As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome （BAC） by BAC strategy. The current physical contigs are expec...As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome （BAC） by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa.展开更多
Apparently balanced chromosomal structural rearrangements are known to cause male infertility and account for approximately 1%of azoospermia or severe oligospermia.However,the underlying mechanisms of pathogenesis and...Apparently balanced chromosomal structural rearrangements are known to cause male infertility and account for approximately 1%of azoospermia or severe oligospermia.However,the underlying mechanisms of pathogenesis and etiologies are still largely unknown.Herein,we investigated apparently balanced interchromosomal structural rearrangements in six cases with azoospermia/severe oligospermia to comprehensively identify and delineate cryptic structural rearrangements and the related copy number variants.In addition,high read-depth genome sequencing(GS)(30-fold)was performed to investigate point mutations causative of male infertility.Mate-pair GS(4-fold)revealed additional structural rearrangements and/or copy number changes in 5 of 6 cases and detected a total of 48 rearrangements.Overall,the breakpoints caused truncations of 30 RefSeq genes,five of which were associated with spermatogenesis.Furthermore,the breakpoints disrupted 43 topological-associated domains.Direct disruptions or potential dysregulations of genes,which play potential roles in male germ cell development,apoptosis,and spermatogenesis,were found in all cases(n=6).In addition,high read-depth GS detected dual molecular findings in case MI6,involving a complex rearrangement and two point mutations in the gene DNAH1.Overall,our study provided the molecular characteristics of apparently balanced interchromosomal structural rearrangements in patients with male infertility.We demonstrated the complexity of chromosomal structural rearrangements,potential gene disruptions/dysregulation and single-gene mutations could be the contributing mechanisms underlie male infertility.展开更多
Medicinal plants are renowned for their abundant production of secondary metabolites,which exhibit notable pharmacological activities and great potential for drug development.The biosynthesis of secondary metabolites ...Medicinal plants are renowned for their abundant production of secondary metabolites,which exhibit notable pharmacological activities and great potential for drug development.The biosynthesis of secondary metabolites is highly intricate and influenced by various intrinsic and extrinsic factors,resulting in substantial species diversity and content variation.Consequently,precise regulation of secondary metabolite synthesis is of utmost importance.In recent years,genome sequencing has emerged as a valuable tool for investigating the synthesis and regulation of secondary metabolites in medicinal plants,facilitated by the widespread use of high-throughput sequencing technologies.This review highlights the latest advancements in genome sequencing within this field and presents several strategies for studying secondary metabolites.Specifically,the article elucidates how genome sequencing can unravel the pathways for secondary metabolite synthesis in medicinal plants,offering insights into the functions and regulatory mechanisms of participating enzymes.Comparative analyses of plant genomes allow identification of shared pathways of metabolite synthesis among species,thereby providing novel avenues for obtaining cost-effective biosynthetic intermediates.By examining individual genomic variations,genes or gene clusters associated with the synthesis of specific compounds can be discovered,indicating potential targets and directions for drug development and the exploration of alternative compound sources.Moreover,the advent of gene-editing technology has enabled the precise modifications of medicinal plant genomes.Optimization of specific secondary metabolite synthesis pathways becomes thus feasible,enabling the precise editing of target genes to regulate secondary metabolite production within cells.These findings serve as valuable references and lessons for future drug development endeavors,conservation of rare resources,and the exploration of new resources.展开更多
Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be a...Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be associated with many physiological and pathological conditions（Bai and Wong,2005）.展开更多
The microbial potential of Penicillium has received critical attention.The present research aimed to elucidate the efficacy of crude enzyme secreted from Penicillium oxalicum WX-209 in degrading citrus segments and ev...The microbial potential of Penicillium has received critical attention.The present research aimed to elucidate the efficacy of crude enzyme secreted from Penicillium oxalicum WX-209 in degrading citrus segments and evaluate the safety of the process.Results showed that citrus segment membranes gradually dissolved after treatment with the crude enzyme solution,indicating good degradation capability.No significant differences in body weight,food ingestion rate,hematology,blood biochemistry,and weight changes of different organs were found between the enzyme intake and control groups.Serial experiments showed that the crude enzyme had high biological safety.Moreover,the whole genome of P.oxalicum WX-209 was sequenced by PacBio and Illumina platforms.Twenty-five scaffolds were assembled to generate 36 Mbp size of genome sequence comprising 11369 predicted genes modeled with a GC content of 48.33%.A total of 592 genes were annotated to encode enzymes related to carbohydrates,and some degradation enzyme genes were identified in strain P.oxalicum WX-209.展开更多
