Fig.1.The GenomeSyn tool for visualizing genome synteny and characterizing structural variations.A:The first synteny visualization map showed the detailed information of two or three genomes and can display structural...Fig.1.The GenomeSyn tool for visualizing genome synteny and characterizing structural variations.A:The first synteny visualization map showed the detailed information of two or three genomes and can display structural variations and other annotation information.B:The second type of visualization map was simple and only showed the synteny relationship between the chromosomes of two or three genomes.C:Multiplatform general GenomeSyn submission page,applicable to Windows,MAC and web platforms;other analysis files can be entered in the"other"option.The publisher would like to apologise for any inconvenience caused.展开更多
Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(...Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(SSB1 and SSB2).However,the functional divergence of these two SSB copies in plants remains largely unknown,and detailed studies regarding their roles in the replication and recombination of organellar genomes are still incomplete.In this study,phylogenetic,gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed plants.Based on accurate long-read sequencing results,ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA(mtDNA)and plastid DNA(ptDNA),accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both genomes.Our findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.展开更多
In-depth knowledge of the microbes responsible for biogenic amine(BA)production during soy sauce fermentation remains limited.Herein,the variations in the BA profiles,microbial communities,and microbes involved in BA ...In-depth knowledge of the microbes responsible for biogenic amine(BA)production during soy sauce fermentation remains limited.Herein,the variations in the BA profiles,microbial communities,and microbes involved in BA production during the fermentation of soy sauce through Japanese-type(JP)and Cantonese-type(CP)processes were compared.BA analysis revealed that the most abundant BA species were putrescine,tyramine,and histamine in the later three stages(1187.68,785.16,and 193.20 mg/kg on average,respectively).The BA profiles differed significantly,with CP samples containing higher contents of putrescine,tyramine,and histamine(P<0.05)at the end of fermentation.Metagenomic analysis indicated that BA-producing genes exhibited different abundance profiles,with most genes,including spe A,spe B,arg,spe E,and tyr DC,having higher abundances in microbial communities during the CP process.In total,15 high-quality metagenome-assembled genomes(MAGs)were retrieved,of which 10 encoded at BA production-related genes.Enterococcus faecium(MAG10)and Weissella paramesenteroides(MAG5)might be the major tyramine producers.The high putrescine content in CP might be associated with the high abundance of Staphylococcus gallinarum(MAG8).This study provides a comprehensive understanding of the diversity and abundance of genes involved in BA synthesis,especially at the species level,during food fermentation.展开更多
Background Traditional genomic analysis relies on a single reference genome,which struggles to effectively characterize the genetic diversity among populations.This is due to the substantial genetic differences betwee...Background Traditional genomic analysis relies on a single reference genome,which struggles to effectively characterize the genetic diversity among populations.This is due to the substantial genetic differences between the genome of the studied species and the reference genome,potentially introducing reference bias.Results In this study,we focused on Guanzhong Black pigs(GZB),Danish Large White pigs(DLW),and their hybrid offspring,Qinchuan Black pigs(QCB).We provided two high-quality parental genomes at the chromosomal level and constructed a parental genomic reference panel to detect SNPs(single nucleotide polymorphisms),INDELs(insertions and deletions),and SVs(structural variations).Compared with the single-reference method,the integrated parental genomic strategy identified 5.48%more SNPs and 67.84%more INDELs.The uniformity of variant distribution and genome functional annotation remained consistent before and after integration,while the ratio of nonreference/non-reference genotypes was also improved.In population genetic structure analysis,principal component analysis(PCA)of the three variant types(SNPs,INDELs,and SVs)exhibited good clustering effects,and ADMIXTURE analysis demonstrated consistent stratification.Selection signal analysis based on the integrated parental genomic strategy successfully identified more differentiated windows and positively selected genes.By leveraging multiple variant types and employing two selection signal methods,we jointly identified several novel intramuscular fat candidate genes(MSMO1,SMC6,CCDC158,KIT,CCNC,etc.),which could not be identified by the single-reference method alone.Functional validation of the gene MSMO1 revealed its role in promoting intramuscular adipocyte proliferation and inhibiting adipogenic differentiation.Conclusions This study is the first to construct a parental genomic reference panel specifically for pig hybrid populations,which significantly reduces reference bias and exhibits superior performance in downstream analyses.This strategy offers new possibilities for genomic selection breeding of livestock and establishes a methodological foundation for precisely dissecting complex traits in hybrid populations.展开更多
