Hybridization and polyploidy are key drivers of species diversity and genome variation in Lycoris,but their cytological and evolutionary consequences remain poorly understood.Here,we investigated chromosome numbers an...Hybridization and polyploidy are key drivers of species diversity and genome variation in Lycoris,but their cytological and evolutionary consequences remain poorly understood.Here,we investigated chromosome numbers and genome sizes in 64 accessions representing the morphological diversity across the genus.Chromosome numbers ranged from 12 to 33,with seven accessions newly identified,including L.chunxiaoensis(2n=33),two putative L.guangxiensis(2n=19),and fivenatural hybrids(2n=16,18,29,33).Genome sizes varied from 18.03 Gb(L.wulingensis)to 32.62 Gb(L.caldwellii).Although no significantcorrelationwas found between genome size and chromosome number across all accessions,a strong correlation within ploidy-level groups(i.e.,diploid or aneuploid)suggested roles for post-polyploid diploidization,aneuploidy,and dysploidy in speciation.Phylogenetic analyses based on chloroplast genomes and nuclear DNA sequences revealed significantdiscordance,indicating a complex reticulate evolution and historical hybridization,which may complicate morphological classification.Chromosome number aligned more closely with morphological groups,underscoring the necessity of integrating cytological,molecular,and morphological data for accurate taxonomy,particularly in largegenome taxa.Based on this evidence,we propose a putative speciation pathway involving multiple hybridization and polyploidization events,with allopolyploidy playing a predominant role.Furthermore,our results indicate that the species L.insularis and L.longifolia are geographic populations of L.sprengeri and L.aurea,respectively,and confirmedthe distribution of L.traubii and L.albiflora in China' Mainland.These findingsoffer new insights into the mechanisms underlying speciation,interspecificrelationships,and the evolutionary history of Lycoris.展开更多
Ferns and lycophytes have remarkably large genomes.However,little is known about how their genome size evolved in fern lineages.To explore the origins and evolution of chromosome numbers and genome size in ferns,we us...Ferns and lycophytes have remarkably large genomes.However,little is known about how their genome size evolved in fern lineages.To explore the origins and evolution of chromosome numbers and genome size in ferns,we used flow cytometry to measure the genomes of 240 species(255 samples)of extant ferns and lycophytes comprising 27 families and 72 genera,of which 228 species(242 samples)represent new reports.We analyzed correlations among genome size,spore size,chromosomal features,phylogeny,and habitat type preference within a phylogenetic framework.We also applied ANOVA and multinomial logistic regression analysis to preference of habitat type and genome size.Using the phylogeny,we conducted ancestral character reconstruction for habitat types and tested whether genome size changes simultaneously with shifts in habitat preference.We found that 2 C values had weak phylogenetic signal,whereas the base number of chromosomes(x)had a strong phylogenetic signal.Furthermore,our analyses revealed a positive correlation between genome size and chromosome traits,indicating that the base number of chromosomes(x),chromosome size,and polyploidization may be primary contributors to genome expansion in ferns and lycophytes.Genome sizes in different habitat types varied significantly and were significantly correlated with habitat types;specifically,multinomial logistic regression indicated that species with larger 2 C values were more likely to be epiphytes.Terrestrial habitat is inferred to be ancestral for both extant ferns and lycophytes,whereas transitions to other habitat types occurred as the major clades emerged.Shifts in habitat types appear be followed by periods of genomic stability.Based on these results,we inferred that habitat type changes and multiple whole-genome duplications have contributed to the formation of large genomes of ferns and their allies during their evolutionary history.展开更多
