To reveal the intraspecific evolution of Leptospirillum ferriphilum isolates which thrived in industrial bioleaching ecosystems and acid mine drainages,genome sequences of L.ferriphilum YSK,L.ferriphilum DX and L.ferr...To reveal the intraspecific evolution of Leptospirillum ferriphilum isolates which thrived in industrial bioleaching ecosystems and acid mine drainages,genome sequences of L.ferriphilum YSK,L.ferriphilum DX and L.ferriphilum ZJ were determined to compare with complete genome of L.ferriphilum ML-04.The genome comparisons reveal that extensive intraspecific variation occurs in their genomes,and that the loss and insertion of novel gene blocks of probable phage origin may mostly contribute to heterogeneity of gene content among L.ferriphilum genomes.Surprisingly,a nif gene cluster is identified in L.ferriphilum YSK and L.ferriphilum ZJ genomes.Intensive analysis and further experiments indicate that the nif gene cluster in L.ferriphilum YSK inherits from ancestor rather than lateral gene transfer.Overall,results suggest that the population of L.ferriphilum undergoes frequent genetic recombination,resulting in many closely related genome types in recent evolution.The combinatorial processes profoundly shape their physiologies and provide the basis for adaptation to different niches.展开更多
Enterococci bacteria are important in environmental, food and clinical microbiology. Enterococcus faecium is a nosocomial pathogen that causes bacteremia, endocarditis and other infections. It is among the most preval...Enterococci bacteria are important in environmental, food and clinical microbiology. Enterococcus faecium is a nosocomial pathogen that causes bacteremia, endocarditis and other infections. It is among the most prevalent organisms encountered in hospital-associated infections accounting for approximately 12% of nosocomial infections in the USA （Linden and Miller, 1999）. However, certain strains of E. faecium are not only non-pathogenic but also have beneficial effects on human health with probiotic potential. For example, E. faecium T-110 is a consortium member in several probiotic products including BIO-THREE~ which is widely prescribed for human, animal and aqua-cultural use. This strain was originally developed by TOA Pharmaceuticals in Japan, and later used in the probiotic products of several other companies.展开更多
Lonicerae Flos(LF)derived from the dried flower buds or opening flowers of four Lonicera plants(Lonicera macranthoides,L.hypoglauca,L.confusa,and L.fulvotnetosa),is a popular traditional Chinese medicine.Because the f...Lonicerae Flos(LF)derived from the dried flower buds or opening flowers of four Lonicera plants(Lonicera macranthoides,L.hypoglauca,L.confusa,and L.fulvotnetosa),is a popular traditional Chinese medicine.Because the four origin plants are very similar in morphology,it is difficult to control the quality of LF in actual production.Over the past decade,many reports have pointed out the differences among them,including the botanical characteristics and active ingredients.However,there is still a lack of rapid methods that can be applied to the identification of the four origins.In this study,comparative analysis of the four chloroplast genomes was performed,and they showed low diversity(Pi=0.00267),three variation hotspots regions(rbcL-accD,rps12-ndhF and rps12-trnN-trnG)were identified as potentially molecular marker of highly informative.Meanwhile,the most obvious difference in SSR comparative analysis is reverse and complement repeats were only identified in L.confusa and L.hypoglauca,respectively.Lastly,the phylogenetic tree showed that L.confusa is more closely related to L.fulvotnetosa,while L.macranthoides is closer to L.hypoglauca.This study systematically revealed the differences among the four chloroplast genomes,and it provides valuable genetic information for identifying the origin of LF.展开更多
Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study ...Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae.The cp genomes,vary-ing in size from 153,366 to 159,895 bp,followed the typical quadripartite organization consisting of a large single-copy(LSC)region(84,545 to 87,883 bp),a small single-copy(SSC)region(18,174 to 19,259 bp),and a pair of inverted repeat(IR)regions(25,310 to 26,396 bp).These genomes contained 132–138 annotated genes,including 87 to 93 protein-coding genes(PCGs),37 tRNA genes,and 8 rRNA genes using MISA software,52 to 121 simple sequence repeat(SSR)loci were identified.D.arbuscular contained the least of SSRs and did not have hexanotides,A.lineata contained the richest SSRs.Long terminal repeats(LTRs)were primarily composed of palindromic and forward repeat sequences,meanwhile,The richest LTRs were found in Argentina lineata.Except for Argentina lineata,Fragariastrum eriocarpum,and Prunus trichostoma,which varied in gene type and position on both sides of the boundary,the remaining species were found to be mostly conserved according to IR boundary analysis.The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1,indicating that this gene was primarily subjected to positive selection during evolution.Additionally,9 hotspots of variation were identified in the LSC and SSC regions.Phylogenetic analysis confirmed the scientific validity of the genus Prunus L.sensu lato(s.l.)within the Rosaceae family.The separation of the three genera Argentina Hill,Fragariastrum Heist.ex Fabr.and Dasiphora Raf.from Potentilla L.may be a more scientific classification.These results offer fresh perspectives on the taxonomy of the Rosaceae.展开更多
The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported...The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported a high-quality genome assembly of G.latifolium.Comparative genome analyses revealed substantial variations in both gene group composition and genomic sequences across 13 cotton genomes,including the expansion of photosynthesis-related gene groups in G.latifolium compared with other races and the pivotal contribution of structural variations(SVs)to G.hirsutum domestication.Based on the resequencing reads and constructed pan-genome of upland cotton,co-selection regions and SVs with significant frequency differences among different populations were identified.Genes located in these regions or affected by these variations may characterize the differences between G.latifolium and other races,and could be involved in maintenance of upland cotton domestication phenotypes.These findings may assist in mining genes for upland cotton improvement and improving the understanding of the genetic basis of upland cotton domestication.展开更多
Bread wheat （Triticum aestivum, AABBDD） is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the whe...Bread wheat （Triticum aestivum, AABBDD） is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path （MTP） of 3176 BAC clones from the short arm ofAe. tauschii chromosome 3 （At3DS）. The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a 247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes. Compared with the orthologous regions of rice, Brachypodium, and sorghum, At3DS contains 38.67% more genes. In comparison to At3DS, the short arm sequence of wheat chromosome 3B （Ta3BS） is 95-Mb large in size, which is primarily due to the expansion of the non-centromeric region, suggesting that transposable element （TE） bursts in Ta3B likely occurred there. Also, the size increase is accompanied by a proportional increase in gene number in Ta3BS. We found that in the sequence of short arm of wheat chromosome 3D （Ta3DS）, there was only less than 0.27% gene loss compared to At3DS. Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.展开更多
