The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis （Betrdn et ah, 20...The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis （Betrdn et ah, 2002; Begun et ah, 2007; Dubruille et ah, 2012）, and thus an ＂out of testis＂ hypothesis for the emergence of new genes has been proposed （Vinckenbosch et ah, 2006; Kaessmann, 2010）. However, such phenomena have not been examined in plant species. Here, by employing a phylostratigraphic method, we dated the origin of protein-coding genes in rice and Arabidopsis thaliana and observed a num- ber of young genes in both species. These young genes tend to encode short extracellular proteins, which may be involved in rapid evolving processes, such as reproductive barriers, species specification, and anti- microbial processes. Further analysis of transcriptome age indexes across different tissues revealed that male reproductive cells express a phylogenetically younger transcriptome than other plant tissues. Compared with sporophytic tissues, the young transcriptomes of the male gametophyte displayed greater complexity and diversity, which included a higher ratio of anti-sense and inter-genic transcripts, reflecting a pervasive transcription state that facilitated the emergence of new genes. Here, we propose that pollen may act as an ＂innovation incubator＂ for the birth of de novo genes. With cases of male-biased expression of young genes reported in animals, the ＂new genes out of the male＂ model revealed a common evolu- tionary force that drives reproductive barriers, species specification, and the upgrading of defensive mech- anisms against pathogens.展开更多
Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types,yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several ord...Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types,yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and families.Thus we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny,with resolved relationships for orders and families with previously uncertain placements.Using this phylogeny as a framework,molecular dating supports a Triassic origin of the crown angiosperms,followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial Revolution.The robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types,revealing a trend of parallel carpel fusions during early diversifications in eudicots,monocots,and magnoliids.Moreover,taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits;such associations of ovary,dry and fleshy fruits define several ovaryfruit"modules"each found in multiple families.One of the frequent modules has an ovary containing multiple ovules,capsules and berries,and another with an ovary having one or two ovules,achenes(or other single-seeded dry fruits)and drupes.This new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types,such as capsule and berry,that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules(such as achenes and drupes).Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications,supporting a possible role of whole-genome duplications,in combination with climate changes and animal behaviors,in angiosperm fruit and ovary diversification.展开更多
目的:分析所有miR-223基因家族成员的序列特征,并对miR-223靶基因进行预测,然后分析miR-223靶基因的生物学功能。方法:利用Clustal X 1.83软件分析miR-223基因序列特征,MEGA 5.0软件分析进化关系,再运用TargetScan、PicTar和miRDB进行...目的:分析所有miR-223基因家族成员的序列特征,并对miR-223靶基因进行预测,然后分析miR-223靶基因的生物学功能。方法:利用Clustal X 1.83软件分析miR-223基因序列特征,MEGA 5.0软件分析进化关系,再运用TargetScan、PicTar和miRDB进行靶基因预测,最后GO和KEGG进行功能分析。结果:在miRBase数据中获得miRNA-223基因家族成员的序列27条,绝大部分位于基因间隔区,少数成员的基因位置未知。大部分定位于X染色体,部分成员位于常染色体。miRNA-223成熟序列长度在20-23nt之间,同源性较高。系统进化树分析表明,miRNA-223基因家族成员分为三支。预测获得人类miRNA-223的可能具有27个靶基因,它们主要与信号转导、转录调控以及细胞生长发育等密切相关。结论:本研究结果不仅有利于理解miR-223基因家族的生物学功能,也可为后续研究提供理论依据。展开更多
Gene gain and loss are crucial factors that shape the evolutionary success of diverse organisms.In the past two decades,more attention has been paid to the significance of gene gain through gene duplication or de novo...Gene gain and loss are crucial factors that shape the evolutionary success of diverse organisms.In the past two decades,more attention has been paid to the significance of gene gain through gene duplication or de novo genes.However,gene loss through natural loss-of-function(LoF)mutations,which isprevalent in the genomes of diverse organisms,has been largely ignored.With the development of sequencing techniques,many genomes have been sequenced across diverse species and can be used to study the evolutionary patterns of gene loss.In this review,we summarize recent advances in research on various aspects of LoF mutations,including their identification,evolutionary dynamics in natural populations,and functional effects.In particular,we discuss how LoF mutations can provide insights into the minimum gene set(or the essential gene set)of an organism.Furthermore,we emphasize their potential impact on adaptation.At the genome level,although most LoF mutations are neutral or deleterious,at least some of them are under positive selection and may contribute to biodiversity and adaptation.Overall,we highlight the importance of natural LoF mutations as a robust framework for understanding biological questions in general.展开更多