Polycyclic aromatic hydrocarbons(PAHs)are ubiquitous priority pollutants that cause great damage to the natural environment and health.Average genome size in a community is critical for shedding light on microbiome...Polycyclic aromatic hydrocarbons(PAHs)are ubiquitous priority pollutants that cause great damage to the natural environment and health.Average genome size in a community is critical for shedding light on microbiome's functional response to pollution stress within an environment.Here,microcosms under different concentrations were performed to evaluate the selection of PAHs stress on the average genome size in a community.We found the distinct communities of significantly larger genome size with the increase of PAHs concentration gradients in soils,and consistent trends were discovered in soils at different latitudes.The abundance of Proteobacteria and Deinococcus-Thermus with relatively larger genomes increased along with PAHs stress and well adapted to polluted environments.In contrast,the abundance of Patescibacteria with a highly streamlined and smaller genome decreased,implying complex interactions between environmental selection and functional fitness resulted in bacteria with larger genomes becoming more abundant.Moreover,we confirmed the increased capacity for horizontal transfer of degrading genes between communities by showing an increased connection number per node positively related to the nid A gene along the concentration gradients in the co-occurrence network.Our findings suggest PAHs tend to select bacterial taxa with larger genome sizes,with significant consequences for community stability and potential biodegradation strategies.展开更多
Eukaryotic genome size data are important both as the basis for comparative research into genome evolution and as estimators of the cost and difficulty of genome sequencing programs for non-model organisms. In this st...Eukaryotic genome size data are important both as the basis for comparative research into genome evolution and as estimators of the cost and difficulty of genome sequencing programs for non-model organisms. In this study, the genome size of 14 species of fireflies （Lampyridae） （two genera in Lampyrinae, three genera in Luciolinae, and one genus in subfamily incertae sedis） were estimated by propidium iodide （PI）-based flow cytometry. The haploid genome sizes of Lampyridae ranged from 0.42 to 1.31 pg, a 3.1-fold span. Genome sizes of the fireflies varied within the tested subfamilies and genera. Lamprigera and Pyrocoelia species had large and small genome sizes, respectively. No correlation was found between genome size and morphological traits such as body length, body width, eye width, and antennal length. Our data provide additional information on genome size estimation of the firefly family Lampyridae. Furthermore, this study will help clarify the cost and difficulty of genome sequencing programs for non-model organisms and will help promote studies on firefly genome evolution.展开更多
Fresh plant material is usually used for genome size estimation by flow cytometry(FCM). Lack of fresh material is cited as one of the main reasons for the dearth of studies on plants from remote locations.Genome sizes...Fresh plant material is usually used for genome size estimation by flow cytometry(FCM). Lack of fresh material is cited as one of the main reasons for the dearth of studies on plants from remote locations.Genome sizes in fresh versus desiccated tissue of 16 Ophiopogoneae species and five model plant species were estimated. Our results indicated that desiccated tissue was suitable for genome size estimation; this method enables broader geographic sampling of plants when fresh tissue collection is not feasible. To be useful, after dessication the Ophiopogoneae sample should be green without brown or yellow markings;it should be stored in deep freezer at à80C, and the storage time should be no more than 6 months.展开更多
Genome size changes significantly among taxonomic levels,and this variation is often related to the patterns shaped by the phylogeny,life histories and ecological factors.However,there are mixed evidences on the main ...Genome size changes significantly among taxonomic levels,and this variation is often related to the patterns shaped by the phylogeny,life histories and ecological factors.However,there are mixed evidences on the main factors affecting molecular evolution in animals.In this study,we used phylogenetic comparative analysis to investigate the evolutionary rate of genome size and the relationships between genome size and life histories(i.e.,hatchling mass,clutch size,clutches per year,age at sexual maturity,lifespan and body mass)among 199 squamata species.Our results showed that the evolutionary rate of genome size in Lacertilia was significantly faster than Serpentes.Moreover,we also found that larger species showed larger hatchling mass,more clutches per year and clutch size and longer lifespan.However,genome size was negatively associated with clutch size and clutches per year,but not associated with body mass we looked at.The findings suggest that larger species do not possess the evolution of large genomes in squamata.展开更多