Genome dynamics of pathogenic organisms are driven by plant host and pathogenic organism co-evolution, in which patho- gen genomes areused to overcome stresses imposed by hosts with various genetic backgrounds through...Genome dynamics of pathogenic organisms are driven by plant host and pathogenic organism co-evolution, in which patho- gen genomes areused to overcome stresses imposed by hosts with various genetic backgrounds through generation of a range of field isolates. This model also applies to the rice host and its fungal pathogen Magnaporthe oryzae. To better understand genetic variation of M. oryzae in nature, the field isolate V86010 from the Philippines was sequenced and ana- lyzed. Genome annotation found that the assembled V86010 genome was composed of 1 931 scaffolds with a combined length of 38.9 Mb. The average GC ratio is 51.3% and repetitive elements constitute 5.1% of the genome. A total of 11 857 genes including 616 effector protein genes were predicted using a combined analysis pipeline. All predicted genes and effector protein genes of isolate V86010 distribute on the eight chromosomes when aligned with the assembled genome of isolate 70-15. Effector protein genes are located disproportionately at several chromosomal ends. The Pot2 elements are abundant in V86010. Seven V86010-specific effector proteins were found to suppress programmed cell death induced by BAX in tobacco leaves using an Agrobacterium-mediated transient assay. Our results may provide useful information for further study of the molecular and genomic dynamics in the evolution of M. oryzae and rice host interactions, and for characterizing novel effectors and AVR genes in the rice blast pathogen.展开更多
The green seaweeds Ulva linza and U.prolifera are closely related species.They usually co-occur widely and have important ecological significance as primary producers thriving in the intertidal zone.In the Yellow Sea,...The green seaweeds Ulva linza and U.prolifera are closely related species.They usually co-occur widely and have important ecological significance as primary producers thriving in the intertidal zone.In the Yellow Sea,a genetically unique floating ecotype of U.prolifera even bloomed to cause serious green tides.However,there is still a lack of appropriate molecular markers to distinguish these two species,partially due to limited evaluations on the intraspecific variations in U.prolifera among dif ferent ecotypes.Since organelle genomes could provide rich genetic resources for phylogenetic analysis and development of genetic markers,in this study,the chloroplast genome from one attached population of U.prolifera was completely sequenced,and comparative genomic analyses were performed with other existing chloroplast genomes from U.linza and the floating ecotype of U.prolifera.The results showed that in spite of the high level of collinearity among three genomes,there were plenty of genetic variations especially within the non-coding regions,including introns and gene spacer regions.A strategy was proposed that only those signals of variation,which were identical between two ecotypes of U.prolifera but divergent between U.linza and U.prolifera,were selected to develop the interspecific markers for U.linza and U.prolifera.Two candidate markers,psa B and pet B,were shown to be able to distinguish these two closely related species and were applicable to more attached populations of U.prolifera from a wide range of geographical sources.In addition to the interspecific marker,this study would also provide resources for the development of intraspecific markers for U.prolifera.These markers might contribute to the surveys for Ulva species composition and green tide monitoring especially in the Yellow Sea region.展开更多
Lactobacillus crispatus is a commonly found species in the urogenital tract(UGT)of healthy females and can also colonize other niches,such as the gastrointestinal tract(GIT).Although its potential protective role in c...Lactobacillus crispatus is a commonly found species in the urogenital tract(UGT)of healthy females and can also colonize other niches,such as the gastrointestinal tract(GIT).Although its potential protective role in cervical cancer has been reported,the anticancer mechanisms involved are still unclear.In this study,we sequenced and characterized the complete genomes of two L.crispatus strains(Lc31 and Lc83)isolated from the UGT of healthy women of reproductive age.Phylogenetic and phylogenomic analyses of these two strains and 15 other L.crispatus strains with complete genome sequences revealed that strains from the UGT and GIT clustered separately.UGT strains had a larger genome size,higher GC contents,and more protein-coding sequences and insertion sequence(Is)elements,indicating the likelihood of active horizontal gene transfer in this niche.We found a universal presence of genes encoding bacteriocins and the absence of virulence factors and antibiotic resistance genes in UGT strains,suggesting the potential of L.crispatus as a urogenital probiotic.Comparative genomic analysis identified an ula gene cluster responsible for L-ascorbate catabolism exclusively in UGT strains,and carbohydrate fermentation experiments confirmed that this substrate supported the growth of L.crispatus Lc31 and Lc83.Our findings improve the understanding of how the genome determines niche adaptation by L.crispatus,providing a foundation for investigating the mechanisms by which urogenital-derived L.crispatus promotes female health.展开更多
Rice blast caused by <em>Magnaporthe oryzae</em> (<em>M. oryzae</em>) is one of the most destructive diseases, which causes significant rice yield losses and affects global food security. To be...Rice blast caused by <em>Magnaporthe oryzae</em> (<em>M. oryzae</em>) is one of the most destructive diseases, which causes significant rice yield losses and affects global food security. To better understand genetic variations among different isolates of <em>M. oryzae</em> in the nature field, we re-sequenced and analyzed the genomes of three field isolates, QJ08-2006, QJ10-10, and QJ10-3001, which showed distinct pathogenicity on Xin-Yin-Zhan, an elite variety in South China. Genome annotation indicated that these three isolates assemblies have similar genome sizes with 38.4 Mb, 38.3 Mb, and 38.4 Mb, respectively. The QJ08-2006 assembly has 2082 contigs with an N50 of 127.4 kb, the QJ10-10 assembly has 2239 contigs with an N50 of 105.13 kb, the QJ10-3001 assembly has 2025 contigs with an N50 of 133.16 kb. A total of 10,432 genes including 1408 putative secreted protein genes were identified from the annotated isolate QJ08-2006 genome, 10,418 genes including 1410 putative secreted protein genes were identified in QJ10-10, and 10,401 genes including 1420 putative secreted protein genes were identified in QJ10-3001. There are as many as 11,076 identical genes in these three isolates and contained only a few unique genes among three isolates, of which 277 unique genes in QJ08-2006 and 264 unique genes in QJ10-10, and 213 unique genes in QJ10-3001. Most of the predicted secreted protein genes had been identified, and the three re-sequenced strains contained 371, 369, and 387 small Indel, respectively. <em>Avr </em>genes were analyzed in several sequenced <em>Magnaporthe</em> strains, the results revealed that <em>Avr-Pi9</em> and <em>Avr-Piz-t </em>were present in all the sequenced isolates. The isolates QJ08-2006 contained <em>AvrPib</em>, QJ10-10, and QJ10-3001 had an insertion of a Pot3 element in the promoter of the <em>AvrPib</em> gene. Our results showed that, the rapid dominancy of virulence mutant isolates via clonal propagation displayed in the field after the release of the elite variety Xin-Yin-Zhan.展开更多