Objective:To surveill emerging variants by nanopore technology-based genome sequencing in different COVID-19 waves in Sri Lanka and to examine the association with the sample characteristics,and vaccination status.Met...Objective:To surveill emerging variants by nanopore technology-based genome sequencing in different COVID-19 waves in Sri Lanka and to examine the association with the sample characteristics,and vaccination status.Methods:The study analyzed 207 RNA positive swab samples received to sequence laboratory during different waves.The N gene cut-off threshold of less than 30 was considered as the major inclusion criteria.Viral RNA was extracted,and elutes were subjected to nanopore sequencing.All the sequencing data were uploaded in the publicly accessible database,GISAID.Results:The Omicron,Delta and Alpha variants accounted for 58%,22%and 4%of the variants throughout the period.Less than 1%were Kappa variant and 16%of the study samples remained unassigned.Omicron variant was circulated among all age groups and in all the provinces.Ct value and variants assigned percentage was 100%in Ct values of 10-15 while only 45%assigned Ct value over 25.Conclusions:The present study examined the emergence,prevalence,and distribution of SARS-CoV-2 variants locally and has shown that nanopore technology-based genome sequencing enables whole genome sequencing in a low resource setting country.展开更多
Objective To evaluate a single-reaction genome amplification method, the multisegment reverse transcription-PCR （M-RTPCR）, for its sensitivity to full genome sequencing of influenza A virus, and the ability to diffe...Objective To evaluate a single-reaction genome amplification method, the multisegment reverse transcription-PCR （M-RTPCR）, for its sensitivity to full genome sequencing of influenza A virus, and the ability to differentiate mix-subtype virus, using the next generation sequencing （NGS） platform. Methods Virus genome copy was quantified and seria（iy diluted to different titers, followed by amplification with the M-RTPCR method and sequencing on the NGS platform. Furthermore, we manually mixed two subtype viruses to different titer rate and amplified the mixed virus with the M-RTPCR protocol, followed by whole genome sequencing on the NGS platform. We also used clinical samples to test the method performance. Results The M-RTPCR method obtained complete genome of testing virus at 125 copies/reaction and determined the virus subtype at titer of 25 copies/reaction. Moreover, the two subtypes in the mixed virus could be discriminated, even though these two virus copies differed by 200-fold using this amplification protocol. The sensitivity of this protocol we detected using virus RNA was also confirmed with clinical samples containing Iow-titer virus. Conclusion The M-RTPCR is a robust and sensitive amplification method for whole genome sequencing of influenza A virus using NGS platform.展开更多
Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the...Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the community by immune evasion mechanisms. Due to mutation within S gene, most Omicron variants have reported S gene target failure (SGTF) with some commercially available PCR kits. Such diagnostic features can be used as markers to screen Omicron. However, Whole Genome Sequencing (WGS) is the only gold standard approach to confirm novel microorganisms at genetically level as similar mutations can also be found in other variants that are circulating at low frequencies worldwide. This Retrospective study is aimed to assess RT-PCR sensitivity in the detection of S gene target failure in comparison with whole genome sequencing to detect variants of Omicron. Methods: We have analysed retrospective data of SARS-CoV-2 positive RT-PCR samples for S gene target failure (SGTF) with TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) and combined with sequencing technologies to study the emerged pattern of SARS-CoV-2 variants during third wave at the tertiary care centre, Surat. Results: From the first day of December 2021 till the end of February 2022, a total of 321,803 diagnostic RT-PCR tests for SARS-CoV-2 were performed, of which 20,566 positive cases were reported at our tertiary care centre with an average cumulative positivity of 6.39% over a period of three months. In the month of December 21 samples characterized by the SGTF (70/129) were suggestive of being infected by the Omicron variant and identified as Omicron (B.1.1.529 lineage) when sequence. In the month of January, we analysed a subset of samples (n = 618) with SGTF (24%) and without SGTF (76%) with Ct values Conclusions: During the COVID-19 pandemic, it took almost more than 15 days to diagnose infection and identify pathogen by sequencing technology. In contrast to that molecular assay provided quick identification with the help of SGTF phenomenon within 5 hours of duration. This strategy helps scientists and health policymakers for the quick isolation and identification of clusters. That ultimately results in a decreased transmission of pathogen among the community.展开更多
Dear Editor,Neurodevelopmental disorders(NDD)are a group of diseases with high phenotypic heterogeneity characterized by inability in cognition,communication,psychological skills,and motor development.The common types...Dear Editor,Neurodevelopmental disorders(NDD)are a group of diseases with high phenotypic heterogeneity characterized by inability in cognition,communication,psychological skills,and motor development.The common types of NDDs include autism spectrum disorder(ASD),attention-deficit/hyperactivity disorder(ADHD),epilepsy,schizophrenia,etc.(Parenti et al.,2020).展开更多