Objective:Dianjixueteng is a geoherb in Yunnan Province,the source plant of which is Kadsura interior.However,the formation of this geoherb is not clear in genetic mechanism,in which genome size is the first step that...Objective:Dianjixueteng is a geoherb in Yunnan Province,the source plant of which is Kadsura interior.However,the formation of this geoherb is not clear in genetic mechanism,in which genome size is the first step that should be known on the genomic level.In this study we aimed to estimate the genome sizes of source plants of K.interior and three related herbs K.heteroclita,K.longipedunculata,and K.coccinea by flow cytometry(FCM)and make a comparison.Methods:The genome sizes of K.interior,K.heteroclita,K.longipedunculata and K.coccinea,i.e.,the source plants of Dianjixueteng and its relative medicinal materials,were estimated by FCM.The nuclei of K.interior were isolated using modified LB01 buffer,for the rest species,by the Galbraith’s buffer.Results:The genome sizes of K.interior,K.heteroclita,K.longipedunculata,and K.coccinea were 7.36,7.12,7.01,and 5.15 pg/1 C,respectively.Genome size of K.interior had no significant variation with those of K.heteroclita and K.longipedunculata(P=0.296),which was significantly larger than that of K.coccinea.Conclusion:Genome size can not distinguish K.interior from K.heteroclita and K.longipedunculata,but could distinguish them from K.coccinea,which lays the foundation for future studies on genetic mechanism of the geoherb formation.展开更多
The dynamic activity of transposable elements(TEs)contributes to the vast diversity of genome size and architecture among plants.Here,we examined the genomic distribution and transposition activity of long terminal re...The dynamic activity of transposable elements(TEs)contributes to the vast diversity of genome size and architecture among plants.Here,we examined the genomic distribution and transposition activity of long terminal repeat retrotransposons(LTR-RTs)in Arabidopsis thaliana(Ath)and three of its relatives,Arabidopsis lyrata(Aly),Eutrema salsugineum(Esa),and Schrenkiella parvula(Spa),in Brassicaceae.Our analyses revealed the distinct evolutionary dynamics of Gypsy retrotransposons,which reflects the different patterns of genome size changes of the four species over the past million years.The rate of Gypsy transposition in Aly is approximately five times more rapid than that of Ath and Esa,suggesting an expanding Aly genome.Gypsy insertions in Esa are strictly confined to pericentromeric heterochromatin and associated with dramatic centromere expansion.In contrast,Gypsy insertions in Spa have been largely suppressed over the last million years,likely as a result of a combination of an inherent molecular mechanism of preferential DNA removal and purifying selection at Gypsy elements.Additionally,species-specific clades of Gypsy elements shaped the distinct genome architectures of Aly and Esa.展开更多
The rapid development of sequencing technology has led to an explosion of plant genome data,opening up more opportunities for research in the field of comparative evolutionary analysis of plant genomes.In this review,...The rapid development of sequencing technology has led to an explosion of plant genome data,opening up more opportunities for research in the field of comparative evolutionary analysis of plant genomes.In this review,we focus on changes in plant genome size and composition,examining the effects of polyploidy,whole-genome duplication,and alternations in transposable elements on plant genome architecture and evolution,respectively.In addition,to address gaps in the available information,we also collected and analyzed 234 representative plant genome data as a supplement.We aim to provide a comprehensive,up-to-date summary of information on plant genome architecture and evolution in this review.展开更多
The mitochondrial genomes(mitogenomes)are purportedly under selection for smaller size to improve their replica-tion and translation efficiency.However,the mitogenomes of Arcidae species are larger than those of other...The mitochondrial genomes(mitogenomes)are purportedly under selection for smaller size to improve their replica-tion and translation efficiency.However,the mitogenomes of Arcidae species are larger than those of other bivalves,and are among the largest metazoan mitogenomes reported to date.In order to explore the differences of base composition and selective constraints between the large and small mitogenomes,we compared the mitogenomes of 9 large arcid mitogenomes and 77 small bivalves mitogenomes.Base composition analyses indicated that Arcidae mitogenomes have significantly greater GC skews in both their whole genomes and coding sequences.This result suggests that the replication of the large mitogenomes in Arcidae may be slower than those in other bivalves,exposing the parental strand to deamination for a longer time.Selection pressure analyses showed that the mitochondrial