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| 1 | Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogenfixing symbiosis in Fabaceae显示文摘Fabaceae are the third largest angiosperm family,with 765 genera and~19500 species.They are important both economically and ecologically,and global Fabaceae crops are intensively studied in part for their nitrogen-fixing ability.However,resolution of the intrasubfamilial Fabaceae phylogeny and divergence times has remained elusive,precluding a reconstruction of the evolutionary history of symbiotic nitrogen fixation in Fabaceae.Here,we report a highly resolved phylogeny using>1500 nuclear genes from newly sequenced transcriptomes and genomes of 391 species,along with other datasets,for a total of 463 legumes spanning all 6 subfamilies and 333 of 765 genera.The subfamilies are maximally supported as mono-phyletic.The clade comprising subfamilies Cercidoideae and Detarioideae is sister to the remaining legumes,and Duparquetioideae and Dialioideae are successive sisters to the clade of Papilionoideae and Caesalpinioideae.Molecular clock estimation revealed an early radiation of subfamilies near the K/Pg boundary,marked by mass extinction,and subsequent divergence of most tribe-level clades within~15 million years.Phylogenomic analyses of thousands of gene families support 28 proposed putative whole-genome duplication/whole-genome triplication events across Fabaceae,including those at the ancestors of Fabaceae and five of the subfamilies,and further analyses supported the Fabaceae ancestral polyploidy.The evolution of rhizobial nitrogen-fixing nodulation in Fabaceae was probed by ancestral character reconstruction and phylogenetic analyses of related gene families and the results support the hypotheses of one or two switches)to rhizobial nodulation followed by multiple losses.Collectively,these results provide a foundation for further morphological and functional evolutionary analyses across Fabaceae. | Yiyong Zhao Rong Zhang Kai-Wen Jiang Ji Qi Yi Hu Jing Guo Renbin Zhu Taikui Zhang Ashley N.Egan Ting-Shuang Yi Chien-Hsun Huang Hong Ma | 2021 | Molecular Plant2021，14，5： | 8 |
| 2 | Angiosperm-wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits显示文摘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. | Yezi Xiang Taikui Zhang Yiyong Zhao Hongjin Dong Hongyi Chen Yi Hu Chien-Hsun Huang Jun Xiang Hong Ma | 2024 | Journal of Integrative Plant Biology2024，66，2： | 0 |
| 3 | The nearly complete assembly of the Cercis chinensis genome and Fabaceae phylogenomic studies provide insights into new gene evolution显示文摘Fabaceae is a large family of angiosperms with high biodiversity that contains a variety of economically important crops and model plants for the study of biological nitrogen fixation.Polyploidization events have been extensively studied in some Fabaceae plants,but the occurrence of new genes is still concealed,owing to a lack of genomic information on certain species of the basal clade of Fabaceae.Cercis chinensis(Cercidoideae)is one such species;it diverged earliest from Fabaceae and is essential for phylogenomic studies and new gene predictions in Fabaceae.To facilitate genomic studies on Fabaceae,we performed genome sequencing of C.chinensis and obtained a 352.84 Mb genome,which was further assembled into seven pseudochromosomes with 30612 predicted protein-coding genes.Compared with other legume genomes,that of C.chinensis exhibits no lineage-specific polyploidization event.Further phylogenomic analyses of 22 legumes and 11 other angiosperms revealed that many gene families are lineage specific before and after the diversification of Fabaceae.Among them,dozens of genes are candidates for new genes that have evolved from intergenic regions and are thus regarded as de novo-originated genes.They differ significantly from established genes in coding sequence length,exon number,guanine–cytosine content,and expression patterns among tissues.Functional analysis revealed that many new genes are related to asparagine metabolism.This study represents an important advance in understanding the evolutionary pattern of new genes in legumes and provides a valuable resource for plant phylogenomic studies. | Jinglong Li Jingting Shen Rui Wang Yamao Chen Taikui Zhang Haifeng Wang Chunce Guo Ji Qi | 2023 | Plant Communications2023，4，1： | 0 |
| 4 | An ancient whole-genome duplication event and its contribution to flavor compounds in the tea plant (Camellia sinensis)显示文摘Tea,coffee,and cocoa are the three most popular nonalcoholic beverages in the world and have extremely high economic and cultural value.The genomes of four tea plant varieties have recently been sequenced,but there is some debate regarding the characterization of a whole-genome duplication(WGD)event in tea plants.Whether the WGD in the tea plant is shared with other plants in order Ericales and how it contributed to tea plant evolution remained unanswered.Here we re-analyzed the tea plant genome and provided evidence that tea experienced only WGD event after the core-eudicot whole-genome triplication(WGT)event.This WGD was shared by the Polemonioids-Primuloids-Core Ericales(PPC)sections,encompassing at least 17 families in the order Ericales.In addition,our study identified eight pairs of duplicated genes in the catechins biosynthesis pathway,four pairs of duplicated genes in the theanine biosynthesis pathway,and one pair of genes in the caffeine biosynthesis pathway,which were expanded and retained following this WGD.Nearly all these gene pairs were expressed in tea plants,implying the contribution of the WGD.This study shows that in addition to the role of the recent tandem gene duplication in the accumulation of tea flavor-related genes,the WGD may have been another main factor driving the evolution of tea flavor. | Ya Wang Fei Chen Yuanchun Ma Taikui Zhang Pengchuan Sun Meifang Lan Fang Li Wanping Fang | 2021 | Horticulture Research2021，8，1： | 0 |
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