Orchid origin and evolution are common topics in evolutionary biology. Orchidaceae have approximately 30 000 orchid species distributed in diverse habitats and account for approximately 10% of the flowering plant spec...Orchid origin and evolution are common topics in evolutionary biology. Orchidaceae have approximately 30 000 orchid species distributed in diverse habitats and account for approximately 10% of the flowering plant species worldwide. Orchids provide us with materials to explore coevolution and organic evolution. In this review, we highlighted the genome study progress of orchids. In addition, we revealed the role of MADS-box gene families in the floral morphology and evolution of orchids. Genomics studies confirmed that all five subfamilies of existing orchids evolved from a common ancestor. Loss of Mβ MADS-box genes resulted in the endosperm from the seed of all existing orchids being absent. Perianth reversion to the ancestral state occurred because Apostasia and Apostasioideae lost B-AP3 and E class paralogous genes. Loss of P-subclade members of MIKC*-Type in Phalaenopsis equestris, Dendrobium catenatum, and Epidendroideae caused the formation of pollinium.In addition, the combined loss of AGL12 and contraction of ANR1 gave orchids the ability to be successfully epiphytic on trees or rocks and to develop a unique root system. Both pollinium and epiphytic production on trees are beneficial for orchid adaptations, and Epidendroideae evolved more species(~ 20 000) than Apostasioideae(16 species). Genome studies shed new light on determining the evolutionary history of orchids and understanding the genetic mechanisms of orchid morphological evolution.展开更多
The bacterial pathogen Xanthomonas oryzae pv.oryzae(Xoo),belonging to Xanthomonas sp.,causes one of the most destructive vascular diseases in rice worldwide,particularly in Asia and Africa.To better understand Xoo pat...The bacterial pathogen Xanthomonas oryzae pv.oryzae(Xoo),belonging to Xanthomonas sp.,causes one of the most destructive vascular diseases in rice worldwide,particularly in Asia and Africa.To better understand Xoo pathogenesis,we performed genome sequencing of the Korea race 1 strain DY89031(J18)and analyzed the phylogenetic tree of 63 Xoo strains.We found that the rich diversity of evolutionary features is likely associated with the rice cultivation regions.Further,virulence effector proteins secreted by the type III secretion system(T3SS)of Xoo showed pathogenesis divergence.The genome of DY89031 shows a remarkable difference from that of the widely prevailed Philippines race 6 strain PXO99A,which is avirulent to rice Xa21,a well-known disease resistance(R)gene that can be broken down by DY89031.Interestingly,plant inoculation experiments with the PXO99A transformants expressing the DY89031 genes enabled us to identify additional TAL(transcription activator-like)and non-TAL effectors that may support DY89031-specific virulence.Characterization of DY89031 genome and identification of new effectors will facilitate the investigation of the rice-Xoo interaction and new mechanisms involved.展开更多
Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly ...Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. Methods In this proof-of-concept study using Enterovirus 71 （EV71） and Coxsackievirus A16 （CA16） strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Results Within the first minute （min） of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min （on average）, 99% identity was achieved for 10 CA16 strains in a single run. Conclusion MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use.展开更多
In this study,the safety of Levilactobacillus brevis CGMCC1.5954 was evaluated,which has probiotic properties,through both in vitro methods such as antibiotic susceptibility testing,biogenic amine testing,and virulenc...In this study,the safety of Levilactobacillus brevis CGMCC1.5954 was evaluated,which has probiotic properties,through both in vitro methods such as antibiotic susceptibility testing,biogenic amine testing,and virulence gene analysis,and in vivo methods including biochemical testing,routine blood index testing,and bacterial displacement capacity analysis.The results of HPLC analysis revealed that during incubation,L.brevis CGMCC1.5954 did not secrete cadaverine,histamine,putrescine,or tyramine.It exhibited sensitivity to tetra-cyclines,macrolides,cephalosporins,β-lactamase inhibitor complex,and other antibiotics,but not to amino-glycosides and quinolones,which is consistent with the behavior of other lactic acid bacteria.Its genome encodes a total of 2314 genes,including 1743 proteins and 109 signal peptides.Notably,no virulence genes were found in this genome.Additionally,the gene encoding the production ofγ-aminobutyric acid was found in it.In vivo experiments indicated that gavage feeding of L.brevis CGMCC1.5954 for 28 d had no significant effect on normal growth,blood hemoglobin level,erythrocytes,white blood cells,and other routine blood parameters in mice.Furthermore,there was no migration of it observed in the liver,kidney,spleen,or blood during the feeding trial,which indicated that it did not cause any infections.Moreover,H&E staining showed no evidence of lesion damage to the liver,kidney,or other organs.To sum up,L.brevis CGMCC1.5954 is considered safe for producing fermented foods,especially those that contain high levels ofγ-aminobutyric acid.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
Pichia fermentans is an important non-Saccharomyces yeast applied in mixed fermentation to enhance fruity and floral traits of wine aroma.In this study,genome sequencing of P.fermentans Z9Y-3 was performed using the P...Pichia fermentans is an important non-Saccharomyces yeast applied in mixed fermentation to enhance fruity and floral traits of wine aroma.In this study,genome sequencing of P.fermentans Z9Y-3 was performed using the PacBio single-molecule real-time sequencing platform,and was further assembled using MECAT.The sequenced genes are annotated by non-redundant protein(Nr),Gene Ontology(GO),Cluster of Orthologous Groups of proteins(COG),Kyoto Encyclopedia of Genes and Genomes(KEGG)and carbohydrate-active enzymes(CAZymes)database.Results indicated that the genome size was about 13.5 Mb with 42.09%GC content and 4730 protein coding genes.The 95.90%genes were annotated to the non-redundant protein(Nr)database,and then annotated to GO database.The 62.64%genes annotated to the COG database revealed 25 functional groups.The 58.22%genes annotated to the KEGG database revealed 5 groups.The 586 genes were annotated to CAZymes,in which two genes bglH and bglC encoding beta-glucosidase were found and further analyzed its motifs.A terpene and a nonribosomal peptides like secondary metabolic gene clusters were predicted using antiSMASH 7.0.0.This study benefits us to understand physiological and biochemical behavior of P.fermentans Z9Y-3 at a molecular level to better use P.fermentans Z9Y-3 in aroma enhancing winemaking.展开更多