protein-coding genes of Arcidae species have significantly higher Ka/Ks ratios than other bivalves,suggesting that they have accumulated more nonsynonymous nucleotide substitutions.Seven protein-coding genes(atp6,cox1-3,nad1,nad4 and nad5)show significant difference for Ka/Ks ratios between the Arcidae and non-Arcidae groups.However,these divergences are not observed in the nuclear gene within histone H3.From these observations,we concluded that the large mitoge-nomes of Arcidae species experienced more relaxed selective constraints.As some Arcidae species are more tolerant to hypoxia that can lead to low metabolic rate,the relaxed selective constraints of mitogenomes may be energy-related.This study provides new insights into the evolution of Arcidae mitogenomes.展开更多
The genome size（C-value） of an organism is referring to the DNA content of its non-replicated haploid chromosome complement,generally deduced from measuring somatic diploid nuclei.We presented genome size（C-value）...The genome size（C-value） of an organism is referring to the DNA content of its non-replicated haploid chromosome complement,generally deduced from measuring somatic diploid nuclei.We presented genome size（C-value） data obtained by flow cytometry for four commercially important crabs（Portunus trituberculatus,Charybdis japonica,Scylla paramamosain,and Eriocheir sinensis） common in the coast of China.Gallus domesticus（2C=2.5 pg） was used as the internal standard.The results showed that the C-value for P.trituberculatus,C.japonica,S.paramamosain,and E.sinensis were（2.31±0.01） pg,（2.33±0.03） pg,（1.64±0.02） pg,and（2.29±0.03） pg,respectively.The C-value of P.trituberculatus,C.japonica and S.paramamosain were reported for the first time.The data represented by the four species indicated that they had lower DNA contents than average DNA values in crustaceans（（4.99±0.48） pg）,and three of the four values were very similar if not identical.The results provide useful data for future studies in the fields of biodiversity,species conservation,and phylogeny of these commercial crabs.They will also be helpful in instructing the hybridization breeding program and estimating the cost of the whole genome sequencing project.展开更多
Relationships between genome size and environmental variables suggest that DNA content might be adaptive and of evolutionary importance in plants.The genus Larrea provides an interesting system to test this hypothesis...Relationships between genome size and environmental variables suggest that DNA content might be adaptive and of evolutionary importance in plants.The genus Larrea provides an interesting system to test this hypothesis,since it shows both intra-and interspecific variation in genome size.Larrea has an amphitropical distribution in North and South American deserts,where it is most speciose.Larrea tridentata in North America shows a gradient of increasing autopolyploidy;while three of the four studied South American species are diploids,Larrea divaricata,Larrea nitida,Larrea ameghinoi,and the fourth is an allopolyploid,Larrea cuneifolia.We downloaded available focal species’georeferenced records from seven data reservoirs.We used these records to extract biologically relevant environmental variables from WorldClim at 30 arc seconds scale,to have a broad characterization of the variable climatic conditions of both regions,and a climatic envelope for each species.We estimated relative DNA content index and relative monoploid genome values,by flow cytometry,of four most abundant Larrea species throughout their respective ranges.Then we winnow the bioclimatic dataset down to uncorrelated variables and sampled locales,to analyse the degree of association between both intra-and interspecific relative DNA content and climatic variables that are functionally relevant in arid environments using Pearson correlations,general linear and mixed effects models.Within the genus Larrea,relative DNA content increases with rising temperature and decreases with rising precipitation.At the intraspecific level,all four species show relative DNA content variation across climatic conditions.Larrea is a genus that shows genome size variation correlated with climate.Our results are also consistent with the hypothesis that extreme environmental pressures may have facilitated repeated whole genome duplication events in North America,while in South America,reticulate evolution,as allopolyploidization,and speciation might have been climate-dependent since the Oligocene.展开更多
基金supported by the ScientificFund of Nanjing Botanical Garden Men.Sun Yat-Sen(JSPKLB202519)Jiangsu Provincial Crop Germplasm Resource Bank(Lycoris)(JS-ZW-K04)Forestry Science and Technology Popularization Demonstration Project of the Central Finance[Su(2024)TG06].