Complete plastid genomes have been proposed as potential“super-barcodes”for plant identification and delineation,particularly in cases where standard DNA barcodes may be insufficient.However,few studies have systema...Complete plastid genomes have been proposed as potential“super-barcodes”for plant identification and delineation,particularly in cases where standard DNA barcodes may be insufficient.However,few studies have systematically addressed how taxonomic complexity,especially in rapidly radiating lineages with intricate evolutionary histories,might influencethe efficacyof plastome-scale barcodes.Pedicularis is a hyperdiverse genus in the Himalaya-Hengduan Mountains,and previous studies have demonstrated high discriminatory power of the standard barcodes within this genus.Therefore,Pedicularis serves as a model for investigating the key plastome-sequence characteristics and biological phenomena that determine species-discrimination capacity.In this study,we evaluated 292 plastomes representing 96 Pedicularis species to compare the discriminatory power of complete plastid genomes with of standard DNA barcodes.Our results revealed that the traditional standard barcode combination(nrITS+matK+rbcL+trnH-psbA)achieved the highest discrimination rates(81.25%),closely followed by the plastid large single copy(LSC)region(80.21%),then by full plastome,the supermatrix of proteincoding genes,and hypervariable regions(79.17%).Notably,the matK and ycf1 gene alone could discriminate 78.13%of species.Key determinants of species discrimination by integrating alignment length(AL)and the proportion of parsimony-informative sites(PPIS),as well as conserved genes under relaxed selection exhibiting stronger discriminatory capacity.Unlike previous studies that demonstrated superior discrimination rates of plastome-scale barcodes,this study reveals a notable exception of minimal differences between traditional DNA and plastome-scale barcodes that appearing linked to Pedicularis’specificbiological habits and potentially reflectingunique evolutionary patterns in the plastid genome.展开更多
Despite most eel gobies(Gobionellidae:Amblyopinae)have inhabited brackish or marine waters,few species(such as Taenioides sp.)have been found to invade multiple inland freshwaters via artificial water transfer project...Despite most eel gobies(Gobionellidae:Amblyopinae)have inhabited brackish or marine waters,few species(such as Taenioides sp.)have been found to invade multiple inland freshwaters via artificial water transfer projects.The habitat transfers from brackish water to freshwater zones of Taenioides sp.have caused severe damage to Chinese aquatic ecosystems in recent years.Unfortunately,the molecular mechanism underlying freshwater invasion remains poorly understood.Considering changes of environmental factors,especially salinity,are bound to adjust the demands for energy affected by mitochondria via oxidative phosphorylation,13 Amblyopinae mitogenomes were compared,including the newly assembled Taenioides sp.mitogenome in this study.Comparative mitogenomic analyses revealed a highly conserved structure,composition and arrangements,with the exception of variable control region(CR).All of the CRs possessed tandem repeat sequences except Trypauchenopsis sp.G341,differing in motifs and number of copies,which was the dominant factor resulting in length heterogeneity of CR.The phylogenetic trees reconfirmed the paraphyletic origin of Amblyopinae with respect to Oxudercinae,supporting that these two subfamilies should be merged as an expansion of phenotypic variation within the“terrestrial goby”clade.Furthermore,four protein coding genes(COI,ND3,ND5 and Cyt b)in Taenioides sp.mitogenome have experienced adaptive evolution,indicating their important roles in enhancing the efficiency of ATP production to cope with the osmotic regulation adjustment and reach its current widespread distribution in multiple inland freshwaters of China.These results revealed the functional importance of mitochondrial genes,and provided fresh insights into the molecular mechanisms underlying the freshwater invasion.Also,our results may provide critical reference value for the future control of other invasive species.展开更多
MATLAB software and optimal complete subgraph algorithm were used to extract and reveal the microsatellite distribution features in the complete genomes of the tobacco vein clearing virus （NC-003 378.1） from the NCB...MATLAB software and optimal complete subgraph algorithm were used to extract and reveal the microsatellite distribution features in the complete genomes of the tobacco vein clearing virus （NC-003 378.1） from the NCBI database.The results showed that the repetitions number and their location of the N-base group has been extracted and displayed.The largest repetitions of N-base group in the complete genomes of the tobacco vein clearing virus was decreased as the exponential function with the increasing of N.The method used in this study could be applied to the extraction and revealing of the microsatellite distribution features in the complete genomes of other viruses,thereby provided a basis for the research of the structure and the law of function,inheritance and variation by the using of the microsatellite distribution features.