Dibutyl phthalate(DBP)is widely used as a plasticizer in plastic food packaging and has attracted extensive attention due to its residual hazards and ability to accumulate.Microbial degradation is a very effective way...Dibutyl phthalate(DBP)is widely used as a plasticizer in plastic food packaging and has attracted extensive attention due to its residual hazards and ability to accumulate.Microbial degradation is a very effective way to remove DBP from a polluted environment.In this study,Stenotrophomonas acidaminiphila BDBP 071,a strain that efficiently degraded DBP was isolated from tomato rhizosphere soil.To obtain a comprehensive understanding of the degradation mechanism of DBP by S.acidaminiphila strain BDBP 071,whole genome sequencing of this strain was performed.The results showed that the genome size of BDBP 071 was 3.87 Mb,the G+C content was 69.43%,and the number of predicted coding sequences was 3484.Based on whole genome sequencing,the metabolic pathway related to DBP biotransformation was obtained,and key genes were subsequently verified by a real-time quantitative polymerase chain reaction to infer the degradation pathway of DBP.It was preliminarily predicted that the relative expression of monoester hydrolase of EstB3 is increased in this strain.This study provides a scientific basis for applying S.acidaminiphila BDBP 071 in environmental pollution bioremediation,as well as a rich resource for DBP biodegradation genes.展开更多
Fundamental improvement was made for genome sequencing since the next-generation sequencing （NGS） came out in the 2000s. The newer technologies make use of the power of massively-parallel short-read DNA sequencing, ...Fundamental improvement was made for genome sequencing since the next-generation sequencing （NGS） came out in the 2000s. The newer technologies make use of the power of massively-parallel short-read DNA sequencing, genome alignment and assembly methods to digitally and rapidly search the genomes on a revolutionary scale, which enable large-scale whole genome sequencing （WGS） accessible and practical for researchers. Nowadays, whole genome sequencing is more and more prevalent in detecting the genetics of diseases, studying causative relations with cancers, making genome-level comparative analysis, reconstruction of human population history, and giving clinical implications and instructions. In this review, we first give a typical pipeline of whole genome sequencing, including the lab template preparation, sequencing, genome assembling and quality control, variants calling and annotations. We compare the difference between whole genome and whole exome sequencing （WES）, and explore a wide range of applications of whole genome sequencing for both mendelian diseases and complex diseases in medical genetics. We highlight the impact of whole genome sequencing in cancer studies, regulatory variant analysis, predictive medicine and precision medicine, as well as discuss the challenges of the whole genome sequencing.展开更多
The first sequenced diploid cotton genome was published in2012 by the group led by the Institute of Cotton Research,Chinese Academy of Agricultural Sciences.Cotton genomics research subsequently entered a period of ra...The first sequenced diploid cotton genome was published in2012 by the group led by the Institute of Cotton Research,Chinese Academy of Agricultural Sciences.Cotton genomics research subsequently entered a period of rapid development.展开更多
In the food industry,bacterial cells usually adhere to equipment surfaces,forming biofilms that may cause persistent contamination.This study aimed to identify the key genes responsible for the stronger biofilm-formin...In the food industry,bacterial cells usually adhere to equipment surfaces,forming biofilms that may cause persistent contamination.This study aimed to identify the key genes responsible for the stronger biofilm-forming capability of the Listeria monocytogenes LMB33426 strain compared to that of the L.monocytogenes CICC 21662 strain through comparative genomics.Additionally,the expression of genes and related metabolic pathways of LMB 33426 and CICC 21662 strains were analyzed at the transcriptional level by high-throughput sequencing technology to uncover key differentially expressed genes between planktonic and biofilm cells of those two strains.Subsequently,the key genes found to present differences that were uncovered by those genome-wide and transcriptomic analyses were used to construct gene deletion strains.The crystalline violet assay and motility assay showed that GL002291,GL002712 and Imo1438 genes were involved in the regulation of biofilm formation as well as motility.The hydrophobicity and auto-aggregation ability assay results demonstrated an association between the clpB,lmo1438,and lmo0294 genes and bacterial adhesion.However,no significant differences were found regarding this association in the GL002291 and GL002712 genes.This study elucidates some potential regulatory genes associated with biofi lm formation in L.monocytogenes,and laying a theoretical foundation for future research.展开更多
基金This work was supported by grants from the National Academy of Agricultural Science(Code #200901FHT020508369)the BioGreen21 Program(Code #20050301034438 and Code #20070301034037),Rural Development Administration, Republic of Korea
文摘As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome （BAC） by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa.
基金supported by the National Natural Science Foundation of China(No.31801042)the Health and Medical Research Fund(No.04152666 and No.07180576)General Research Fund(No.14115418),and Direct Grant(No.2020.052).