文摘Hybridization and polyploidy are key drivers of species diversity and genome variation in Lycoris,but their cytological and evolutionary consequences remain poorly understood.Here,we investigated chromosome numbers and genome sizes in 64 accessions representing the morphological diversity across the genus.Chromosome numbers ranged from 12 to 33,with seven accessions newly identified,including L.chunxiaoensis(2n=33),two putative L.guangxiensis(2n=19),and fivenatural hybrids(2n=16,18,29,33).Genome sizes varied from 18.03 Gb(L.wulingensis)to 32.62 Gb(L.caldwellii).Although no significantcorrelationwas found between genome size and chromosome number across all accessions,a strong correlation within ploidy-level groups(i.e.,diploid or aneuploid)suggested roles for post-polyploid diploidization,aneuploidy,and dysploidy in speciation.Phylogenetic analyses based on chloroplast genomes and nuclear DNA sequences revealed significantdiscordance,indicating a complex reticulate evolution and historical hybridization,which may complicate morphological classification.Chromosome number aligned more closely with morphological groups,underscoring the necessity of integrating cytological,molecular,and morphological data for accurate taxonomy,particularly in largegenome taxa.Based on this evidence,we propose a putative speciation pathway involving multiple hybridization and polyploidization events,with allopolyploidy playing a predominant role.Furthermore,our results indicate that the species L.insularis and L.longifolia are geographic populations of L.sprengeri and L.aurea,respectively,and confirmedthe distribution of L.traubii and L.albiflora in China' Mainland.These findingsoffer new insights into the mechanisms underlying speciation,interspecificrelationships,and the evolutionary history of Lycoris.
基金the National Natural Science Foundation of China(grant number 31870188,31800174,31700172,41571056)to Wang,Shen,Wang and XingShanghai Landscaping and City Appearance Administrative Bureau of China,Scientific Research Grants(G182411)to Yan+1 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences(grant number XDA13020603,XDA13020500)to Chen and JianGuangdong Natural Science Foundation(grant number 2015A030308015)to Wang。
文摘Ferns and lycophytes have remarkably large genomes.However,little is known about how their genome size evolved in fern lineages.To explore the origins and evolution of chromosome numbers and genome size in ferns,we used flow cytometry to measure the genomes of 240 species(255 samples)of extant ferns and lycophytes comprising 27 families and 72 genera,of which 228 species(242 samples)represent new reports.We analyzed correlations among genome size,spore size,chromosomal features,phylogeny,and habitat type preference within a phylogenetic framework.We also applied ANOVA and multinomial logistic regression analysis to preference of habitat type and genome size.Using the phylogeny,we conducted ancestral character reconstruction for habitat types and tested whether genome size changes simultaneously with shifts in habitat preference.We found that 2 C values had weak phylogenetic signal,whereas the base number of chromosomes(x)had a strong phylogenetic signal.Furthermore,our analyses revealed a positive correlation between genome size and chromosome traits,indicating that the base number of chromosomes(x),chromosome size,and polyploidization may be primary contributors to genome expansion in ferns and lycophytes.Genome sizes in different habitat types varied significantly and were significantly correlated with habitat types;specifically,multinomial logistic regression indicated that species with larger 2 C values were more likely to be epiphytes.Terrestrial habitat is inferred to be ancestral for both extant ferns and lycophytes,whereas transitions to other habitat types occurred as the major clades emerged.Shifts in habitat types appear be followed by periods of genomic stability.Based on these results,we inferred that habitat type changes and multiple whole-genome duplications have contributed to the formation of large genomes of ferns and their allies during their evolutionary history.