Genetic information has been instrumental in elucidating the relationship between the East Asian Summer Monsoon(EASM)and subtropical evergreen broad-leaved forests(EBLFs).However,how the genomic insights of EBLFs’spe...Genetic information has been instrumental in elucidating the relationship between the East Asian Summer Monsoon(EASM)and subtropical evergreen broad-leaved forests(EBLFs).However,how the genomic insights of EBLFs’species correspond to environmental shifts induced by the EASM remains limited.In this study,we investigated the adaptive mechanisms of evergreen Engelhardia species in response to the EASM through genome sequencing and comparative genomic analyses from the de novo genome assemblies of fiveclosely related Engelhardia taxa and one Rhoiptelea species.Our findingsrevealed that the divergence of evergreen trees from their sister deciduous species is closely associated with the onset and intensification of the EASM.This genomic transitionmayhave coincided with a significantexpansion of the terpene synthase(TPS)gene family in E.fenzelii,driven by four distinct modes of gene duplication.This expansion enhances the biosynthesis of terpene volatiles,providing a defensive mechanism against potential herbivory in EASM affected environments.We also identifieda shared whole-genome duplication(WGD)event across Engelhardia,along with substantial differences in transposable element(TE)composition and activity,which contributed to genome size variation between E.fenzelii and E.roxburghiana.In addition,demographic analyses revealed a continuous population decline over the past 10 million years,further exacerbated by recenthumandisturbance,underscoring the conservation urgency for these species.These results not only provide preliminary insights into the complex evolutionary dynamics within the Engelhardia genus from genomic insights(e.g.,the intricate relationships between genomic variations,environmental changes,and adaptive responses driven by significantclimatic events such as the EASM),but also provides valuable insights into the conservation significance of EBLFs.展开更多
Selaginella moellendorffii Hieron.,a lycophyte of significant medicinal and evolutionary importance,is recognized as one of the earliest vascular plants.However,the absence of a high-quality reference genome has hinde...Selaginella moellendorffii Hieron.,a lycophyte of significant medicinal and evolutionary importance,is recognized as one of the earliest vascular plants.However,the absence of a high-quality reference genome has hindered the comprehensive exploration of its unique phylogenetic position and therapeutic potential,thereby limiting our understanding of its genomic structure and metabolic capabilities.In this study,we present the first chromosome-level,telomere-to-telomere(T2T)genome assembly of S.moellendorffii,constructed utilizing PacBio HiFi,Oxford Nanopore(ONT),and Hi-C technologies.The assembled genome,spanning 112.83 Mb across 10 chromosomes with a contig N50 of 11.11 Mb,exhibited exceptional completeness(BUSCO score:95.7%)and accuracy(QV=48.11).Comparative genomic analysis identified 3515 gene families unique to S.moellendorffii,with significant enrichment in secondary metabolismpathways,including those related to flavonoid biosynthesis.Phylogenetic analysis revealed that S.moellendorffii diverged from Isoetes approximately 339.6 million years ago(MYA),representing a key evolutionary transition in early vascular plants.By integrating tissue-specific transcriptome and metabolome analyses,we uncovered the molecular basis of biflavone biosynthesis,identifying key enzymes and regulatory networks that govern the production of these bioactive compounds.We observed a correlation between the tissue-specific accumulation patterns of six major biflavones,including amentoflavone and ginkgetin,and the expression of their biosynthetic genes.This high-quality genome assembly,coupled with multi-omics analyses,offers unprecedented insights into the evolution of early vascular plants and elucidates the molecular mechanisms behind their specialized metabolism.展开更多
The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannot...The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannotating and utilizing plastome sequences remain challenging.Therefore,a streamlined phylogenomic pipeline spanning plastome annotation,phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome.Here,we develop PlastidHub,a novel web application employing innovative tools to analyze plastome sequences.In comparison with existing tools,key novel functionalities in PlastidHub include:(1)standardization of quadripartite structure;(2)improvement of annotation flexibility and consistency;(3)quantitative assessment of annotation completeness;(4)diverse extraction modes for canonical and specialized sequences;(5)intelligent screening of molecular markers for biodiversity studies;(6)genelevel visual comparison of structural variations and annotation completeness.PlastidHub features cloud-based web applications that do not require users to install,update,or maintain tools;detailed help documents including user guides,test examples,a static pop-up prompt box,and dynamic pop-up warning prompts when entering unreasonable parameter values;batch processing capabilities for all tools;intermediate results for secondary use;and easy-to-operate task flows between fileupload and download.A key feature of PlastidHub is its interrelated task-based user interface design.Give that PlastidHub is easy to use without specialized computational skills or resources,this new platform should be widely used among botanists and evolutionary biologists,improving and expediting research employing the plastome.PlastidHub is available at https://www.plastidhub.cn.展开更多
The black wolfberry(Lycium ruthenicum;2n=2x=24)is an important medicinal plant with ecological and economic value.Its fruits have numerous beneficial pharmacological activities,especially those of anthocyanins,polysac...The black wolfberry(Lycium ruthenicum;2n=2x=24)is an important medicinal plant with ecological and economic value.Its fruits have numerous beneficial pharmacological activities,especially those of anthocyanins,polysaccharides,and alkaloids,and have high nutritional value.However,the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary mechanisms.In this study,we developed the telomere-to-telomere(T2T)nearly gapless genome of L.ruthenicum(2.26 Gb)by integrating PacBio HiFi,Nanopore Ultra-Long,and Hi-C technologies.The assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally annotated.Approximately 80%of the repetitive sequences were identified,of which long terminal repeats(LTRs)were the most abundant,accounting for 73.01%.The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium species.The species-specific genes of L.ruthenicum were related to defense mechanisms,salt tolerance,drought resistance,and oxidative stress,further demonstrating their superior adaptability to arid environments.Based on the assembled genome and fruit transcriptome data,we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of L.ruthenicum,most of which were highly expressed at a later stage in fruit development.Furthermore,154 potential disease resistance-related nucleotidebinding genes have been identified in the L.ruthenicum genome.The whole-genome and proximal,dispersed,and tandem duplication genes in the L.ruthenicum genome enriched the number of genes involved in anthocyanin synthesis and resistance-related pathways.These results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.展开更多
Lactococcus lactis,a major starter culture in the dairy industry,has been widely applied in food fermentation.While current research has primarily focused on evaluating its role during fermentation,genomic investigati...Lactococcus lactis,a major starter culture in the dairy industry,has been widely applied in food fermentation.While current research has primarily focused on evaluating its role during fermentation,genomic investigations into its genetic diversity and functional adaptability remain limited.In this study,199 L.lactis strains isolated from Chinese traditional artisanal cheeses(72 bovine,71 goat,and 56 yak milk cheese isolates)were subjected to comparative genomic analysis.Genomic characteristic analysis indicated that bovine milk strains possess larger genomes and the highest number of unique genes.Functional characterization further demonstrated notable differences in carbohydrate metabolism among strains from different sources,with yak milk strains enriched in enzymes involved in complex polysaccharide degradation,including members of the carbohydrate esterases family.Moreover,strains from different sources exhibit distinct strategies for lactose hydrolysis and metabolic utilization,reflecting adaptive evolution to their specific nutritional niches.Analysis of the antibiotic resistance profile suggests that L.lactis predominantly harbors glycopeptide and lincosamide resistance genes,encompassing four distinct resistance mechanisms.Collectively,this study reveals the genetic diversity and adaptive evolution of L.lactis strains from different sources and identifies key genes associated with carbohydrate degradation,lactose metabolism,and antibiotic resistance,providing concrete genetic evidence for the selection of efficient and safe industrial fermentation strains.展开更多