文摘Apparently balanced chromosomal structural rearrangements are known to cause male infertility and account for approximately 1%of azoospermia or severe oligospermia.However,the underlying mechanisms of pathogenesis and etiologies are still largely unknown.Herein,we investigated apparently balanced interchromosomal structural rearrangements in six cases with azoospermia/severe oligospermia to comprehensively identify and delineate cryptic structural rearrangements and the related copy number variants.In addition,high read-depth genome sequencing(GS)(30-fold)was performed to investigate point mutations causative of male infertility.Mate-pair GS(4-fold)revealed additional structural rearrangements and/or copy number changes in 5 of 6 cases and detected a total of 48 rearrangements.Overall,the breakpoints caused truncations of 30 RefSeq genes,five of which were associated with spermatogenesis.Furthermore,the breakpoints disrupted 43 topological-associated domains.Direct disruptions or potential dysregulations of genes,which play potential roles in male germ cell development,apoptosis,and spermatogenesis,were found in all cases(n=6).In addition,high read-depth GS detected dual molecular findings in case MI6,involving a complex rearrangement and two point mutations in the gene DNAH1.Overall,our study provided the molecular characteristics of apparently balanced interchromosomal structural rearrangements in patients with male infertility.We demonstrated the complexity of chromosomal structural rearrangements,potential gene disruptions/dysregulation and single-gene mutations could be the contributing mechanisms underlie male infertility.
基金funded by the National Natural Science Foundation of China,grant number 81603221.
文摘Medicinal plants are renowned for their abundant production of secondary metabolites,which exhibit notable pharmacological activities and great potential for drug development.The biosynthesis of secondary metabolites is highly intricate and influenced by various intrinsic and extrinsic factors,resulting in substantial species diversity and content variation.Consequently,precise regulation of secondary metabolite synthesis is of utmost importance.In recent years,genome sequencing has emerged as a valuable tool for investigating the synthesis and regulation of secondary metabolites in medicinal plants,facilitated by the widespread use of high-throughput sequencing technologies.This review highlights the latest advancements in genome sequencing within this field and presents several strategies for studying secondary metabolites.Specifically,the article elucidates how genome sequencing can unravel the pathways for secondary metabolite synthesis in medicinal plants,offering insights into the functions and regulatory mechanisms of participating enzymes.Comparative analyses of plant genomes allow identification of shared pathways of metabolite synthesis among species,thereby providing novel avenues for obtaining cost-effective biosynthetic intermediates.By examining individual genomic variations,genes or gene clusters associated with the synthesis of specific compounds can be discovered,indicating potential targets and directions for drug development and the exploration of alternative compound sources.Moreover,the advent of gene-editing technology has enabled the precise modifications of medicinal plant genomes.Optimization of specific secondary metabolite synthesis pathways becomes thus feasible,enabling the precise editing of target genes to regulate secondary metabolite production within cells.These findings serve as valuable references and lessons for future drug development endeavors,conservation of rare resources,and the exploration of new resources.
文摘Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be associated with many physiological and pathological conditions（Bai and Wong,2005）.
基金the financial support of the National Natural Science Foundation of China[32201960,32073020]Science and Technology Innovation Program of Hunan Province[2022RC1150]+2 种基金Changsha Municipal Natural Science Foundation[kq2202332]Hunan innovative province construction project[2019NK2041]Agricultural Science and Technology Innovation Project of Hunan Province[2021CX05].
文摘The microbial potential of Penicillium has received critical attention.The present research aimed to elucidate the efficacy of crude enzyme secreted from Penicillium oxalicum WX-209 in degrading citrus segments and evaluate the safety of the process.Results showed that citrus segment membranes gradually dissolved after treatment with the crude enzyme solution,indicating good degradation capability.No significant differences in body weight,food ingestion rate,hematology,blood biochemistry,and weight changes of different organs were found between the enzyme intake and control groups.Serial experiments showed that the crude enzyme had high biological safety.Moreover,the whole genome of P.oxalicum WX-209 was sequenced by PacBio and Illumina platforms.Twenty-five scaffolds were assembled to generate 36 Mbp size of genome sequence comprising 11369 predicted genes modeled with a GC content of 48.33%.A total of 592 genes were annotated to encode enzymes related to carbohydrates,and some degradation enzyme genes were identified in strain P.oxalicum WX-209.
文摘Objective:To surveill emerging variants by nanopore technology-based genome sequencing in different COVID-19 waves in Sri Lanka and to examine the association with the sample characteristics,and vaccination status.Methods:The study analyzed 207 RNA positive swab samples received to sequence laboratory during different waves.The N gene cut-off threshold of less than 30 was considered as the major inclusion criteria.Viral RNA was extracted,and elutes were subjected to nanopore sequencing.All the sequencing data were uploaded in the publicly accessible database,GISAID.Results:The Omicron,Delta and Alpha variants accounted for 58%,22%and 4%of the variants throughout the period.Less than 1%were Kappa variant and 16%of the study samples remained unassigned.Omicron variant was circulated among all age groups and in all the provinces.Ct value and variants assigned percentage was 100%in Ct values of 10-15 while only 45%assigned Ct value over 25.Conclusions:The present study examined the emergence,prevalence,and distribution of SARS-CoV-2 variants locally and has shown that nanopore technology-based genome sequencing enables whole genome sequencing in a low resource setting country.