After more than one hundred fifty years of the publication of On the Origin of Species by Darwin, scientists are still arguing on the relative importance of mutation and natural selection, on the driving force of orga...After more than one hundred fifty years of the publication of On the Origin of Species by Darwin, scientists are still arguing on the relative importance of mutation and natural selection, on the driving force of organismal evolution, on microevo- lution and macroevolution, etc. Such periodically repeated debates appeared to have introduced more chaos than musings. What happened and why？ Have we really considered our views, opinions and arguments under the big picture of evolution before pos- ing the questions？ Or are we talking past each other？ We do need some reflections. While we believe that the current evolutionary theory is doing fine, perhaps a refinement or re-encapsulation of its knowledge framework can help promote a better understanding of the evolutionary science as a whole and blow offthe mist over the big picture [Current Zoology 61 （1）： 217-220, 2015 ].展开更多
In order to explore the genomic basis for liver cancer metastasis,whole-exome sequencing(WES)was performed on patient-derived hepatocellular carcinoma(HCC)cell lines with differential metastatic potentials and analyze...In order to explore the genomic basis for liver cancer metastasis,whole-exome sequencing(WES)was performed on patient-derived hepatocellular carcinoma(HCC)cell lines with differential metastatic potentials and analyzed their clonal evolution relationships.An evolutionary tree based on genomic single nucleotide polymorphism(SNP)was constructed in MegaX software.The WES data showed that the average percentage of heterogeneous mutations in each HCC cell lines was 16.55%(range,15.38%e18.17%).C:G>T:A and T:A>C:G somatic transitions were the two most frequent substitutions.In these metastatic HCC cell lines,non-silent gene mutations were found in 21.88%of known driver genes and 10 classical signaling pathways.The protein interaction network was constructed by STRING,and hub genes were found in the shared trunk mutation genes and the heterogeneous branch mutations respectively.In cBioPortal database,some of the selected hub genes were found to be associated with poor overall survival(OS)of HCC patients.Among the mutated HCC driver genes,a novel KEAP1 mutation with a homozygous frameshift truncation at the c-terminal Nrf2 binding region was detected and verified in MHCC97-H and HCC97LM3 cells.In conclusion,WES data demonstrate that HCC cell lines from tumor biopsy specimens of the same patient have obtained different metastatic potentials through repeated selection in rodents in vivo,and they do indeed have a genetic relationship at the genomic level.展开更多
Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships.In this study,785 singl...Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships.In this study,785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato,an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events.The nuclear phylogeny recovered the monophyly of Malus s.l.(including Docynia);however,the genus was supported to be biphyletic in the plastid phylogeny.An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance.Our conflict analysis demonstrated that ILS,hybridization,and allopolyploidy could explain the widespread nuclear gene tree discordance.One deep hybridization event(Malus doumeri)and one recent event(Malus coronaria)were detected in Malus s.l.Furthermore,our historical biogeographic analysis integrating living and fossil data supported a widespread East Asianwestern North American origin of Malus s.l.in the Eocene,followed by several extinction and dispersal events in the Northern Hemisphere.We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.展开更多
The homeobox （Hox） genes form an evolutionarily conserved family encoding transcription factors that play major roles in segmental identity and organ specification across species. The canonical grouping of Hox genes...The homeobox （Hox） genes form an evolutionarily conserved family encoding transcription factors that play major roles in segmental identity and organ specification across species. The canonical grouping of Hox genes present in the HOM-C cluster of Drosophila or related clusters in other organisms includes eight “typical” genes, which are localized in the order labial （lab）, proboscipedia （pb ）, Deformed （ Dfd）, Sex combs reduced （Scr）, Antennapedia （Antp）, Ultrabithorux （Ubx）, abdominalA （abdA）, and AbdominalB （AbdB）. The members of Hox cluster are expressed in a distinct anterior to posterior order in the embryo. Analysis of the relatedness of different members of the Hox gene cluster to each other in four evolutionarily diverse insect taxa revealed that the loci pb/Dfd and AbdB, which are farthest apart in linkage, had a high degree of evolutionary relatedness, indicating that pb/Dfd type anterior genes and AbdB are closest to the ancestral anterior and posterior Hox genes, respectively. The greater relatedness of other posterior genes Ubx and abdA to the more anterior genes such as Antp and Scr suggested that they arose by gene duplications in the more anterior members rather than the posterior AbdB.展开更多