In this study, we isolated an environmental clone of Ochrobactrum intermedium, strain 2745-2, from the formation water of Changqing oilfield in Shanxi, China, which can degrade crude oil. Strain 2745-2 is aerobic and ...In this study, we isolated an environmental clone of Ochrobactrum intermedium, strain 2745-2, from the formation water of Changqing oilfield in Shanxi, China, which can degrade crude oil. Strain 2745-2 is aerobic and rod-shaped with optimum growth at 42 ℃ and pH 5.5. We sequenced the genome and found a single chromosome of 4800175 bp, with a G＋C content of 57.63%. Sixty RNAs and 4737 protein-coding genes were identified： many of the genes are responsible for the degradation, emulsification, and metabolizing of crude oil. A comparative genomic analysis with related clinical strains （M86, 229E, and LMG3301T） showed that genes involved in virulence, disease, defense, phages, prophages, transposable elements, plasmids, and antibiotic resistance are also present in strain 2745-2.展开更多
AIM: To characterize cytogenetic alterations in esophageal squamous cell carcinoma (ESCC) and its metastasis. METHODS: A total of 37 cases of primary ESCC and 15 pairs of primary ESCC tumors and their matched metastat...AIM: To characterize cytogenetic alterations in esophageal squamous cell carcinoma (ESCC) and its metastasis. METHODS: A total of 37 cases of primary ESCC and 15 pairs of primary ESCC tumors and their matched metastatic lymph nodes cases were enrolled from Linzhou, the high incidence area for ESCC in Henan, northern China. The comparative genomic hybridization (CGH) was applied to determine the chromosomal aberrations on the DNA extracted from the frozen ESCC and metastatic lymph node samples from these patients. RESULTS: CGH showed chromosomal aberrations in all the cases. In 37 cases of primary ESCC, chromosomal profile of DNA copy number was characterized by frequently detected gains at 8q (29/37, 78%), 3q (24/37, 65%), 5p (19/37, 51%); and frequently detected losses at 3p (21/37, 57%), 8p and 9q (14/37, 38%). In 15 pairs of primary ESCC tumors and their matched metastatic lymph node cases, the majority of the chromosomal aberrations in both primary tumor and metastatic lymph node lesions were consistent with the primary ESCC cases, but new candidate regions of interest were also detected. The most significant finding is the gains of chromosome 6p with a minimum high-level amplification region at 6p12-6q12 in 7 metastatic lymph nodes butonly in 2 corresponding primary tumors (P = 0.05) and 20p with a minimum high-level amplification region at 20p12 in 11 metastatic lymph nodes but only in 5 corresponding primary tumors (P < 0.05). Another interesting finding is the loss of chromosome 10p and 10q in 8 and 7 metastatic lymph nodes but only in 2 corresponding primary tumors (P < 0.05). CONCLUSION: Using the CGH technique to detect chromosomal aberrations in both the primary tumor and its metastatic lymph nodes of ESCC, gains of 8q, 3q and 5p and loss of 3p, 8p, 9q and 13q were specifically implicated in ESCC in Linzhou population. Gains of 6p and 20p and loss of 10pq may contribute to the lymph node metastasis of ESCC. These findings suggest that the gains and losses of chromosomal regions may contain ESCC-related oncogenes and tumor suppressor genes and provide important theoretic information for identifying and cloning novel ESCC-related oncogenes and tumor suppressor genes.展开更多
In the present study,the complete genomes of four common（4/EV71/Wenzhou/CHN/2014,15/EV71/Wenzhou/CHN/2014,116/EV71/Wenzhou/CHN/2014,and 120/EV71/Wenzhou/CHN/2014）and two virulent（11/EV71/Wenzhou/CHN/2014and 109/EV7...In the present study,the complete genomes of four common（4/EV71/Wenzhou/CHN/2014,15/EV71/Wenzhou/CHN/2014,116/EV71/Wenzhou/CHN/2014,and 120/EV71/Wenzhou/CHN/2014）and two virulent（11/EV71/Wenzhou/CHN/2014and 109/EV71/Wenzhou/CHN/2014）enterovirus 71（EV71）isolates were sequenced and described.They are 7405 bp in length and belong to EV71 sub-genotype C4 （C4a cluster）.展开更多
Approximately 30% of pregnancies after implantation end up in spontaneous abortions, and 50% of them are caused by chromosomal abnormalities. However, the spectrum of genomic copy number variants （CNVs） in products ...Approximately 30% of pregnancies after implantation end up in spontaneous abortions, and 50% of them are caused by chromosomal abnormalities. However, the spectrum of genomic copy number variants （CNVs） in products of conception （POC） and the underlying gene- dosage-sensitive mechanisms causing spontaneous abortions remain largely unknown. In this study, array comparative genornic hybridiza- tion （aCGH） analysis was performed as a salvage procedure for 128 POC culture failure （POC-CF） samples and as a supplemental procedure for 106 POC normal karyotype （POC-NK） samples. Chromosomal abnormalities were detected in 10% of POC-CF and pathogenic CNVs were detected in 3.9% of POC-CF and 5.7% of POC-NK samples. Compiled results from this study and relevant case series through a literature review demonstrated an abnormality detection rate （ADR） of 35% for chromosomal abnormalities in POC-CF samples, 3.7% for pathogenic CNVs in POC-CF samples, and 4.6% for pathogenic CNVs in POC-NK samples. Ingenuity Pathway Analysis （IPA） was performed on the genes from pathogenic CNVs found in POC samples. The denoted primary gene networks suggested that apoptosis and cell proliferation pathways are involved in miscarriage. In summary, a similar spectrum of cytogenomic abnormalities was observed in POC culture success and POC-CF samples. A threshold effect correlating the number of dosage-sensitive genes in a chromosome with the observed frequency of autosomai trisomy is proposed. A rationalized approach using firstly fluorescence in situ hybridization （FISH） testing with probes of chromosomes X/Y/ 18, 13/21, and 15/16/22 for common aneuploidies and polyploidies and secondly aCGH for other cytogenomic abnormalities is recommended for POC-CF samples.展开更多
基金Project(2018YFC1801804)supported by the National Key R&D Program of ChinaProjects(2016JJ3146,2017JJ3160)supported by the Natural Science Foundation of Hunan Province,China。
文摘To reveal the intraspecific evolution of Leptospirillum ferriphilum isolates which thrived in industrial bioleaching ecosystems and acid mine drainages,genome sequences of L.ferriphilum YSK,L.ferriphilum DX and L.ferriphilum ZJ were determined to compare with complete genome of L.ferriphilum ML-04.The genome comparisons reveal that extensive intraspecific variation occurs in their genomes,and that the loss and insertion of novel gene blocks of probable phage origin may mostly contribute to heterogeneity of gene content among L.ferriphilum genomes.Surprisingly,a nif gene cluster is identified in L.ferriphilum YSK and L.ferriphilum ZJ genomes.Intensive analysis and further experiments indicate that the nif gene cluster in L.ferriphilum YSK inherits from ancestor rather than lateral gene transfer.Overall,results suggest that the population of L.ferriphilum undergoes frequent genetic recombination,resulting in many closely related genome types in recent evolution.The combinatorial processes profoundly shape their physiologies and provide the basis for adaptation to different niches.