基金funded by a project(2014ZX10004002)of the Chinese National Key Program of Mega Infectious Disease of the National 12th Five-Year Plan
文摘Objective To evaluate a single-reaction genome amplification method, the multisegment reverse transcription-PCR （M-RTPCR）, for its sensitivity to full genome sequencing of influenza A virus, and the ability to differentiate mix-subtype virus, using the next generation sequencing （NGS） platform. Methods Virus genome copy was quantified and seria（iy diluted to different titers, followed by amplification with the M-RTPCR method and sequencing on the NGS platform. Furthermore, we manually mixed two subtype viruses to different titer rate and amplified the mixed virus with the M-RTPCR protocol, followed by whole genome sequencing on the NGS platform. We also used clinical samples to test the method performance. Results The M-RTPCR method obtained complete genome of testing virus at 125 copies/reaction and determined the virus subtype at titer of 25 copies/reaction. Moreover, the two subtypes in the mixed virus could be discriminated, even though these two virus copies differed by 200-fold using this amplification protocol. The sensitivity of this protocol we detected using virus RNA was also confirmed with clinical samples containing Iow-titer virus. Conclusion The M-RTPCR is a robust and sensitive amplification method for whole genome sequencing of influenza A virus using NGS platform.
文摘Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the community by immune evasion mechanisms. Due to mutation within S gene, most Omicron variants have reported S gene target failure (SGTF) with some commercially available PCR kits. Such diagnostic features can be used as markers to screen Omicron. However, Whole Genome Sequencing (WGS) is the only gold standard approach to confirm novel microorganisms at genetically level as similar mutations can also be found in other variants that are circulating at low frequencies worldwide. This Retrospective study is aimed to assess RT-PCR sensitivity in the detection of S gene target failure in comparison with whole genome sequencing to detect variants of Omicron. Methods: We have analysed retrospective data of SARS-CoV-2 positive RT-PCR samples for S gene target failure (SGTF) with TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) and combined with sequencing technologies to study the emerged pattern of SARS-CoV-2 variants during third wave at the tertiary care centre, Surat. Results: From the first day of December 2021 till the end of February 2022, a total of 321,803 diagnostic RT-PCR tests for SARS-CoV-2 were performed, of which 20,566 positive cases were reported at our tertiary care centre with an average cumulative positivity of 6.39% over a period of three months. In the month of December 21 samples characterized by the SGTF (70/129) were suggestive of being infected by the Omicron variant and identified as Omicron (B.1.1.529 lineage) when sequence. In the month of January, we analysed a subset of samples (n = 618) with SGTF (24%) and without SGTF (76%) with Ct values Conclusions: During the COVID-19 pandemic, it took almost more than 15 days to diagnose infection and identify pathogen by sequencing technology. In contrast to that molecular assay provided quick identification with the help of SGTF phenomenon within 5 hours of duration. This strategy helps scientists and health policymakers for the quick isolation and identification of clusters. That ultimately results in a decreased transmission of pathogen among the community.
基金supported by the National Key Research and Development Program of China(2022YFC2703900)the CAMS Innovation Fund for Medical Sciences(2021-I2M-1018)+1 种基金the National Natural Science Foundation of China(82394420 and 82394423)the Theranostics and Translational Research Facility of National Infrastructures for Translational Medicine,Institute of Clinical Medicine,Peking Union Medical College Hospital,Chinese Academy of Medical Sciences&Peking Union Medical College for the support。
文摘Dear Editor,Neurodevelopmental disorders(NDD)are a group of diseases with high phenotypic heterogeneity characterized by inability in cognition,communication,psychological skills,and motor development.The common types of NDDs include autism spectrum disorder(ASD),attention-deficit/hyperactivity disorder(ADHD),epilepsy,schizophrenia,etc.(Parenti et al.,2020).
基金supported by the Teamwork Projects Funded by Guangdong Natural Science Foundation,China(Grant No.2017A030312004)The National Natural Science Foundation of China(Grant No.31870199)+2 种基金The National Key Research and Development Program of China(Grant No.2018YFD1000401)Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization Construction Funds(Grant No.115/118990050115/KJG18016A)。
文摘Orchid origin and evolution are common topics in evolutionary biology. Orchidaceae have approximately 30 000 orchid species distributed in diverse habitats and account for approximately 10% of the flowering plant species worldwide. Orchids provide us with materials to explore coevolution and organic evolution. In this review, we highlighted the genome study progress of orchids. In addition, we revealed the role of MADS-box gene families in the floral morphology and evolution of orchids. Genomics studies confirmed that all five subfamilies of existing orchids evolved from a common ancestor. Loss of Mβ MADS-box genes resulted in the endosperm from the seed of all existing orchids being absent. Perianth reversion to the ancestral state occurred because Apostasia and Apostasioideae lost B-AP3 and E class paralogous genes. Loss of P-subclade members of MIKC*-Type in Phalaenopsis equestris, Dendrobium catenatum, and Epidendroideae caused the formation of pollinium.In addition, the combined loss of AGL12 and contraction of ANR1 gave orchids the ability to be successfully epiphytic on trees or rocks and to develop a unique root system. Both pollinium and epiphytic production on trees are beneficial for orchid adaptations, and Epidendroideae evolved more species(~ 20 000) than Apostasioideae(16 species). Genome studies shed new light on determining the evolutionary history of orchids and understanding the genetic mechanisms of orchid morphological evolution.