Gene duplication plays an important role in the evolution of organisms by allowing functional innovation and the divergence of duplicate genes. Previous studies found two PI-like genes in grass species, sug- gesting f...Gene duplication plays an important role in the evolution of organisms by allowing functional innovation and the divergence of duplicate genes. Previous studies found two PI-like genes in grass species, sug- gesting functional divergence between the paralogous copies. Here, we reconstructed the evolutionary history of two PI genes from major lineages of grasses and other monocot species, and demonstrated that two PI genes （PI1 and PI2） arose from a whole genome duplication that occurred in a common ancestor of extant grasses. Molecular evolutionary analyses at the family and tribal levels found strong purifying selection acting on two genes in grasses, consistent with the conserved class B function of the PI genes. Importantly, we detected different patterns of selective relaxation between the duplicated PI genes although no signature of positive selection was found. Likelihood ratio tests revealed that the ω ratio for M domain is significantly higher in PI1 than in PI2 but that for K domain is significantly higher in PI2 than in PI1. These findings imply that complementary selective relaxation occurs in two PI genes after duplication, and provide additional molecular evidence for the subfunctionalization of the duplicated PI genes in grasses.展开更多
文摘The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis （Betrdn et ah, 2002; Begun et ah, 2007; Dubruille et ah, 2012）, and thus an ＂out of testis＂ hypothesis for the emergence of new genes has been proposed （Vinckenbosch et ah, 2006; Kaessmann, 2010）. However, such phenomena have not been examined in plant species. Here, by employing a phylostratigraphic method, we dated the origin of protein-coding genes in rice and Arabidopsis thaliana and observed a num- ber of young genes in both species. These young genes tend to encode short extracellular proteins, which may be involved in rapid evolving processes, such as reproductive barriers, species specification, and anti- microbial processes. Further analysis of transcriptome age indexes across different tissues revealed that male reproductive cells express a phylogenetically younger transcriptome than other plant tissues. Compared with sporophytic tissues, the young transcriptomes of the male gametophyte displayed greater complexity and diversity, which included a higher ratio of anti-sense and inter-genic transcripts, reflecting a pervasive transcription state that facilitated the emergence of new genes. Here, we propose that pollen may act as an ＂innovation incubator＂ for the birth of de novo genes. With cases of male-biased expression of young genes reported in animals, the ＂new genes out of the male＂ model revealed a common evolu- tionary force that drives reproductive barriers, species specification, and the upgrading of defensive mech- anisms against pathogens.
基金supported by funds from the National Natural Science Foundation of China(31670209,31770242,and 31970224)China Postdoctoral Science Foundation(2019M661344)+2 种基金funds from the Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering at Fudan Universityfunds from the National Top Talent Undergraduate Training Program for outstanding undergraduates and the Wangdao Program for undergraduate research at Fudan Universityfunds from the Eberly College of Science(Department of Biology)and the Huck Institutes for the Life Sciences at the Pennsylvania State University。
文摘Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types,yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and families.Thus we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny,with resolved relationships for orders and families with previously uncertain placements.Using this phylogeny as a framework,molecular dating supports a Triassic origin of the crown angiosperms,followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial Revolution.The robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types,revealing a trend of parallel carpel fusions during early diversifications in eudicots,monocots,and magnoliids.Moreover,taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits;such associations of ovary,dry and fleshy fruits define several ovaryfruit"modules"each found in multiple families.One of the frequent modules has an ovary containing multiple ovules,capsules and berries,and another with an ovary having one or two ovules,achenes(or other single-seeded dry fruits)and drupes.This new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types,such as capsule and berry,that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules(such as achenes and drupes).Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications,supporting a possible role of whole-genome duplications,in combination with climate changes and animal behaviors,in angiosperm fruit and ovary diversification.