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 genomes of three groups of grass carp, namely the Xiangjiang River grass carp group （Xiangjiang group）, a one-generation artificially induced meio-gynogenetic grass carp group （meio-gynogenetic-1 group）, and a...The genomes of three groups of grass carp, namely the Xiangjiang River grass carp group （Xiangjiang group）, a one-generation artificially induced meio-gynogenetic grass carp group （meio-gynogenetic-1 group）, and a two-generation artificially induced meio-gynogenetic grass carp group （meio-gynogenetic-2 group）, were comparatively analyzed with microsatellite markers. Genetic polymorphism had been observed in the Xiangjiang group and most of the examined loci had more than two alleles. But the degree of genetic diversity was not very high. Although all the examined genetic loci in the analyzed individuals were in homozygous state, the genotypes of different individuals of the group were not identical in the meio-gynogenetic-1 group. In the meio-gynogenetic-2 group, not only the examined genetic loci of each individual were homozygous but also the genotypes of all the analyzed individuals of the group were the same. These results suggested that the examined meio-gynogenetic-2 group is a homozygous group and homozygous clone could be produced by continuous artificial induction of gynogenesis for two generations. It was found that the polymorphism existed not only at the allele level but also at the locus level; many alleles of the microsatellite loci and some of the microsatellite loci had been lost during the process of artificial gynogenesis. Therefore, both protection of the diversity of natural grass carp resource and selection of homozygous traits with desired economic genotypes are very important aspects for grass carp breeding.展开更多
The genus Oryza consists of two cultivated species (O. sativa L. and O. glaberrima Steud.) and approximately 20 wild relative species widely distributed in the pan-tropics. These species have been classified into four...The genus Oryza consists of two cultivated species (O. sativa L. and O. glaberrima Steud.) and approximately 20 wild relative species widely distributed in the pan-tropics. These species have been classified into four complexes following the Vaughan's taxonomic system([1]). The O. officinalis complex is the largest complex in the genus, which includes ten species, having BE, CC, on, and EE genomes in the diploids as well as BBCC and CCDD genomes in the tetraploids. The relationships among the BE, CC, and EE genomes still remain unclear, although previous studies have indicated certain affinities of these genomes([2-4]). Genomic in situ hybridization (GISH) is a powerful technique to detect the relationships among the related genomes at chromosome and DNA levels. The objective of the present study was to investigate the relationships among the BE, CC and EE genomes in the genus Oryza by the two-probe GISH.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
Various types of gene rearrangements have been discovered in the mitogenoes of the frog family Ranidae. In this study, we determined the complete mitogenome sequence of three Rana frogs. By combining the available mit...Various types of gene rearrangements have been discovered in the mitogenoes of the frog family Ranidae. In this study, we determined the complete mitogenome sequence of three Rana frogs. By combining the available mitogenomic data sets from GenBank, we evaluated the phylogenetic relationships of Ranidae at the mitogenome level and analyzed mitogenome rearrangement cases within Ranidae. The three frogs shared an identical mitogenome organization that was extremely similar to the typical Neobatrachian-type arrangement. Except for the genus Babina, the monophyly of each genus was well supported. The genus Amnirana occupied the most basal position among the Ranidae. The [Lithobates ＋ Rana] was the closest sister group of Odorrana. The diversity of mitochondrial gene arrangements in ranid species was unexpectedly high, with 47 mitogenomes from 40 ranids being classified into 10 different gene rearrangement types. Some taxa owned their unique gene rearrangement characteristics, which had significant implication for their phylogeny analysis. All rearrangement events discovered in the Ranidae mitogenomes can be explained by the duplication and random loss model.展开更多
Common wheat （Triticum aestivum L.） is one of the most important crops, and intra-specific wheat hybrids have obvious heterosis in yield and protein quality. Therefore, utilization of hybrid wheat varieties offers a...Common wheat （Triticum aestivum L.） is one of the most important crops, and intra-specific wheat hybrids have obvious heterosis in yield and protein quality. Therefore, utilization of hybrid wheat varieties offers an effective way to increase yield and nutrition. Cytoplasmic male sterility （CMS） systems are a useful genetic tool for hybrid crop breeding, and are ideal models for studying the genetic interaction and cooperative function of mitochondrial and nuclear genomes in plants （Schnable and Wise, 1998; Hanson and Bentolila, 2004）.展开更多
Only in recent years, the draft sequences for several agricultural animals have been assembled. Assembling an individual animal＇s entire genome sequence or specific region（s） of interest is increasingly important f...Only in recent years, the draft sequences for several agricultural animals have been assembled. Assembling an individual animal＇s entire genome sequence or specific region（s） of interest is increasingly important for agricultura researchers to perform genetic comparisons between animals with different performance. We review the current status for several sequenced agricultural species and suggest that next generation sequencing （NGS） technology with decreased sequencing cost and increased speed of sequencing can benefit agricultural researchers. By taking advantage of advanced NGS technologies, genes and chromosomal regions that are more labile to the influence of environmental factors could be pinpointed. A more long term goal would be addressing the question of how animals respond at the molecular and cellular levels to different environmental models （e.g. nutrition）. Upon revealing important genes and gene-environment interactions, the rate of genetic improvement can also be accelerated. It is clear that NGS technologies will be able to assist animal scientists to efficiently raise animals and to better prevent infectious diseases so that overall costs of animal production can be decreased.展开更多