基金supported by Chinese Academy of Sciences(XDB27040201)the National Natural Science Foundation of China(3181101746)。
文摘The bacterial pathogen Xanthomonas oryzae pv.oryzae(Xoo),belonging to Xanthomonas sp.,causes one of the most destructive vascular diseases in rice worldwide,particularly in Asia and Africa.To better understand Xoo pathogenesis,we performed genome sequencing of the Korea race 1 strain DY89031(J18)and analyzed the phylogenetic tree of 63 Xoo strains.We found that the rich diversity of evolutionary features is likely associated with the rice cultivation regions.Further,virulence effector proteins secreted by the type III secretion system(T3SS)of Xoo showed pathogenesis divergence.The genome of DY89031 shows a remarkable difference from that of the widely prevailed Philippines race 6 strain PXO99A,which is avirulent to rice Xa21,a well-known disease resistance(R)gene that can be broken down by DY89031.Interestingly,plant inoculation experiments with the PXO99A transformants expressing the DY89031 genes enabled us to identify additional TAL(transcription activator-like)and non-TAL effectors that may support DY89031-specific virulence.Characterization of DY89031 genome and identification of new effectors will facilitate the investigation of the rice-Xoo interaction and new mechanisms involved.
基金supported by the National key research and development plan(2016TFC1202700,2016YFC1200900)Beijing Municipal Science&Technology Commission project(grant numbers D151100002115003)Guangzhou Municipal Science&Technology Commission project(grant numbers 2015B2150820)
文摘Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. Methods In this proof-of-concept study using Enterovirus 71 （EV71） and Coxsackievirus A16 （CA16） strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Results Within the first minute （min） of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min （on average）, 99% identity was achieved for 10 CA16 strains in a single run. Conclusion MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use.
基金supported by the Natural Science Funding of China(31972048,32272339)the outstanding youth fund of Zhejiang Prov-ince(LR22C200001)National Key R&D Program of China(2021YFD2100104).
文摘In this study,the safety of Levilactobacillus brevis CGMCC1.5954 was evaluated,which has probiotic properties,through both in vitro methods such as antibiotic susceptibility testing,biogenic amine testing,and virulence gene analysis,and in vivo methods including biochemical testing,routine blood index testing,and bacterial displacement capacity analysis.The results of HPLC analysis revealed that during incubation,L.brevis CGMCC1.5954 did not secrete cadaverine,histamine,putrescine,or tyramine.It exhibited sensitivity to tetra-cyclines,macrolides,cephalosporins,β-lactamase inhibitor complex,and other antibiotics,but not to amino-glycosides and quinolones,which is consistent with the behavior of other lactic acid bacteria.Its genome encodes a total of 2314 genes,including 1743 proteins and 109 signal peptides.Notably,no virulence genes were found in this genome.Additionally,the gene encoding the production ofγ-aminobutyric acid was found in it.In vivo experiments indicated that gavage feeding of L.brevis CGMCC1.5954 for 28 d had no significant effect on normal growth,blood hemoglobin level,erythrocytes,white blood cells,and other routine blood parameters in mice.Furthermore,there was no migration of it observed in the liver,kidney,spleen,or blood during the feeding trial,which indicated that it did not cause any infections.Moreover,H&E staining showed no evidence of lesion damage to the liver,kidney,or other organs.To sum up,L.brevis CGMCC1.5954 is considered safe for producing fermented foods,especially those that contain high levels ofγ-aminobutyric acid.
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financially supported by the Basic Research Program of Natural Science in Shaanxi Province(2023-JC-YB-145)the National Natural Science Foundation of China(31801528 and 31972199)+2 种基金the Shaanxi Provincial Science and Technology Project for Innovation Team(2023-CX-TD-59)the Key Science and Technology Project of Xinjiang Uygur Autonomous Region(2022A02002-4)the Key Research and Development Project of Xinjiang Uygur Autonomous Region in the 14th Five Year Plan(2020B01005-2).
文摘Pichia fermentans is an important non-Saccharomyces yeast applied in mixed fermentation to enhance fruity and floral traits of wine aroma.In this study,genome sequencing of P.fermentans Z9Y-3 was performed using the PacBio single-molecule real-time sequencing platform,and was further assembled using MECAT.The sequenced genes are annotated by non-redundant protein(Nr),Gene Ontology(GO),Cluster of Orthologous Groups of proteins(COG),Kyoto Encyclopedia of Genes and Genomes(KEGG)and carbohydrate-active enzymes(CAZymes)database.Results indicated that the genome size was about 13.5 Mb with 42.09%GC content and 4730 protein coding genes.The 95.90%genes were annotated to the non-redundant protein(Nr)database,and then annotated to GO database.The 62.64%genes annotated to the COG database revealed 25 functional groups.The 58.22%genes annotated to the KEGG database revealed 5 groups.The 586 genes were annotated to CAZymes,in which two genes bglH and bglC encoding beta-glucosidase were found and further analyzed its motifs.A terpene and a nonribosomal peptides like secondary metabolic gene clusters were predicted using antiSMASH 7.0.0.This study benefits us to understand physiological and biochemical behavior of P.fermentans Z9Y-3 at a molecular level to better use P.fermentans Z9Y-3 in aroma enhancing winemaking.