文摘目的:分析所有miR-223基因家族成员的序列特征,并对miR-223靶基因进行预测,然后分析miR-223靶基因的生物学功能。方法:利用Clustal X 1.83软件分析miR-223基因序列特征,MEGA 5.0软件分析进化关系,再运用TargetScan、PicTar和miRDB进行靶基因预测,最后GO和KEGG进行功能分析。结果:在miRBase数据中获得miRNA-223基因家族成员的序列27条,绝大部分位于基因间隔区,少数成员的基因位置未知。大部分定位于X染色体,部分成员位于常染色体。miRNA-223成熟序列长度在20-23nt之间,同源性较高。系统进化树分析表明,miRNA-223基因家族成员分为三支。预测获得人类miRNA-223的可能具有27个靶基因,它们主要与信号转导、转录调控以及细胞生长发育等密切相关。结论:本研究结果不仅有利于理解miR-223基因家族的生物学功能,也可为后续研究提供理论依据。
基金supported by the National Natural Science Foundation of China(31925004)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB27010305)the Innovative Academy of Seed Design,Chinese Academy of Sciences.
文摘Gene gain and loss are crucial factors that shape the evolutionary success of diverse organisms.In the past two decades,more attention has been paid to the significance of gene gain through gene duplication or de novo genes.However,gene loss through natural loss-of-function(LoF)mutations,which isprevalent in the genomes of diverse organisms,has been largely ignored.With the development of sequencing techniques,many genomes have been sequenced across diverse species and can be used to study the evolutionary patterns of gene loss.In this review,we summarize recent advances in research on various aspects of LoF mutations,including their identification,evolutionary dynamics in natural populations,and functional effects.In particular,we discuss how LoF mutations can provide insights into the minimum gene set(or the essential gene set)of an organism.Furthermore,we emphasize their potential impact on adaptation.At the genome level,although most LoF mutations are neutral or deleterious,at least some of them are under positive selection and may contribute to biodiversity and adaptation.Overall,we highlight the importance of natural LoF mutations as a robust framework for understanding biological questions in general.
文摘After more than one hundred fifty years of the publication of On the Origin of Species by Darwin, scientists are still arguing on the relative importance of mutation and natural selection, on the driving force of organismal evolution, on microevo- lution and macroevolution, etc. Such periodically repeated debates appeared to have introduced more chaos than musings. What happened and why？ Have we really considered our views, opinions and arguments under the big picture of evolution before pos- ing the questions？ Or are we talking past each other？ We do need some reflections. While we believe that the current evolutionary theory is doing fine, perhaps a refinement or re-encapsulation of its knowledge framework can help promote a better understanding of the evolutionary science as a whole and blow offthe mist over the big picture [Current Zoology 61 （1）： 217-220, 2015 ].
基金This work was supported by the National Natural Science Foundation of China(NSFC,NO.81172066,NO.81472858NO.91529103)+1 种基金Innovation Team Fund of Second Affiliated Hospital of Chongqing Medical UniversityThe authors would like to thank Dr.Zhou-You Tang,Professor&Director,Liver Cancer Institute,Fudan University,for providing the three HCC cell lines(MHCC97-L,MHCC97-H,HCC97LM3).