文摘Enterococci bacteria are important in environmental, food and clinical microbiology. Enterococcus faecium is a nosocomial pathogen that causes bacteremia, endocarditis and other infections. It is among the most prevalent organisms encountered in hospital-associated infections accounting for approximately 12% of nosocomial infections in the USA （Linden and Miller, 1999）. However, certain strains of E. faecium are not only non-pathogenic but also have beneficial effects on human health with probiotic potential. For example, E. faecium T-110 is a consortium member in several probiotic products including BIO-THREE~ which is widely prescribed for human, animal and aqua-cultural use. This strain was originally developed by TOA Pharmaceuticals in Japan, and later used in the probiotic products of several other companies.
基金the Science and Technology Project of Changsha City(No.kq2004038)Program for Innovative Leading Talents for Science and Technology of Xianyang City。
文摘Lonicerae Flos(LF)derived from the dried flower buds or opening flowers of four Lonicera plants(Lonicera macranthoides,L.hypoglauca,L.confusa,and L.fulvotnetosa),is a popular traditional Chinese medicine.Because the four origin plants are very similar in morphology,it is difficult to control the quality of LF in actual production.Over the past decade,many reports have pointed out the differences among them,including the botanical characteristics and active ingredients.However,there is still a lack of rapid methods that can be applied to the identification of the four origins.In this study,comparative analysis of the four chloroplast genomes was performed,and they showed low diversity(Pi=0.00267),three variation hotspots regions(rbcL-accD,rps12-ndhF and rps12-trnN-trnG)were identified as potentially molecular marker of highly informative.Meanwhile,the most obvious difference in SSR comparative analysis is reverse and complement repeats were only identified in L.confusa and L.hypoglauca,respectively.Lastly,the phylogenetic tree showed that L.confusa is more closely related to L.fulvotnetosa,while L.macranthoides is closer to L.hypoglauca.This study systematically revealed the differences among the four chloroplast genomes,and it provides valuable genetic information for identifying the origin of LF.
基金funded by the Jiangxi Provincial Natural Science Foundation,Grant Number 20232BAB216119.
文摘Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae.The cp genomes,vary-ing in size from 153,366 to 159,895 bp,followed the typical quadripartite organization consisting of a large single-copy(LSC)region(84,545 to 87,883 bp),a small single-copy(SSC)region(18,174 to 19,259 bp),and a pair of inverted repeat(IR)regions(25,310 to 26,396 bp).These genomes contained 132–138 annotated genes,including 87 to 93 protein-coding genes(PCGs),37 tRNA genes,and 8 rRNA genes using MISA software,52 to 121 simple sequence repeat(SSR)loci were identified.D.arbuscular contained the least of SSRs and did not have hexanotides,A.lineata contained the richest SSRs.Long terminal repeats(LTRs)were primarily composed of palindromic and forward repeat sequences,meanwhile,The richest LTRs were found in Argentina lineata.Except for Argentina lineata,Fragariastrum eriocarpum,and Prunus trichostoma,which varied in gene type and position on both sides of the boundary,the remaining species were found to be mostly conserved according to IR boundary analysis.The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1,indicating that this gene was primarily subjected to positive selection during evolution.Additionally,9 hotspots of variation were identified in the LSC and SSC regions.Phylogenetic analysis confirmed the scientific validity of the genus Prunus L.sensu lato(s.l.)within the Rosaceae family.The separation of the three genera Argentina Hill,Fragariastrum Heist.ex Fabr.and Dasiphora Raf.from Potentilla L.may be a more scientific classification.These results offer fresh perspectives on the taxonomy of the Rosaceae.
基金supported by the National Natural Science Foundation of China(32201873)the Key Research and Development Plan of Hubei Province(2023BBB050)。
文摘The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported a high-quality genome assembly of G.latifolium.Comparative genome analyses revealed substantial variations in both gene group composition and genomic sequences across 13 cotton genomes,including the expansion of photosynthesis-related gene groups in G.latifolium compared with other races and the pivotal contribution of structural variations(SVs)to G.hirsutum domestication.Based on the resequencing reads and constructed pan-genome of upland cotton,co-selection regions and SVs with significant frequency differences among different populations were identified.Genes located in these regions or affected by these variations may characterize the differences between G.latifolium and other races,and could be involved in maintenance of upland cotton domestication phenotypes.These findings may assist in mining genes for upland cotton improvement and improving the understanding of the genetic basis of upland cotton domestication.
基金supported by funding from the National Natural Science Foundation of China(Nos.31290210,31210103902)the Unites States National Science Foundation grant(No.IOS 1238231)+1 种基金the USDA-Agricultural Research Service CRIS project(No.5325-21000-019)the Ministry of Education of China(111 project)
文摘Bread wheat （Triticum aestivum, AABBDD） is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path （MTP） of 3176 BAC clones from the short arm ofAe. tauschii chromosome 3 （At3DS）. The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a 247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes. Compared with the orthologous regions of rice, Brachypodium, and sorghum, At3DS contains 38.67% more genes. In comparison to At3DS, the short arm sequence of wheat chromosome 3B （Ta3BS） is 95-Mb large in size, which is primarily due to the expansion of the non-centromeric region, suggesting that transposable element （TE） bursts in Ta3B likely occurred there. Also, the size increase is accompanied by a proportional increase in gene number in Ta3BS. We found that in the sequence of short arm of wheat chromosome 3D （Ta3DS）, there was only less than 0.27% gene loss compared to At3DS. Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.
基金supported by the grants from the National Natural Science Foundation of China (31528017 and 31461143019)
文摘Genome dynamics of pathogenic organisms are driven by plant host and pathogenic organism co-evolution, in which patho- gen genomes areused to overcome stresses imposed by hosts with various genetic backgrounds through generation of a range of field isolates. This model also applies to the rice host and its fungal pathogen Magnaporthe oryzae. To better understand genetic variation of M. oryzae in nature, the field isolate V86010 from the Philippines was sequenced and ana- lyzed. Genome annotation found that the assembled V86010 genome was composed of 1 931 scaffolds with a combined length of 38.9 Mb. The average GC ratio is 51.3% and repetitive elements constitute 5.1% of the genome. A total of 11 857 genes including 616 effector protein genes were predicted using a combined analysis pipeline. All predicted genes and effector protein genes of isolate V86010 distribute on the eight chromosomes when aligned with the assembled genome of isolate 70-15. Effector protein genes are located disproportionately at several chromosomal ends. The Pot2 elements are abundant in V86010. Seven V86010-specific effector proteins were found to suppress programmed cell death induced by BAX in tobacco leaves using an Agrobacterium-mediated transient assay. Our results may provide useful information for further study of the molecular and genomic dynamics in the evolution of M. oryzae and rice host interactions, and for characterizing novel effectors and AVR genes in the rice blast pathogen.