基金funded by the National Nature Science Foundation of China(32102094)Application Foundation Project of Sichuan Provincial Department of Science and Technology(2019YJ0389)+4 种基金Science and Technology Support Project of Sichuan Province(No.2019ZYZF0170)Technological Innovation Project of Chengdu Science and Technology Bureau(2018-YF05-00522-SN)Key Scientifc Research Fund of Xihua University(Z1310525)Science and Technology Programme Project of Sichuan Province(2019ZYZF0170)the Natural Science Foundation of Sichuan Province(Grant number 2022NSFSC0105).
文摘Dibutyl phthalate(DBP)is widely used as a plasticizer in plastic food packaging and has attracted extensive attention due to its residual hazards and ability to accumulate.Microbial degradation is a very effective way to remove DBP from a polluted environment.In this study,Stenotrophomonas acidaminiphila BDBP 071,a strain that efficiently degraded DBP was isolated from tomato rhizosphere soil.To obtain a comprehensive understanding of the degradation mechanism of DBP by S.acidaminiphila strain BDBP 071,whole genome sequencing of this strain was performed.The results showed that the genome size of BDBP 071 was 3.87 Mb,the G+C content was 69.43%,and the number of predicted coding sequences was 3484.Based on whole genome sequencing,the metabolic pathway related to DBP biotransformation was obtained,and key genes were subsequently verified by a real-time quantitative polymerase chain reaction to infer the degradation pathway of DBP.It was preliminarily predicted that the relative expression of monoester hydrolase of EstB3 is increased in this strain.This study provides a scientific basis for applying S.acidaminiphila BDBP 071 in environmental pollution bioremediation,as well as a rich resource for DBP biodegradation genes.
基金ACKNOWLEDGEMENTS This research was partially supported by the National Basic Research Program of China （No. 2012CB316504）, the National High Technology Research and Development Program of China （No. 2012AA020401）, the National Natural Science Foundation of China （Nos. 61573207 and 61175002） and Beijing Collaborative Innovation Center for Cardiovascular Disorders.
文摘Fundamental improvement was made for genome sequencing since the next-generation sequencing （NGS） came out in the 2000s. The newer technologies make use of the power of massively-parallel short-read DNA sequencing, genome alignment and assembly methods to digitally and rapidly search the genomes on a revolutionary scale, which enable large-scale whole genome sequencing （WGS） accessible and practical for researchers. Nowadays, whole genome sequencing is more and more prevalent in detecting the genetics of diseases, studying causative relations with cancers, making genome-level comparative analysis, reconstruction of human population history, and giving clinical implications and instructions. In this review, we first give a typical pipeline of whole genome sequencing, including the lab template preparation, sequencing, genome assembling and quality control, variants calling and annotations. We compare the difference between whole genome and whole exome sequencing （WES）, and explore a wide range of applications of whole genome sequencing for both mendelian diseases and complex diseases in medical genetics. We highlight the impact of whole genome sequencing in cancer studies, regulatory variant analysis, predictive medicine and precision medicine, as well as discuss the challenges of the whole genome sequencing.
基金supported by the Funds for Creative Research Groups of China(31621005)Young Elite Scientist Sponsorship Program by CAST
文摘The first sequenced diploid cotton genome was published in2012 by the group led by the Institute of Cotton Research,Chinese Academy of Agricultural Sciences.Cotton genomics research subsequently entered a period of rapid development.
基金supported by the National Natural Science Foundation of China(32272295)the Agricultural Independent Innovation Program in Jiangsu Province(CX(23)3043)the Postgraduate Research&Practice Innovation Program of Jiangsu Province(KYCX23_0770).
文摘In the food industry,bacterial cells usually adhere to equipment surfaces,forming biofilms that may cause persistent contamination.This study aimed to identify the key genes responsible for the stronger biofilm-forming capability of the Listeria monocytogenes LMB33426 strain compared to that of the L.monocytogenes CICC 21662 strain through comparative genomics.Additionally,the expression of genes and related metabolic pathways of LMB 33426 and CICC 21662 strains were analyzed at the transcriptional level by high-throughput sequencing technology to uncover key differentially expressed genes between planktonic and biofilm cells of those two strains.Subsequently,the key genes found to present differences that were uncovered by those genome-wide and transcriptomic analyses were used to construct gene deletion strains.The crystalline violet assay and motility assay showed that GL002291,GL002712 and Imo1438 genes were involved in the regulation of biofilm formation as well as motility.The hydrophobicity and auto-aggregation ability assay results demonstrated an association between the clpB,lmo1438,and lmo0294 genes and bacterial adhesion.However,no significant differences were found regarding this association in the GL002291 and GL002712 genes.This study elucidates some potential regulatory genes associated with biofi lm formation in L.monocytogenes,and laying a theoretical foundation for future research.