Chaos game representation (CGR) of DNA sequences and linked protein sequences from genomes was proposed by Jeffrey (1990) and Yu et al. (2004), respectively. In this paper, we consider the CGR of three kinds of sequen...Chaos game representation (CGR) of DNA sequences and linked protein sequences from genomes was proposed by Jeffrey (1990) and Yu et al. (2004), respectively. In this paper, we consider the CGR of three kinds of sequences from complete genomes: whole genome DNA sequences, linked coding DNA sequences and linked protein sequences. Some fractal patterns are found in these CGRs. A recurrent iterated function systems (RIFS) model is proposed to simulate the CGRs of these sequences from genomes and their induced measures. Numerical results on 50 genomes show that the RIFS model can simulate very well the CGRs and their induced measures. The parameters estimated in the RIFS model reflect information on species classification.展开更多
Pyropia species grow in the intertidal zone and are cold-water adapted. To date, most of the information about the whole plastid and mitochondrial genomes(ptDNA and mtDNA) of this genus is limited to Northern Hemisphe...Pyropia species grow in the intertidal zone and are cold-water adapted. To date, most of the information about the whole plastid and mitochondrial genomes(ptDNA and mtDNA) of this genus is limited to Northern Hemisphere species. Here, we report the sequencing of the ptDNA and mtDNA of the Antarctic red alga Pyropia endiviifolia using the Illumina platform. The plastid genome(195 784 bp, 33.28% GC content) contains 210 protein-coding genes, 37 tRNA genes and 6 rRNA genes. The mitochondrial genome(34 603 bp, 30.5% GC content) contains 26 protein-coding genes, 25 tRNA genes and 2 rRNA genes. Our results suggest that the organellar genomes of Py. endiviifolia have a compact organization. Although the collinearity of these genomes is conserved compared with other Pyropia species, the genome sizes show significant differences, mainly because of the different copy numbers of rDNA operons in the pt DNA and group II introns in the mtDNA. The other Pyropia species have 2–3 distinct intronic ORFs in their cox 1 genes, but Py. endiviifolia has no introns in its cox 1 gene. This has led to a smaller mtDNA than in other Pyropia species. The phylogenetic relationships within Pyropia were examined using concatenated gene sets from most of the available organellar genomes with both the maximum likelihood and Bayesian methods. The analysis revealed a sister taxa affiliation between the Antarctic species Py. endiviifolia and the North American species Py. kanakaensis.展开更多
Distributions of triplet separator lengths for two bacterial complete genomes are analyzed. The theoretical distributions for the independent random sequence and the first-order Markov chain are derived and compared w...Distributions of triplet separator lengths for two bacterial complete genomes are analyzed. The theoretical distributions for the independent random sequence and the first-order Markov chain are derived and compared with the distributions of the bacterial genomes. A prominent double band structure, which does not exist in the theoretical distributions, is observed in the bacterial distributions for most triplets.展开更多
Species of the Pinus genus provide a classical model for studying hybrid speciation.Although studies on two narrowly distributed species(P inus funebris and P.takahasii)concluded that they originated from two widespre...Species of the Pinus genus provide a classical model for studying hybrid speciation.Although studies on two narrowly distributed species(P inus funebris and P.takahasii)concluded that they originated from two widespread species(P.sylvestris and P.densiflora)via hybrid speciation,the conclusion was based on a low number of informative restriction sites.In this study,we analyzed the sequences of four Pinus chloroplast(cp)genomes(P.sylvestris,P.densiflora,P.funebris and P.takahasii)to clarify whether hybrid speciation was involved.The complete cp-genomes of Pinus species ranged in size from 119,865 to 119,890 bp,similar to other Pinus species.Phylogenetic results based on the whole cp-genomes showed P.sylvestris clustered with P.funebris and P.takahasii,which suggested that P.sylvestris was the paternal parent in hybridization events.In an analysis of simple sequence repeats(SSRs),we detected a total of 69 SSRs repeats among the four Pinus cp-genomes;most were A or T bases.In addition,we identified divergent hotspot regions among the four Pinus cp-genomes(trnE-clpP,cemA-ycf4,petD-rpoA,psbD-trnT,and trnN-chlL),in P.sylvestris(psbD-trnT,trnN-chlL,psbB and rps8)and in P.densiflora(trnE-clpP,petD-rpoA,ycf3 intron,psbD-trnT,and trnN-chlL).The genome information found in this study provides new insights into hybrid speciation in P inus and contributes to a better understanding of the phylogenetic relationships within the Pinus genus.展开更多
文摘Fig.1.The GenomeSyn tool for visualizing genome synteny and characterizing structural variations.A:The first synteny visualization map showed the detailed information of two or three genomes and can display structural variations and other annotation information.B:The second type of visualization map was simple and only showed the synteny relationship between the chromosomes of two or three genomes.C:Multiplatform general GenomeSyn submission page,applicable to Windows,MAC and web platforms;other analysis files can be entered in the"other"option.The publisher would like to apologise for any inconvenience caused.
