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Widespread whole genome duplications Contribute to genome Complexity and Species Diversity in Angiosperms

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Molecular Plant 2018年第3期11卷 414-428页

作者： Ren Ren Haifeng Wang Chunce Guo Ning Zhang Liping Zeng Yamao Chen Hong Ma Ji Qi State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Science Institute of Plant Biology Center for Evolutionary Biology School of Life Sciences Fudan University Shanghai China State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops Fujian Agriculture and Forestry University Fuzhou Fujian 350002 China Department of Botany National Museum of Natural History MRC 166 Smithsonian Institution Washington DC USA Institutes of Biomedical Sciences Fudan University Shanghai China These authors contributed equally to this article.

Gene duplications provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication （WGD） doubles the chromosomes initially and results in hundreds to thousands of retained duplicates. WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes, and thus are considered as a major driving force in species diversification. We per- formed comparative genomic and phylogenomic analyses of 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms to detect large-scale gene dupli- cation events by surveying tens of thousands of gene family trees. These analyses confirmed most of the previously reported WGDs and provided strong evidence for novel ones in many lineages. The detected WGDs supported a model of exponential gene loss during evolution with an estimated half-life of approx- imately 21.6 million years, and were correlated with both the emergence of lineages with high degrees of diversification and periods of global climate changes. The new datasets and analyses detected many novel WGDs widely spread during angiosperm evolution, uncovered preferential retention of gene functions in essential cellular metabolisms, and provided clues for the roles of WGD in promoting angiosperm radiation and enhancing their adaptation to environmental changes.

关键词： whole genome duplication duplicate gene polyploidization angiosperm phylogenomics

Functional Divergence between Subgenomes anc Gene Pairs after whole genome duplications

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Molecular Plant 2018年第3期11卷 388-397页

作者： Zhikai Liang James C. Schnable Plant Science innovation & Department of Agronomy and Horticulture University of Nebraska-Lincoln Lincoln NE 68503 USA

Gene loss following whole genome duplication （WGD） is often biased, with one subgenome retaining more ancestral genes and the other sustaining more gene deletions. While bias toward the greater expression of gene copies on one subgenome can explain bias in gene loss, this raises the question to what drives differences in gene expression levels between subgenomes. Differences in chromatin modifications and epigenetic markers between subgenomes in several model species are now being identified, providing an explanation for bias in gene expression between subgenomes. WGDs can be classified into duplications with higher, biased gene loss and bias in gene expression between subgenomes versus those with lower, unbiased rates of gene loss and an absence of detectable bias between subgenomes; however, the origi- nally proposed link between these two classes and whether WGD results from an allo- or autopolyploid event is inconsistent with recent data from the allopolyploid Capsella bursa-pastoris. The gene balance hypothesis can explain bias in the functional categories of genes retained following WGD, the difference in gene loss rates between unbiased and biased WGDs, and how plant genomes have avoided being overrun with genes encoding dose-sensitive subunits of multiprotein complexes. Comparisons of gene expression patterns between retained transcription factor pairs in maize suggest the high degree of retention for WGD-derived pairs of transcription factors may instead be explained by the older duplication-degeneration-complementation model.

关键词： whole genome duplication fractionation subgenome polypioidy

Upgraded durian genome reveals the role of chromosome reshuffling during ancestral karyotype evolution,lignin biosynthesis regulation,and stress tolerance

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Science China(Life Sciences) 2024年第6期67卷 1266-1279页

作者： Wanwan Li Xin Chen Jianing Yu Yuxian Zhu College of Life Sciences Shaanxi Normal UniversityXi’an 710119China The State Key Laboratory of Protein and Gene Research College of Life SciencesPeking UniversityBeijing 100871China The Institute for Advanced Studies Wuhan UniversityWuhan 430072China

Durian(Durio zibethinus)is a tropical fruit that has a unique flavor and *** occupies a significant phylogenetic position within the Malvaceae *** core-eudicot plants are reported to share seven ancestral karyotypes that have undergone reshuffling,resulting in an abundant genomic ***,the ancestral karyotypes of the Malvaceae family,as well as the evolution trajectory leading to the28 chromosomes in durian,remain poorly ***,we report the high-quality assembly of the durian genome with comprehensive comparative genomic *** analyzing the collinear blocks between cacao and durian,we inferred 11 Malvaceae ancestral *** blocks were present in a single-copy form in cacao and mainly in triplicates in durian,possibly resulting from a recent whole genome triplication(WGT)event that led to hexaploidization of the durian genome around 20(17–24)million years ago.A large proportion of the duplicated genes in durian,such as those involved in the lignin biosynthesis module for phenylpropane biosynthesis,are derived directly from whole genome duplication,which makes it an important force in reshaping its genomic *** studies have revealed that genes involved in feruloyl-Co A formations were highly preferentially expressed in fruit peels,indicating that the thorns produced on durian fruit may comprise guaiacyl and syringyl *** all the analyzed transcription factors(TFs),members of the heat shock factor family(HSF)were the most significantly upregulated under heat *** subfamilies of genes encoding heat shock proteins(HSPs)in the durian genome appear to have undergone *** potential interactions between HSF Dzi05.397 and HSPs were examined and experimentally *** study provides a high-quality durian genome and reveals the reshuffling mechanism of ancestral Malvaceae chromosomes to produce the durian *** also provide insights into the mechanism underlying lignin bi