基金supported by the National Natural Science Foundation of China(No.31670507)National Key R&D Program of China(No.2019YFC1805803)+1 种基金the National Natural Science Foundation of China(Nos.41907273 and 91951108)the Strategic Priority Research Program of Chinese Academy of Sciences(No.XDA23010400)。
文摘Polycyclic aromatic hydrocarbons(PAHs)are ubiquitous priority pollutants that cause great damage to the natural environment and health.Average genome size in a community is critical for shedding light on microbiome's functional response to pollution stress within an environment.Here,microcosms under different concentrations were performed to evaluate the selection of PAHs stress on the average genome size in a community.We found the distinct communities of significantly larger genome size with the increase of PAHs concentration gradients in soils,and consistent trends were discovered in soils at different latitudes.The abundance of Proteobacteria and Deinococcus-Thermus with relatively larger genomes increased along with PAHs stress and well adapted to polluted environments.In contrast,the abundance of Patescibacteria with a highly streamlined and smaller genome decreased,implying complex interactions between environmental selection and functional fitness resulted in bacteria with larger genomes becoming more abundant.Moreover,we confirmed the increased capacity for horizontal transfer of degrading genes between communities by showing an increased connection number per node positively related to the nid A gene along the concentration gradients in the co-occurrence network.Our findings suggest PAHs tend to select bacterial taxa with larger genome sizes,with significant consequences for community stability and potential biodegradation strategies.
基金supported by grants from the National Natural Science Foundation of China(No.31472035)Yunnan Provincial Science and Technology Department(No.2014FB179)to LXY
文摘Eukaryotic genome size data are important both as the basis for comparative research into genome evolution and as estimators of the cost and difficulty of genome sequencing programs for non-model organisms. In this study, the genome size of 14 species of fireflies （Lampyridae） （two genera in Lampyrinae, three genera in Luciolinae, and one genus in subfamily incertae sedis） were estimated by propidium iodide （PI）-based flow cytometry. The haploid genome sizes of Lampyridae ranged from 0.42 to 1.31 pg, a 3.1-fold span. Genome sizes of the fireflies varied within the tested subfamilies and genera. Lamprigera and Pyrocoelia species had large and small genome sizes, respectively. No correlation was found between genome size and morphological traits such as body length, body width, eye width, and antennal length. Our data provide additional information on genome size estimation of the firefly family Lampyridae. Furthermore, this study will help clarify the cost and difficulty of genome sequencing programs for non-model organisms and will help promote studies on firefly genome evolution.
基金supported by grants from the General Project of Natural Science Research in Anhui Province (AQKJ2015B018)Major projects of the National Natural Science Foundation of China (31590823)
文摘Fresh plant material is usually used for genome size estimation by flow cytometry(FCM). Lack of fresh material is cited as one of the main reasons for the dearth of studies on plants from remote locations.Genome sizes in fresh versus desiccated tissue of 16 Ophiopogoneae species and five model plant species were estimated. Our results indicated that desiccated tissue was suitable for genome size estimation; this method enables broader geographic sampling of plants when fresh tissue collection is not feasible. To be useful, after dessication the Ophiopogoneae sample should be green without brown or yellow markings;it should be stored in deep freezer at à80C, and the storage time should be no more than 6 months.
基金Financial support was provided by the National Natural Sciences Foundation of China(31772451,31970393)the Science and Technology Youth Innovation Team of Sichuan Province(2019JDTD0012)。
文摘Genome size changes significantly among taxonomic levels,and this variation is often related to the patterns shaped by the phylogeny,life histories and ecological factors.However,there are mixed evidences on the main factors affecting molecular evolution in animals.In this study,we used phylogenetic comparative analysis to investigate the evolutionary rate of genome size and the relationships between genome size and life histories(i.e.,hatchling mass,clutch size,clutches per year,age at sexual maturity,lifespan and body mass)among 199 squamata species.Our results showed that the evolutionary rate of genome size in Lacertilia was significantly faster than Serpentes.Moreover,we also found that larger species showed larger hatchling mass,more clutches per year and clutch size and longer lifespan.However,genome size was negatively associated with clutch size and clutches per year,but not associated with body mass we looked at.The findings suggest that larger species do not possess the evolution of large genomes in squamata.