基金supported by grants from the National Natural Science Foundation of China(32170238,32400191)Guangdong Basic and Applied Basic Research Foundation(2023A1515111029)+2 种基金the Science,Technology and Innovation Commission of Shenzhen Municipality(RCYX20200714114538196)the Chinese Academy of Agricultural Sciences Elite Youth Program(grant 110243160001007)the Guangdong Pearl River Talent Program(2021QN02N792)。
文摘Single-stranded DNA-binding proteins(SSBs)play essential roles in the replication,recombination and repair processes of organellar DNA molecules.In Arabidopsis thaliana,SSBs are encoded by a small family of two genes(SSB1 and SSB2).However,the functional divergence of these two SSB copies in plants remains largely unknown,and detailed studies regarding their roles in the replication and recombination of organellar genomes are still incomplete.In this study,phylogenetic,gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed plants.Based on accurate long-read sequencing results,ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA(mtDNA)and plastid DNA(ptDNA),accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both genomes.Our findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.
基金supported by the Natural Science Foundation of Guangdong Province(2022A1515012158)the National Science Foundation of China(41977138)+3 种基金the Construction Project of Teaching Quality and Teaching Reform in Guangdong Province(SJD202001)the General University Project of Guangdong Provincial Department of Education(2021KCXTD070 and 2021ZDZX4072)the Key Project of Social Welfare and Basic Research of Zhongshan City(2020B2010)the Start-up Fund from the Zhongshan Institute at the University of Electronic Science and Technology in China(419YKQN12)。
文摘In-depth knowledge of the microbes responsible for biogenic amine(BA)production during soy sauce fermentation remains limited.Herein,the variations in the BA profiles,microbial communities,and microbes involved in BA production during the fermentation of soy sauce through Japanese-type(JP)and Cantonese-type(CP)processes were compared.BA analysis revealed that the most abundant BA species were putrescine,tyramine,and histamine in the later three stages(1187.68,785.16,and 193.20 mg/kg on average,respectively).The BA profiles differed significantly,with CP samples containing higher contents of putrescine,tyramine,and histamine(P<0.05)at the end of fermentation.Metagenomic analysis indicated that BA-producing genes exhibited different abundance profiles,with most genes,including spe A,spe B,arg,spe E,and tyr DC,having higher abundances in microbial communities during the CP process.In total,15 high-quality metagenome-assembled genomes(MAGs)were retrieved,of which 10 encoded at BA production-related genes.Enterococcus faecium(MAG10)and Weissella paramesenteroides(MAG5)might be the major tyramine producers.The high putrescine content in CP might be associated with the high abundance of Staphylococcus gallinarum(MAG8).This study provides a comprehensive understanding of the diversity and abundance of genes involved in BA synthesis,especially at the species level,during food fermentation.
基金supported by the National Key Research and Development Program(2021YFD1301200 and 2021YFF1000602).
文摘Background Traditional genomic analysis relies on a single reference genome,which struggles to effectively characterize the genetic diversity among populations.This is due to the substantial genetic differences between the genome of the studied species and the reference genome,potentially introducing reference bias.Results In this study,we focused on Guanzhong Black pigs(GZB),Danish Large White pigs(DLW),and their hybrid offspring,Qinchuan Black pigs(QCB).We provided two high-quality parental genomes at the chromosomal level and constructed a parental genomic reference panel to detect SNPs(single nucleotide polymorphisms),INDELs(insertions and deletions),and SVs(structural variations).Compared with the single-reference method,the integrated parental genomic strategy identified 5.48%more SNPs and 67.84%more INDELs.The uniformity of variant distribution and genome functional annotation remained consistent before and after integration,while the ratio of nonreference/non-reference genotypes was also improved.In population genetic structure analysis,principal component analysis(PCA)of the three variant types(SNPs,INDELs,and SVs)exhibited good clustering effects,and ADMIXTURE analysis demonstrated consistent stratification.Selection signal analysis based on the integrated parental genomic strategy successfully identified more differentiated windows and positively selected genes.By leveraging multiple variant types and employing two selection signal methods,we jointly identified several novel intramuscular fat candidate genes(MSMO1,SMC6,CCDC158,KIT,CCNC,etc.),which could not be identified by the single-reference method alone.Functional validation of the gene MSMO1 revealed its role in promoting intramuscular adipocyte proliferation and inhibiting adipogenic differentiation.Conclusions This study is the first to construct a parental genomic reference panel specifically for pig hybrid populations,which significantly reduces reference bias and exhibits superior performance in downstream analyses.This strategy offers new possibilities for genomic selection breeding of livestock and establishes a methodological foundation for precisely dissecting complex traits in hybrid populations.