关键词： Durio zibethinus whole genome duplication whole genome triplication Malvaceae ancestral karyotypes chromosome reshuffling lignin biosynthesis heat stress

The impact of tandem duplication on gene evolution in Solanaceae species

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Journal of Integrative Agriculture 2022年第4期21卷 1004-1014页

作者： HUANG Yi-le ZHANG Ling-kui ZHANG Kang CHEN Shu-min HU Jian-bin CHENG Feng College of Horticulture Henan Agricultural UniversityZhengzhou 450002P.R.China Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesBeijing 100097P.R.China

whole genome duplication(WGD) and tandem duplication(TD) are important modes of gene amplification and functional innovation, and they are common in plant genome evolution. We analyzed the genomes of three Solanaceae species(Solanum lycopersicum, Capsicum annuum, and Petunia inflata), which share a common distant ancestor with Vitis vinifera, Theobroma cacao, and Coffea canephora but have undergone an extra whole genome triplication(WGT) event. The analysis was used to investigate the phenomenon of tandem gene evolution with(S. lycopersicum) or without WGT(V. vinifera). Among the tandem gene arrays in these genomes, we found that V. vinifera, which has not experienced the WGT event, retained relatively more and larger tandem duplicated gene(TDG) clusters than the Solanaceae species that experienced the WGT event. Larger TDG clusters tend to be derived from older TD events, so this indicates that continuous TDGs(absolute dosage) accumulated during long-term evolution. In addition, WGD and TD show a significant bias in the functional categories of the genes retained. WGD tends to retain dose-sensitive genes related to biological processes, including DNA-binding and transcription factor activity, while TD tends to retain genes involved in stress resistance. WGD and TD also provide more possibilities for gene functional innovation through gene fusion and fission. The TDG cluster containing the tomato fusarium wilt resistance gene I3 contains 15 genes, and one of these genes, Solyc07g055560, has undergone a fusion event after the duplication events. These data provide evidence that helps explain the new functionalization of TDGs in adapting to environmental changes.

关键词： tandem duplication whole genome duplication Solanaceae species gene retention gene fusion

Comparative DNA-methylome and transcriptome analysis reveals heterosis-and polyploidy-associated epigenetic changes in rice

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The Crop Journal 2023年第2期11卷 427-437页

作者： Xiaolan Rao Jun Ren Wei Wang Rongrong Chen Qian Xie Yanqing Xu Dongmei Li Zhaojian Song Yuchi He Detian Cai Pingfang Yang Shiyou Lyu Li Li Wei Liu Xianhua Zhang School of Life Sciences Hubei UniversityWuhan 430062HubeiChina Wuhan Polyploid Bio-Technology Limited Company Wuhan 430345HubeiChina State Key Laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterChangsha 410125HunanChina Institute for Regenerative Medicine Shanghai East HospitalSchool of Life Sciences and TechnologyTongji UniversityShanghai 200123China

Heterosis and polyploidy have an overwhelming influence on plant ***,polyploid rice hybrids have been used to breed new rice varieties because they combine the advantages of both heterosis and *** this study,we generated six rice lines:autotetraploid rice hybrids and their autotetraploid parents,diploid donors,and hybrids of the diploid *** investigate the molecular mechanism controlling the effects of both hybridization and polyploidization,we performed bisulfite and RNA sequencing on young panicles at the pollen meiosis stage to compare the DNA metabolomes and transcriptomes among the six rice *** hybrids lines were hypermethylated compared to their corresponding parents and the autotetraploid lines showed globally increased DNA methylation of their transposable elements compared to the diploid *** alteration in DNA methylation level corresponded to the differential gene expressions among the rice genotypes,suggesting that methylation changes induced by polyploidization and hybridization may affect gene *** of gene candidates were identified that may be associated with heterosis and *** results provide DNA information that can be used to investigate epigenetic modification during heterosis and polyploidy in rice.