基金financially supported by the National Natural Science Foundation of China(Grant No.81872965,81703650)。
文摘Objective:Dianjixueteng is a geoherb in Yunnan Province,the source plant of which is Kadsura interior.However,the formation of this geoherb is not clear in genetic mechanism,in which genome size is the first step that should be known on the genomic level.In this study we aimed to estimate the genome sizes of source plants of K.interior and three related herbs K.heteroclita,K.longipedunculata,and K.coccinea by flow cytometry(FCM)and make a comparison.Methods:The genome sizes of K.interior,K.heteroclita,K.longipedunculata and K.coccinea,i.e.,the source plants of Dianjixueteng and its relative medicinal materials,were estimated by FCM.The nuclei of K.interior were isolated using modified LB01 buffer,for the rest species,by the Galbraith’s buffer.Results:The genome sizes of K.interior,K.heteroclita,K.longipedunculata,and K.coccinea were 7.36,7.12,7.01,and 5.15 pg/1 C,respectively.Genome size of K.interior had no significant variation with those of K.heteroclita and K.longipedunculata(P=0.296),which was significantly larger than that of K.coccinea.Conclusion:Genome size can not distinguish K.interior from K.heteroclita and K.longipedunculata,but could distinguish them from K.coccinea,which lays the foundation for future studies on genetic mechanism of the geoherb formation.
基金the“Innovation Project for the Postdoctoral Researchers”in Chinathe“Open Research Fund Program”of Beijing Key Lab of Plant Resource Research and Development,Beijing Technology and Business University。
文摘The dynamic activity of transposable elements(TEs)contributes to the vast diversity of genome size and architecture among plants.Here,we examined the genomic distribution and transposition activity of long terminal repeat retrotransposons(LTR-RTs)in Arabidopsis thaliana(Ath)and three of its relatives,Arabidopsis lyrata(Aly),Eutrema salsugineum(Esa),and Schrenkiella parvula(Spa),in Brassicaceae.Our analyses revealed the distinct evolutionary dynamics of Gypsy retrotransposons,which reflects the different patterns of genome size changes of the four species over the past million years.The rate of Gypsy transposition in Aly is approximately five times more rapid than that of Ath and Esa,suggesting an expanding Aly genome.Gypsy insertions in Esa are strictly confined to pericentromeric heterochromatin and associated with dramatic centromere expansion.In contrast,Gypsy insertions in Spa have been largely suppressed over the last million years,likely as a result of a combination of an inherent molecular mechanism of preferential DNA removal and purifying selection at Gypsy elements.Additionally,species-specific clades of Gypsy elements shaped the distinct genome architectures of Aly and Esa.
基金supported by special funds for the science technology innovation and industrial development of Shenzhen’Dapeng New District,China(Grant No.PT202101-02)the National Natural Science Foundation of China(Grant No.32072101)+1 种基金the National Key Projects in Agricultural Biological Breeding,China(Grant No.2022ZD0401702)the Guangdong Basic and Applied Basic ResearchFoundation,China(Grant No.2019A1515111150).
文摘The rapid development of sequencing technology has led to an explosion of plant genome data,opening up more opportunities for research in the field of comparative evolutionary analysis of plant genomes.In this review,we focus on changes in plant genome size and composition,examining the effects of polyploidy,whole-genome duplication,and alternations in transposable elements on plant genome architecture and evolution,respectively.In addition,to address gaps in the available information,we also collected and analyzed 234 representative plant genome data as a supplement.We aim to provide a comprehensive,up-to-date summary of information on plant genome architecture and evolution in this review.
基金This work was supported by research grants from the National Natural Science Foundation of China(No.31772414)the Natural Science Foundation of Qingdao City(No.20-3-4-16-nsh)the Fundamental Research Funds for the Central Universities(No.201964001).
文摘The mitochondrial genomes(mitogenomes)are purportedly under selection for smaller size to improve their replica-tion and translation efficiency.However,the mitogenomes of Arcidae species are larger than those of other bivalves,and are among the largest metazoan mitogenomes reported to date.In order to explore the differences of base composition and selective constraints between the large and small mitogenomes,we compared the mitogenomes of 9 large arcid mitogenomes and 77 small bivalves mitogenomes.Base composition analyses indicated that Arcidae mitogenomes have significantly greater GC skews in both their whole genomes and coding sequences.This result suggests that the replication of the large mitogenomes in Arcidae may be slower than those in other bivalves,exposing the parental strand to deamination for a longer time.Selection pressure analyses showed that the mitochondrial protein-coding genes of Arcidae species have significantly higher Ka/Ks ratios than other bivalves,suggesting that they have accumulated more nonsynonymous nucleotide substitutions.Seven protein-coding genes(atp6,cox1-3,nad1,nad4 and nad5)show significant difference for Ka/Ks ratios between the Arcidae and non-Arcidae groups.However,these divergences are not observed in the nuclear gene within histone H3.From these observations,we concluded that the large mitoge-nomes of Arcidae species experienced more relaxed selective constraints.As some Arcidae species are more tolerant to hypoxia that can lead to low metabolic rate,the relaxed selective constraints of mitogenomes may be energy-related.This study provides new insights into the evolution of Arcidae mitogenomes.