基金supported by the National Natural Science Foundation of China(32371700,32071670 and 31870196)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31000000)+4 种基金the Science and Technology Basic Resources Investigation Program of China(2021FY100200)Yunnan Revitalization Talent Support Program“Young Talent”and“Innovation Team”Projects(202405AS350019)the 14th Five-Year Plan of Xishuangbanna Tropical Botanical Garden,Chinese Academy of Science(XTBG-1450101)the Key R&D program of Yunnan Province,China(202103AC100003)the Key Basic Research program of Yunnan Province,China(202101BC070003).
文摘Complete plastid genomes have been proposed as potential“super-barcodes”for plant identification and delineation,particularly in cases where standard DNA barcodes may be insufficient.However,few studies have systematically addressed how taxonomic complexity,especially in rapidly radiating lineages with intricate evolutionary histories,might influencethe efficacyof plastome-scale barcodes.Pedicularis is a hyperdiverse genus in the Himalaya-Hengduan Mountains,and previous studies have demonstrated high discriminatory power of the standard barcodes within this genus.Therefore,Pedicularis serves as a model for investigating the key plastome-sequence characteristics and biological phenomena that determine species-discrimination capacity.In this study,we evaluated 292 plastomes representing 96 Pedicularis species to compare the discriminatory power of complete plastid genomes with of standard DNA barcodes.Our results revealed that the traditional standard barcode combination(nrITS+matK+rbcL+trnH-psbA)achieved the highest discrimination rates(81.25%),closely followed by the plastid large single copy(LSC)region(80.21%),then by full plastome,the supermatrix of proteincoding genes,and hypervariable regions(79.17%).Notably,the matK and ycf1 gene alone could discriminate 78.13%of species.Key determinants of species discrimination by integrating alignment length(AL)and the proportion of parsimony-informative sites(PPIS),as well as conserved genes under relaxed selection exhibiting stronger discriminatory capacity.Unlike previous studies that demonstrated superior discrimination rates of plastome-scale barcodes,this study reveals a notable exception of minimal differences between traditional DNA and plastome-scale barcodes that appearing linked to Pedicularis’specificbiological habits and potentially reflectingunique evolutionary patterns in the plastid genome.
基金The National Natural Science Foundation of China under contract Nos 42171069 and 41976121.
文摘Despite most eel gobies(Gobionellidae:Amblyopinae)have inhabited brackish or marine waters,few species(such as Taenioides sp.)have been found to invade multiple inland freshwaters via artificial water transfer projects.The habitat transfers from brackish water to freshwater zones of Taenioides sp.have caused severe damage to Chinese aquatic ecosystems in recent years.Unfortunately,the molecular mechanism underlying freshwater invasion remains poorly understood.Considering changes of environmental factors,especially salinity,are bound to adjust the demands for energy affected by mitochondria via oxidative phosphorylation,13 Amblyopinae mitogenomes were compared,including the newly assembled Taenioides sp.mitogenome in this study.Comparative mitogenomic analyses revealed a highly conserved structure,composition and arrangements,with the exception of variable control region(CR).All of the CRs possessed tandem repeat sequences except Trypauchenopsis sp.G341,differing in motifs and number of copies,which was the dominant factor resulting in length heterogeneity of CR.The phylogenetic trees reconfirmed the paraphyletic origin of Amblyopinae with respect to Oxudercinae,supporting that these two subfamilies should be merged as an expansion of phenotypic variation within the“terrestrial goby”clade.Furthermore,four protein coding genes(COI,ND3,ND5 and Cyt b)in Taenioides sp.mitogenome have experienced adaptive evolution,indicating their important roles in enhancing the efficiency of ATP production to cope with the osmotic regulation adjustment and reach its current widespread distribution in multiple inland freshwaters of China.These results revealed the functional importance of mitochondrial genes,and provided fresh insights into the molecular mechanisms underlying the freshwater invasion.Also,our results may provide critical reference value for the future control of other invasive species.
基金Supported by the Eleventh Five-year Development Planning Project for Instructional Science in Hubei Province (2006B131)~~
文摘MATLAB software and optimal complete subgraph algorithm were used to extract and reveal the microsatellite distribution features in the complete genomes of the tobacco vein clearing virus （NC-003 378.1） from the NCBI database.The results showed that the repetitions number and their location of the N-base group has been extracted and displayed.The largest repetitions of N-base group in the complete genomes of the tobacco vein clearing virus was decreased as the exponential function with the increasing of N.The method used in this study could be applied to the extraction and revealing of the microsatellite distribution features in the complete genomes of other viruses,thereby provided a basis for the research of the structure and the law of function,inheritance and variation by the using of the microsatellite distribution features.