关键词： Oryza sativa Neotetraploid rice Heterosis whole genome duplication Epigenetic changes

Lycophyte transcriptomes reveal two whole-genome duplications in Lycopodiaceae:Insights into the polyploidization of Phlegmariurus

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Plant Diversity 2022年第3期44卷 262-270页

作者： Zeng-Qiang Xia Zuo-Ying Wei Hui Shen Jiang-Ping Shu Ting Wang Yu-Feng Gu Amit Jaisi Yue-Hong Yan Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of ShenzhenShenzhen518114China CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and EcologyChinese Academy of Sciences300 Fenglin RoadShanghai200032China Shanghai Chenshan Plant Science Research Center Chinese Academy of Sciences3888 Chenhua Road SongjiangShanghai201602China University of Chinese Academy of Sciences Beijing100049China College of Life and Sciences Shanghai Normal UniversityShanghai201602China Life Science and Technology College Harbin Normal UniversityHarbinHeilongjiang 150025China Drug and Cosmetics Excellence Center School of PharmacyWalailak UniversityNakhon Si Thammarat80160Thailand

Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to *** are an excellent study system for examining whole-genome duplications(WGDs),or polyploidization,in spore-dispersed vascular ***,a lack of genome sequence data limits the reliable detection of very ancient WGDs,small-scale duplications(SSDs),and recent ***,we integrated phylogenomic analysis and the distribution of synonymous substitutions per synonymous sites(Ks)of the transcriptomes of 13 species of lycophytes to identify,locate,and date multiple WGDs in the lycophyte family ***,we examined the genus Phlegmariurus for signs of genetic discordance,which can provide valuable insight into the underlying causes of such conflict(e.g.,hybridization,incomplete lineage sorting,or horizontal gene transfer).We found strong evidence that two WGD events occurred along the phylogenetic backbone of Lycopodiaceae,with one occurring in the common ancestor of extant Phlegmariurus(Lycopodiaceae)approximately 22-23 million years ago(Mya)and the other occurring in the common ancestor of Lycopodiaceae around 206-214 ***,we found significant genetic discordance in the genus Phlegmariurus,indicating that the genus has a complex evolutionary *** study provides molecular evidence for multiple WGDs in Lycopodiaceae and offers phylogenetic clues to the evolutionary history of Lycopodiaceae.

关键词： Lycophytes whole genome duplication Polyploidization Phylogenomics Gene tree conflict

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Polyploid organisms

Science China(Life Sciences) 2012年第4期55卷 301-311页

作者： SONG Can LIU ShaoJun XIAO Jun HE WeiGuo ZHOU Yi QIN QinBo ZHANG Chun LIU Yun Key Laboratory of Protein Chemistry and Fish Developmental Biology of Ministry of Education of China College of Life Sciences Hunan Normal University Changsha 410081 China

Polyploids are organisms with three or more complete chromosome sets. Polyploidization is widespread in plants and animals, and is an important mechanism of speciation. genome sequencing and related molecular systematics and bioinformatics studies on plants and animals in recent years support the view that species have been shaped by whole genome duplication during evolution. The stability of polyploids depends on rapid genome recombination and changes in gene expression after formation. The formation of polyploids and subsequent diploidization are important aspects in long-term evolution. Polyploids can be formed in various ways. Among them, hybrid organisms formed by distant hybridization could produce unreduced gametes and thus generate offspring with doubled chromosomes, which is a fast, efficient method of polyploidization. The formation of fertile polyploids not only promoted the interflow of genetic materials among species and enriched the species diversity, but also laid the foundation for polyploidy breeding. The study of polyploids has both important theoretical significance and valuable applications. The production and application of polyploidy breeding have brought remarkable economic and social benefits.

关键词： polyploid whole genome duplication diploidization distant hybridization polyploidy breeding

Hox Gene Clusters of Early Vertebrates:Do They Serve as Reliable Markers for genome Evolution?

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Genomics, Proteomics & Bioinformatics 2011年第3期9卷 97-103页

作者： Shigehiro Kuraku Laboratory for Zoology and Evolutionary Biology Department of Biology University of Konstanz 78464 Konstanz Germany

Hox genes, responsible for regional specification along the anteroposterior axis in embryogenesis, are found as clusters in most eumetazoan genomes sequenced to date. Invertebrates possess a single Hox gene cluster with some exceptions of secondary cluster breakages, while osteichthyans （bony vertebrates） have multiple Hox clusters. In tetrapods, four Hox clusters, derived from the so-called two-round whole genome duplications （2R-WGDs）, are observed. Overall, the number of Hox gene clusters has been regarded as a reliable marker of ploidy levels in animal genomes. In fact, this scheme also fits the situations in teleost fishes that experienced an additional WGD. In this review, I focus on cyclostomes and cartilaginous fishes as lineages that would fill the gap between invertebrates and osteichthyans. A recent study highlighted a possible loss of the HoxC cluster in the galeomorph shark lineage, while other aspects of cartilaginous fish Hox clusters usually mark their conserved nature. In contrast, existing resources suggest that the cyclostomes exhibit a different mode of Hox cluster organization. For this group of species, whose genomes could have differently responded to the 2R-WGDs from jawed vertebrates, therefore the number of Hox clusters may not serve as a good indicator of their ploidy level.

关键词： Hox cluster Chondrichthyes Cyclostomata whole genome duplication hidden paralogy

Ancient two expansions of GYPSY-LTR transposons underlie the large genome of Norway spruce

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Ancient two expansions of GYPSY-LTR transposons underlie the...