文摘In order to explore the genomic basis for liver cancer metastasis,whole-exome sequencing(WES)was performed on patient-derived hepatocellular carcinoma(HCC)cell lines with differential metastatic potentials and analyzed their clonal evolution relationships.An evolutionary tree based on genomic single nucleotide polymorphism(SNP)was constructed in MegaX software.The WES data showed that the average percentage of heterogeneous mutations in each HCC cell lines was 16.55%(range,15.38%e18.17%).C:G>T:A and T:A>C:G somatic transitions were the two most frequent substitutions.In these metastatic HCC cell lines,non-silent gene mutations were found in 21.88%of known driver genes and 10 classical signaling pathways.The protein interaction network was constructed by STRING,and hub genes were found in the shared trunk mutation genes and the heterogeneous branch mutations respectively.In cBioPortal database,some of the selected hub genes were found to be associated with poor overall survival(OS)of HCC patients.Among the mutated HCC driver genes,a novel KEAP1 mutation with a homozygous frameshift truncation at the c-terminal Nrf2 binding region was detected and verified in MHCC97-H and HCC97LM3 cells.In conclusion,WES data demonstrate that HCC cell lines from tumor biopsy specimens of the same patient have obtained different metastatic potentials through repeated selection in rodents in vivo,and they do indeed have a genetic relationship at the genomic level.
基金National Natural Science Foundation of China supports this research (32000163 and 31620103902)
文摘Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships.In this study,785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato,an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events.The nuclear phylogeny recovered the monophyly of Malus s.l.(including Docynia);however,the genus was supported to be biphyletic in the plastid phylogeny.An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance.Our conflict analysis demonstrated that ILS,hybridization,and allopolyploidy could explain the widespread nuclear gene tree discordance.One deep hybridization event(Malus doumeri)and one recent event(Malus coronaria)were detected in Malus s.l.Furthermore,our historical biogeographic analysis integrating living and fossil data supported a widespread East Asianwestern North American origin of Malus s.l.in the Eocene,followed by several extinction and dispersal events in the Northern Hemisphere.We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.
文摘The homeobox （Hox） genes form an evolutionarily conserved family encoding transcription factors that play major roles in segmental identity and organ specification across species. The canonical grouping of Hox genes present in the HOM-C cluster of Drosophila or related clusters in other organisms includes eight “typical” genes, which are localized in the order labial （lab）, proboscipedia （pb ）, Deformed （ Dfd）, Sex combs reduced （Scr）, Antennapedia （Antp）, Ultrabithorux （Ubx）, abdominalA （abdA）, and AbdominalB （AbdB）. The members of Hox cluster are expressed in a distinct anterior to posterior order in the embryo. Analysis of the relatedness of different members of the Hox gene cluster to each other in four evolutionarily diverse insect taxa revealed that the loci pb/Dfd and AbdB, which are farthest apart in linkage, had a high degree of evolutionary relatedness, indicating that pb/Dfd type anterior genes and AbdB are closest to the ancestral anterior and posterior Hox genes, respectively. The greater relatedness of other posterior genes Ubx and abdA to the more anterior genes such as Antp and Scr suggested that they arose by gene duplications in the more anterior members rather than the posterior AbdB.
基金supported by the National Natural Science Foundation of China(30990242 and 30121003)the State Key Basic Research and Development Plant of China(9732007CB815704)
文摘Gene duplication plays an important role in the evolution of organisms by allowing functional innovation and the divergence of duplicate genes. Previous studies found two PI-like genes in grass species, sug- gesting functional divergence between the paralogous copies. Here, we reconstructed the evolutionary history of two PI genes from major lineages of grasses and other monocot species, and demonstrated that two PI genes （PI1 and PI2） arose from a whole genome duplication that occurred in a common ancestor of extant grasses. Molecular evolutionary analyses at the family and tribal levels found strong purifying selection acting on two genes in grasses, consistent with the conserved class B function of the PI genes. Importantly, we detected different patterns of selective relaxation between the duplicated PI genes although no signature of positive selection was found. Likelihood ratio tests revealed that the ω ratio for M domain is significantly higher in PI1 than in PI2 but that for K domain is significantly higher in PI2 than in PI1. These findings imply that complementary selective relaxation occurs in two PI genes after duplication, and provide additional molecular evidence for the subfunctionalization of the duplicated PI genes in grasses.