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This work was supported by National Natural Sciences Foundation of China (No. 39830300 )the Ministry of Education (No. 20065-14)
文摘The genomes of three groups of grass carp, namely the Xiangjiang River grass carp group （Xiangjiang group）, a one-generation artificially induced meio-gynogenetic grass carp group （meio-gynogenetic-1 group）, and a two-generation artificially induced meio-gynogenetic grass carp group （meio-gynogenetic-2 group）, were comparatively analyzed with microsatellite markers. Genetic polymorphism had been observed in the Xiangjiang group and most of the examined loci had more than two alleles. But the degree of genetic diversity was not very high. Although all the examined genetic loci in the analyzed individuals were in homozygous state, the genotypes of different individuals of the group were not identical in the meio-gynogenetic-1 group. In the meio-gynogenetic-2 group, not only the examined genetic loci of each individual were homozygous but also the genotypes of all the analyzed individuals of the group were the same. These results suggested that the examined meio-gynogenetic-2 group is a homozygous group and homozygous clone could be produced by continuous artificial induction of gynogenesis for two generations. It was found that the polymorphism existed not only at the allele level but also at the locus level; many alleles of the microsatellite loci and some of the microsatellite loci had been lost during the process of artificial gynogenesis. Therefore, both protection of the diversity of natural grass carp resource and selection of homozygous traits with desired economic genotypes are very important aspects for grass carp breeding.
文摘The genus Oryza consists of two cultivated species (O. sativa L. and O. glaberrima Steud.) and approximately 20 wild relative species widely distributed in the pan-tropics. These species have been classified into four complexes following the Vaughan's taxonomic system([1]). The O. officinalis complex is the largest complex in the genus, which includes ten species, having BE, CC, on, and EE genomes in the diploids as well as BBCC and CCDD genomes in the tetraploids. The relationships among the BE, CC, and EE genomes still remain unclear, although previous studies have indicated certain affinities of these genomes([2-4]). Genomic in situ hybridization (GISH) is a powerful technique to detect the relationships among the related genomes at chromosome and DNA levels. The objective of the present study was to investigate the relationships among the BE, CC and EE genomes in the genus Oryza by the two-probe GISH.
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supported by the Innovative Research Team in University of Sichuan Bureau of Education (No.14TD0002)the Scientific Research Fund of Sichuan Provincial Education Department (No.11ZA077)
文摘Various types of gene rearrangements have been discovered in the mitogenoes of the frog family Ranidae. In this study, we determined the complete mitogenome sequence of three Rana frogs. By combining the available mitogenomic data sets from GenBank, we evaluated the phylogenetic relationships of Ranidae at the mitogenome level and analyzed mitogenome rearrangement cases within Ranidae. The three frogs shared an identical mitogenome organization that was extremely similar to the typical Neobatrachian-type arrangement. Except for the genus Babina, the monophyly of each genus was well supported. The genus Amnirana occupied the most basal position among the Ranidae. The [Lithobates ＋ Rana] was the closest sister group of Odorrana. The diversity of mitochondrial gene arrangements in ranid species was unexpectedly high, with 47 mitogenomes from 40 ranids being classified into 10 different gene rearrangement types. Some taxa owned their unique gene rearrangement characteristics, which had significant implication for their phylogeny analysis. All rearrangement events discovered in the Ranidae mitogenomes can be explained by the duplication and random loss model.
基金supported by the National Natural Science Foundation of China(No.30971844)the Fundamental Research Funds of Northwest A & F University(No. QN2011003)+1 种基金China Postdoctoral Science Foundation to Wang Junwei(No.20070410835)the Tang Zhong-Ying Breeding Funding Project of Northwest A & F University
文摘Common wheat （Triticum aestivum L.） is one of the most important crops, and intra-specific wheat hybrids have obvious heterosis in yield and protein quality. Therefore, utilization of hybrid wheat varieties offers an effective way to increase yield and nutrition. Cytoplasmic male sterility （CMS） systems are a useful genetic tool for hybrid crop breeding, and are ideal models for studying the genetic interaction and cooperative function of mitochondrial and nuclear genomes in plants （Schnable and Wise, 1998; Hanson and Bentolila, 2004）.