基金Shandong Provincial Natural Science Foundation under contract No.ZR2014CP006Zhejiang Major Special Program of Breeding under contract No.2012C12907-3+2 种基金the Open Fund of Zhejiang Provincial Top Key Discipline of Aquaculture under contract No.xkzsc02the Independent Innovation Program of Qingdao under contract No.15-9-1-44-jchsponsored by K.C.Wong Magna Fund in Ningbo University
文摘The genome size（C-value） of an organism is referring to the DNA content of its non-replicated haploid chromosome complement,generally deduced from measuring somatic diploid nuclei.We presented genome size（C-value） data obtained by flow cytometry for four commercially important crabs（Portunus trituberculatus,Charybdis japonica,Scylla paramamosain,and Eriocheir sinensis） common in the coast of China.Gallus domesticus（2C=2.5 pg） was used as the internal standard.The results showed that the C-value for P.trituberculatus,C.japonica,S.paramamosain,and E.sinensis were（2.31±0.01） pg,（2.33±0.03） pg,（1.64±0.02） pg,and（2.29±0.03） pg,respectively.The C-value of P.trituberculatus,C.japonica and S.paramamosain were reported for the first time.The data represented by the four species indicated that they had lower DNA contents than average DNA values in crustaceans（（4.99±0.48） pg）,and three of the four values were very similar if not identical.The results provide useful data for future studies in the fields of biodiversity,species conservation,and phylogeny of these commercial crabs.They will also be helpful in instructing the hybridization breeding program and estimating the cost of the whole genome sequencing project.
基金supported by Argentine National Found for Science and Technology,under Grant PICT 2014-3478-BID and 20190149 BIDCouncil of Science and Technology-CONICET under Grant PIP-0712.R.V.R.,M.T.,and C.P.S.are members of CONICET. Grant Agency of the Czech Republic 17-12420S
文摘Relationships between genome size and environmental variables suggest that DNA content might be adaptive and of evolutionary importance in plants.The genus Larrea provides an interesting system to test this hypothesis,since it shows both intra-and interspecific variation in genome size.Larrea has an amphitropical distribution in North and South American deserts,where it is most speciose.Larrea tridentata in North America shows a gradient of increasing autopolyploidy;while three of the four studied South American species are diploids,Larrea divaricata,Larrea nitida,Larrea ameghinoi,and the fourth is an allopolyploid,Larrea cuneifolia.We downloaded available focal species’georeferenced records from seven data reservoirs.We used these records to extract biologically relevant environmental variables from WorldClim at 30 arc seconds scale,to have a broad characterization of the variable climatic conditions of both regions,and a climatic envelope for each species.We estimated relative DNA content index and relative monoploid genome values,by flow cytometry,of four most abundant Larrea species throughout their respective ranges.Then we winnow the bioclimatic dataset down to uncorrelated variables and sampled locales,to analyse the degree of association between both intra-and interspecific relative DNA content and climatic variables that are functionally relevant in arid environments using Pearson correlations,general linear and mixed effects models.Within the genus Larrea,relative DNA content increases with rising temperature and decreases with rising precipitation.At the intraspecific level,all four species show relative DNA content variation across climatic conditions.Larrea is a genus that shows genome size variation correlated with climate.Our results are also consistent with the hypothesis that extreme environmental pressures may have facilitated repeated whole genome duplication events in North America,while in South America,reticulate evolution,as allopolyploidization,and speciation might have been climate-dependent since the Oligocene.