基金Supported by the Science&Technology Basic Resources Investigation Program of China(No.2018FY100205)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA23050302)+2 种基金the National Key R&D Program of China(No.2018YFD0901500)the National Natural Science Foundation of China(No.41776153)the Key R&D Program of Shandong Province(No.2019GSF107012)。
文摘The green seaweeds Ulva linza and U.prolifera are closely related species.They usually co-occur widely and have important ecological significance as primary producers thriving in the intertidal zone.In the Yellow Sea,a genetically unique floating ecotype of U.prolifera even bloomed to cause serious green tides.However,there is still a lack of appropriate molecular markers to distinguish these two species,partially due to limited evaluations on the intraspecific variations in U.prolifera among dif ferent ecotypes.Since organelle genomes could provide rich genetic resources for phylogenetic analysis and development of genetic markers,in this study,the chloroplast genome from one attached population of U.prolifera was completely sequenced,and comparative genomic analyses were performed with other existing chloroplast genomes from U.linza and the floating ecotype of U.prolifera.The results showed that in spite of the high level of collinearity among three genomes,there were plenty of genetic variations especially within the non-coding regions,including introns and gene spacer regions.A strategy was proposed that only those signals of variation,which were identical between two ecotypes of U.prolifera but divergent between U.linza and U.prolifera,were selected to develop the interspecific markers for U.linza and U.prolifera.Two candidate markers,psa B and pet B,were shown to be able to distinguish these two closely related species and were applicable to more attached populations of U.prolifera from a wide range of geographical sources.In addition to the interspecific marker,this study would also provide resources for the development of intraspecific markers for U.prolifera.These markers might contribute to the surveys for Ulva species composition and green tide monitoring especially in the Yellow Sea region.
基金supported by grants from the Natural Science Foundation of Anhui Province(grant number 2208085MH253)the National Natural Science Foundation(grant number 81702560)the Fundamental Research Funds for the Central Universities(grant number WK9110000110),People's Republic of China.
文摘Lactobacillus crispatus is a commonly found species in the urogenital tract(UGT)of healthy females and can also colonize other niches,such as the gastrointestinal tract(GIT).Although its potential protective role in cervical cancer has been reported,the anticancer mechanisms involved are still unclear.In this study,we sequenced and characterized the complete genomes of two L.crispatus strains(Lc31 and Lc83)isolated from the UGT of healthy women of reproductive age.Phylogenetic and phylogenomic analyses of these two strains and 15 other L.crispatus strains with complete genome sequences revealed that strains from the UGT and GIT clustered separately.UGT strains had a larger genome size,higher GC contents,and more protein-coding sequences and insertion sequence(Is)elements,indicating the likelihood of active horizontal gene transfer in this niche.We found a universal presence of genes encoding bacteriocins and the absence of virulence factors and antibiotic resistance genes in UGT strains,suggesting the potential of L.crispatus as a urogenital probiotic.Comparative genomic analysis identified an ula gene cluster responsible for L-ascorbate catabolism exclusively in UGT strains,and carbohydrate fermentation experiments confirmed that this substrate supported the growth of L.crispatus Lc31 and Lc83.Our findings improve the understanding of how the genome determines niche adaptation by L.crispatus,providing a foundation for investigating the mechanisms by which urogenital-derived L.crispatus promotes female health.
文摘Rice blast caused by <em>Magnaporthe oryzae</em> (<em>M. oryzae</em>) is one of the most destructive diseases, which causes significant rice yield losses and affects global food security. To better understand genetic variations among different isolates of <em>M. oryzae</em> in the nature field, we re-sequenced and analyzed the genomes of three field isolates, QJ08-2006, QJ10-10, and QJ10-3001, which showed distinct pathogenicity on Xin-Yin-Zhan, an elite variety in South China. Genome annotation indicated that these three isolates assemblies have similar genome sizes with 38.4 Mb, 38.3 Mb, and 38.4 Mb, respectively. The QJ08-2006 assembly has 2082 contigs with an N50 of 127.4 kb, the QJ10-10 assembly has 2239 contigs with an N50 of 105.13 kb, the QJ10-3001 assembly has 2025 contigs with an N50 of 133.16 kb. A total of 10,432 genes including 1408 putative secreted protein genes were identified from the annotated isolate QJ08-2006 genome, 10,418 genes including 1410 putative secreted protein genes were identified in QJ10-10, and 10,401 genes including 1420 putative secreted protein genes were identified in QJ10-3001. There are as many as 11,076 identical genes in these three isolates and contained only a few unique genes among three isolates, of which 277 unique genes in QJ08-2006 and 264 unique genes in QJ10-10, and 213 unique genes in QJ10-3001. Most of the predicted secreted protein genes had been identified, and the three re-sequenced strains contained 371, 369, and 387 small Indel, respectively. <em>Avr </em>genes were analyzed in several sequenced <em>Magnaporthe</em> strains, the results revealed that <em>Avr-Pi9</em> and <em>Avr-Piz-t </em>were present in all the sequenced isolates. The isolates QJ08-2006 contained <em>AvrPib</em>, QJ10-10, and QJ10-3001 had an insertion of a Pot3 element in the promoter of the <em>AvrPib</em> gene. Our results showed that, the rapid dominancy of virulence mutant isolates via clonal propagation displayed in the field after the release of the elite variety Xin-Yin-Zhan.
基金supported by the National Natural Science Foundation of China(No.42171063)Southeast Asia Biodiversity Research Institute,Chinese Academy of Sciences(No.Y4ZK111B01)+6 种基金the Special Fund for ScientificResearch of Shanghai Landscaping&City Appearance Administrative Bureau(G242414,G242416)the“Yunnan Revitalization Talent Support Program”in Yunnan Province(XDYC-QNRC-2022-0028)Yunnan Revitalization Talent Support Program“Innovation Team”Project(202405AS350019)the CAS“Light of West China”Programthe 14th Five-Year Plan of Xishuangbanna Tropical Botanical Garden,Chinese Academy Sciences(XTBG-1450303)the European Research Council(ERC)under the European Union's Horizon 2020 research and innovation program(No.833522)GhentUniversity(Methusalem funding,BOF.MET.2021.0005.01).