基金supported by the National Institutes of Health Grant #U54 DA021519
文摘Only in recent years, the draft sequences for several agricultural animals have been assembled. Assembling an individual animal＇s entire genome sequence or specific region（s） of interest is increasingly important for agricultura researchers to perform genetic comparisons between animals with different performance. We review the current status for several sequenced agricultural species and suggest that next generation sequencing （NGS） technology with decreased sequencing cost and increased speed of sequencing can benefit agricultural researchers. By taking advantage of advanced NGS technologies, genes and chromosomal regions that are more labile to the influence of environmental factors could be pinpointed. A more long term goal would be addressing the question of how animals respond at the molecular and cellular levels to different environmental models （e.g. nutrition）. Upon revealing important genes and gene-environment interactions, the rate of genetic improvement can also be accelerated. It is clear that NGS technologies will be able to assist animal scientists to efficiently raise animals and to better prevent infectious diseases so that overall costs of animal production can be decreased.
文摘Chaos game representation (CGR) of DNA sequences and linked protein sequences from genomes was proposed by Jeffrey (1990) and Yu et al. (2004), respectively. In this paper, we consider the CGR of three kinds of sequences from complete genomes: whole genome DNA sequences, linked coding DNA sequences and linked protein sequences. Some fractal patterns are found in these CGRs. A recurrent iterated function systems (RIFS) model is proposed to simulate the CGRs of these sequences from genomes and their induced measures. Numerical results on 50 genomes show that the RIFS model can simulate very well the CGRs and their induced measures. The parameters estimated in the RIFS model reflect information on species classification.
基金Supported by the National Natural Science Foundation of China(No.31372517)the Scientific and Technological Innovation Project Financially Supported by Qingdao National Laboratory for Marine Science and Technology(No.2015ASKJ02)the National Infrastructure of Fishery Germplasm Resources(No.2016DKA30470)
文摘Pyropia species grow in the intertidal zone and are cold-water adapted. To date, most of the information about the whole plastid and mitochondrial genomes(ptDNA and mtDNA) of this genus is limited to Northern Hemisphere species. Here, we report the sequencing of the ptDNA and mtDNA of the Antarctic red alga Pyropia endiviifolia using the Illumina platform. The plastid genome(195 784 bp, 33.28% GC content) contains 210 protein-coding genes, 37 tRNA genes and 6 rRNA genes. The mitochondrial genome(34 603 bp, 30.5% GC content) contains 26 protein-coding genes, 25 tRNA genes and 2 rRNA genes. Our results suggest that the organellar genomes of Py. endiviifolia have a compact organization. Although the collinearity of these genomes is conserved compared with other Pyropia species, the genome sizes show significant differences, mainly because of the different copy numbers of rDNA operons in the pt DNA and group II introns in the mtDNA. The other Pyropia species have 2–3 distinct intronic ORFs in their cox 1 genes, but Py. endiviifolia has no introns in its cox 1 gene. This has led to a smaller mtDNA than in other Pyropia species. The phylogenetic relationships within Pyropia were examined using concatenated gene sets from most of the available organellar genomes with both the maximum likelihood and Bayesian methods. The analysis revealed a sister taxa affiliation between the Antarctic species Py. endiviifolia and the North American species Py. kanakaensis.
基金the Special Funds for Major National Basic Research Projects，国家自然科学基金，北京市创新工程项目
文摘Distributions of triplet separator lengths for two bacterial complete genomes are analyzed. The theoretical distributions for the independent random sequence and the first-order Markov chain are derived and compared with the distributions of the bacterial genomes. A prominent double band structure, which does not exist in the theoretical distributions, is observed in the bacterial distributions for most triplets.
基金funded by Kunyu Mountain National Nature Reserve Administration。
文摘Species of the Pinus genus provide a classical model for studying hybrid speciation.Although studies on two narrowly distributed species(P inus funebris and P.takahasii)concluded that they originated from two widespread species(P.sylvestris and P.densiflora)via hybrid speciation,the conclusion was based on a low number of informative restriction sites.In this study,we analyzed the sequences of four Pinus chloroplast(cp)genomes(P.sylvestris,P.densiflora,P.funebris and P.takahasii)to clarify whether hybrid speciation was involved.The complete cp-genomes of Pinus species ranged in size from 119,865 to 119,890 bp,similar to other Pinus species.Phylogenetic results based on the whole cp-genomes showed P.sylvestris clustered with P.funebris and P.takahasii,which suggested that P.sylvestris was the paternal parent in hybridization events.In an analysis of simple sequence repeats(SSRs),we detected a total of 69 SSRs repeats among the four Pinus cp-genomes;most were A or T bases.In addition,we identified divergent hotspot regions among the four Pinus cp-genomes(trnE-clpP,cemA-ycf4,petD-rpoA,psbD-trnT,and trnN-chlL),in P.sylvestris(psbD-trnT,trnN-chlL,psbB and rps8)and in P.densiflora(trnE-clpP,petD-rpoA,ycf3 intron,psbD-trnT,and trnN-chlL).The genome information found in this study provides new insights into hybrid speciation in P inus and contributes to a better understanding of the phylogenetic relationships within the Pinus genus.