文摘Genetic information has been instrumental in elucidating the relationship between the East Asian Summer Monsoon(EASM)and subtropical evergreen broad-leaved forests(EBLFs).However,how the genomic insights of EBLFs’species correspond to environmental shifts induced by the EASM remains limited.In this study,we investigated the adaptive mechanisms of evergreen Engelhardia species in response to the EASM through genome sequencing and comparative genomic analyses from the de novo genome assemblies of fiveclosely related Engelhardia taxa and one Rhoiptelea species.Our findingsrevealed that the divergence of evergreen trees from their sister deciduous species is closely associated with the onset and intensification of the EASM.This genomic transitionmayhave coincided with a significantexpansion of the terpene synthase(TPS)gene family in E.fenzelii,driven by four distinct modes of gene duplication.This expansion enhances the biosynthesis of terpene volatiles,providing a defensive mechanism against potential herbivory in EASM affected environments.We also identifieda shared whole-genome duplication(WGD)event across Engelhardia,along with substantial differences in transposable element(TE)composition and activity,which contributed to genome size variation between E.fenzelii and E.roxburghiana.In addition,demographic analyses revealed a continuous population decline over the past 10 million years,further exacerbated by recenthumandisturbance,underscoring the conservation urgency for these species.These results not only provide preliminary insights into the complex evolutionary dynamics within the Engelhardia genus from genomic insights(e.g.,the intricate relationships between genomic variations,environmental changes,and adaptive responses driven by significantclimatic events such as the EASM),but also provides valuable insights into the conservation significance of EBLFs.
基金funded by the National Natural Science Foundation of China(Grant No.81903921)the Key project at central government level:The ability establishment of sustainable use for valuable Chinese medicine resources(2060302)the Distinguished Young Scholars of Hubei University of Chinese Medicine(Grant No.2022ZZXJ002).
文摘Selaginella moellendorffii Hieron.,a lycophyte of significant medicinal and evolutionary importance,is recognized as one of the earliest vascular plants.However,the absence of a high-quality reference genome has hindered the comprehensive exploration of its unique phylogenetic position and therapeutic potential,thereby limiting our understanding of its genomic structure and metabolic capabilities.In this study,we present the first chromosome-level,telomere-to-telomere(T2T)genome assembly of S.moellendorffii,constructed utilizing PacBio HiFi,Oxford Nanopore(ONT),and Hi-C technologies.The assembled genome,spanning 112.83 Mb across 10 chromosomes with a contig N50 of 11.11 Mb,exhibited exceptional completeness(BUSCO score:95.7%)and accuracy(QV=48.11).Comparative genomic analysis identified 3515 gene families unique to S.moellendorffii,with significant enrichment in secondary metabolismpathways,including those related to flavonoid biosynthesis.Phylogenetic analysis revealed that S.moellendorffii diverged from Isoetes approximately 339.6 million years ago(MYA),representing a key evolutionary transition in early vascular plants.By integrating tissue-specific transcriptome and metabolome analyses,we uncovered the molecular basis of biflavone biosynthesis,identifying key enzymes and regulatory networks that govern the production of these bioactive compounds.We observed a correlation between the tissue-specific accumulation patterns of six major biflavones,including amentoflavone and ginkgetin,and the expression of their biosynthetic genes.This high-quality genome assembly,coupled with multi-omics analyses,offers unprecedented insights into the evolution of early vascular plants and elucidates the molecular mechanisms behind their specialized metabolism.
基金the Natural Science Foundation of Shandong Province(ZR2020QC022)the Science and Technology Basic Resources Investigation Program of China(No.2019FY100900)+2 种基金the Major Program for Basic Research Project of Yunnan Province(202401BC070001)Yunnan Revitalization Talent Support Program:Yunling Scholar Project to Tingshuang Yithe open research project of“Cross Cooperative Team”of the Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciences.
文摘The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannotating and utilizing plastome sequences remain challenging.Therefore,a streamlined phylogenomic pipeline spanning plastome annotation,phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome.Here,we develop PlastidHub,a novel web application employing innovative tools to analyze plastome sequences.In comparison with existing tools,key novel functionalities in PlastidHub include:(1)standardization of quadripartite structure;(2)improvement of annotation flexibility and consistency;(3)quantitative assessment of annotation completeness;(4)diverse extraction modes for canonical and specialized sequences;(5)intelligent screening of molecular markers for biodiversity studies;(6)genelevel visual comparison of structural variations and annotation completeness.PlastidHub features cloud-based web applications that do not require users to install,update,or maintain tools;detailed help documents including user guides,test examples,a static pop-up prompt box,and dynamic pop-up warning prompts when entering unreasonable parameter values;batch processing capabilities for all tools;intermediate results for secondary use;and easy-to-operate task flows between fileupload and download.A key feature of PlastidHub is its interrelated task-based user interface design.Give that PlastidHub is easy to use without specialized computational skills or resources,this new platform should be widely used among botanists and evolutionary biologists,improving and expediting research employing the plastome.PlastidHub is available at https://www.plastidhub.cn.
基金supported by the National Natural Science Foundation of China(32360058)the Central Government Guides Local Science and Technology Development Projects,China(2023ZYZX1224)Xinjiang University Excellent Doctoral Student Innovation Project(XJU2022BS051)。
文摘The black wolfberry(Lycium ruthenicum;2n=2x=24)is an important medicinal plant with ecological and economic value.Its fruits have numerous beneficial pharmacological activities,especially those of anthocyanins,polysaccharides,and alkaloids,and have high nutritional value.However,the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary mechanisms.In this study,we developed the telomere-to-telomere(T2T)nearly gapless genome of L.ruthenicum(2.26 Gb)by integrating PacBio HiFi,Nanopore Ultra-Long,and Hi-C technologies.The assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally annotated.Approximately 80%of the repetitive sequences were identified,of which long terminal repeats(LTRs)were the most abundant,accounting for 73.01%.The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium species.The species-specific genes of L.ruthenicum were related to defense mechanisms,salt tolerance,drought resistance,and oxidative stress,further demonstrating their superior adaptability to arid environments.Based on the assembled genome and fruit transcriptome data,we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of L.ruthenicum,most of which were highly expressed at a later stage in fruit development.Furthermore,154 potential disease resistance-related nucleotidebinding genes have been identified in the L.ruthenicum genome.The whole-genome and proximal,dispersed,and tandem duplication genes in the L.ruthenicum genome enriched the number of genes involved in anthocyanin synthesis and resistance-related pathways.These results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.
基金supported by the National Key Research and Development Project(2022YFD2100703)the National Natural Science Foundation of China(32394051 and U23A20259)the Fundamental Research Funds for the Central Universities(JUSRP622013).
文摘Lactococcus lactis,a major starter culture in the dairy industry,has been widely applied in food fermentation.While current research has primarily focused on evaluating its role during fermentation,genomic investigations into its genetic diversity and functional adaptability remain limited.In this study,199 L.lactis strains isolated from Chinese traditional artisanal cheeses(72 bovine,71 goat,and 56 yak milk cheese isolates)were subjected to comparative genomic analysis.Genomic characteristic analysis indicated that bovine milk strains possess larger genomes and the highest number of unique genes.Functional characterization further demonstrated notable differences in carbohydrate metabolism among strains from different sources,with yak milk strains enriched in enzymes involved in complex polysaccharide degradation,including members of the carbohydrate esterases family.Moreover,strains from different sources exhibit distinct strategies for lactose hydrolysis and metabolic utilization,reflecting adaptive evolution to their specific nutritional niches.Analysis of the antibiotic resistance profile suggests that L.lactis predominantly harbors glycopeptide and lincosamide resistance genes,encompassing four distinct resistance mechanisms.Collectively,this study reveals the genetic diversity and adaptive evolution of L.lactis strains from different sources and identifies key genes associated with carbohydrate degradation,lactose metabolism,and antibiotic resistance,providing concrete genetic evidence for the selection of efficient and safe industrial fermentation strains.
基金supported by the National High-Tech R&D Program(863)of China(No.2013AA064402)the National Natural Science Foundation of China(Nos.81301461 and 51474034)+1 种基金the Zhejiang Provincial Natural Science Foundation of China(No.LQ13H190002)the Scientific Research Foundation of Zhejiang Provincial Health Bureau(No.2012KYB083),China
文摘In this study, we isolated an environmental clone of Ochrobactrum intermedium, strain 2745-2, from the formation water of Changqing oilfield in Shanxi, China, which can degrade crude oil. Strain 2745-2 is aerobic and rod-shaped with optimum growth at 42 ℃ and pH 5.5. We sequenced the genome and found a single chromosome of 4800175 bp, with a G＋C content of 57.63%. Sixty RNAs and 4737 protein-coding genes were identified： many of the genes are responsible for the degradation, emulsification, and metabolizing of crude oil. A comparative genomic analysis with related clinical strains （M86, 229E, and LMG3301T） showed that genes involved in virulence, disease, defense, phages, prophages, transposable elements, plasmids, and antibiotic resistance are also present in strain 2745-2.
基金Supported by The Science and Technology Fund of Henan Health Department, No. 2007-026
文摘AIM: To characterize cytogenetic alterations in esophageal squamous cell carcinoma (ESCC) and its metastasis. METHODS: A total of 37 cases of primary ESCC and 15 pairs of primary ESCC tumors and their matched metastatic lymph nodes cases were enrolled from Linzhou, the high incidence area for ESCC in Henan, northern China. The comparative genomic hybridization (CGH) was applied to determine the chromosomal aberrations on the DNA extracted from the frozen ESCC and metastatic lymph node samples from these patients. RESULTS: CGH showed chromosomal aberrations in all the cases. In 37 cases of primary ESCC, chromosomal profile of DNA copy number was characterized by frequently detected gains at 8q (29/37, 78%), 3q (24/37, 65%), 5p (19/37, 51%); and frequently detected losses at 3p (21/37, 57%), 8p and 9q (14/37, 38%). In 15 pairs of primary ESCC tumors and their matched metastatic lymph node cases, the majority of the chromosomal aberrations in both primary tumor and metastatic lymph node lesions were consistent with the primary ESCC cases, but new candidate regions of interest were also detected. The most significant finding is the gains of chromosome 6p with a minimum high-level amplification region at 6p12-6q12 in 7 metastatic lymph nodes butonly in 2 corresponding primary tumors (P = 0.05) and 20p with a minimum high-level amplification region at 20p12 in 11 metastatic lymph nodes but only in 5 corresponding primary tumors (P < 0.05). Another interesting finding is the loss of chromosome 10p and 10q in 8 and 7 metastatic lymph nodes but only in 2 corresponding primary tumors (P < 0.05). CONCLUSION: Using the CGH technique to detect chromosomal aberrations in both the primary tumor and its metastatic lymph nodes of ESCC, gains of 8q, 3q and 5p and loss of 3p, 8p, 9q and 13q were specifically implicated in ESCC in Linzhou population. Gains of 6p and 20p and loss of 10pq may contribute to the lymph node metastasis of ESCC. These findings suggest that the gains and losses of chromosomal regions may contain ESCC-related oncogenes and tumor suppressor genes and provide important theoretic information for identifying and cloning novel ESCC-related oncogenes and tumor suppressor genes.
基金funded by Natural Science Foundation of Zhejiang(LQ14C010006)National Natural Science Foundation of China(81501363)Planned Science and Technology Project of Zhejiang(2014C33261)
文摘In the present study,the complete genomes of four common（4/EV71/Wenzhou/CHN/2014,15/EV71/Wenzhou/CHN/2014,116/EV71/Wenzhou/CHN/2014,and 120/EV71/Wenzhou/CHN/2014）and two virulent（11/EV71/Wenzhou/CHN/2014and 109/EV71/Wenzhou/CHN/2014）enterovirus 71（EV71）isolates were sequenced and described.They are 7405 bp in length and belong to EV71 sub-genotype C4 （C4a cluster）.
基金partially supported by Guangdong Innovative and Entrepreneurial Research Team Program (No. 201301S0105240297)by 111 Project
文摘Approximately 30% of pregnancies after implantation end up in spontaneous abortions, and 50% of them are caused by chromosomal abnormalities. However, the spectrum of genomic copy number variants （CNVs） in products of conception （POC） and the underlying gene- dosage-sensitive mechanisms causing spontaneous abortions remain largely unknown. In this study, array comparative genornic hybridiza- tion （aCGH） analysis was performed as a salvage procedure for 128 POC culture failure （POC-CF） samples and as a supplemental procedure for 106 POC normal karyotype （POC-NK） samples. Chromosomal abnormalities were detected in 10% of POC-CF and pathogenic CNVs were detected in 3.9% of POC-CF and 5.7% of POC-NK samples. Compiled results from this study and relevant case series through a literature review demonstrated an abnormality detection rate （ADR） of 35% for chromosomal abnormalities in POC-CF samples, 3.7% for pathogenic CNVs in POC-CF samples, and 4.6% for pathogenic CNVs in POC-NK samples. Ingenuity Pathway Analysis （IPA） was performed on the genes from pathogenic CNVs found in POC samples. The denoted primary gene networks suggested that apoptosis and cell proliferation pathways are involved in miscarriage. In summary, a similar spectrum of cytogenomic abnormalities was observed in POC culture success and POC-CF samples. A threshold effect correlating the number of dosage-sensitive genes in a chromosome with the observed frequency of autosomai trisomy is proposed. A rationalized approach using firstly fluorescence in situ hybridization （FISH） testing with probes of chromosomes X/Y/ 18, 13/21, and 15/16/22 for common aneuploidies and polyploidies and secondly aCGH for other cytogenomic abnormalities is recommended for POC-CF samples.
