An Overlooked Paleotetraploidization in Cucurbitaceae

Wang, Jinpeng; Sun, Pengchuan; Li, Yuxian; Liu, Yinzhe; Yang, Ning; Yu, Jigao; Ma, Xuelian; Sun, Shiqun; Xia, Ruiyan; Liu, Xiaojian; Ge, Dongcen; Luo, Sainan; Liu, Yinmeng; Kong, Youting; Cui, Xiaobo; Lei, Tianyu; Wang, Li; Wang, Zhenyi; Ge, Weina; Zhang, Lan; Song, Xiaoming; Yuan, Min; Guo, Di; Jin, Dianchuan; Chen, Wei; Pan, Yuxin; Liu, Tao; Yang, Guixian; Xiao, Yue; Sun, Jinshuai; Zhang, Cong; Li, Zhibo; Xu, Haiyan; Duan, Xiaoyang; Shen, Shaoqi; Zhang, Zhonghua; Huang, Sanwen; Wang, Xiyin

doi:10.1093/molbev/msx242

Cited by 100 publications

(126 citation statements)

References 33 publications

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“…BLASTP search was performed to find putative homologous genes within a genome or between genomes. When running ColinearScan, maximal gap length between genes in colinearity along a chromosome sequence was set to 50 genes according to previous reports (Wang et al, ; Wang et al, ; Wang et al, ; Wang et al, ; Wang et al, ; Wang et al, ). Since large gene families lead to difficulty to infer gene colinearity, families with > 30 genes were removed before running ColinearScan.…”

Section: Methodsmentioning

confidence: 99%

Deciphering the high‐quality genome sequence of coriander that causes controversial feelings

Song

Wang

et al. 2020

Plant Biotechnology Journal

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Coriander (Coriandrum sativum L. 2n = 2x = 22), a plant from the Apiaceae family, also called cilantro or Chinese parsley, is a globally important crop used as vegetable, spice, fragrance and traditional medicine. Here, we report a high-quality assembly and analysis of its genome sequence, anchored to 11 chromosomes, with total length of 2118.68 Mb and N50 scaffold length of 160.99 Mb. We found that two whole-genome duplication events, respectively, dated to~45-52 and~54-61 million years ago, were shared by the Apiaceae family after their split from lettuce. Unbalanced gene loss and expression are observed between duplicated copies produced by these two events. Gene retention, expression, metabolomics and comparative genomic analyses of terpene synthase (TPS) gene family, involved in terpenoid biosynthesis pathway contributing to coriander's special flavour, revealed that tandem duplication contributed to coriander TPS gene family expansion, especially compared to their carrot counterparts. Notably, a TPS gene highly expressed in all 4 tissues and 3 development stages studied is likely a major-effect gene encoding linalool synthase and myrcene synthase. The present genome sequencing, transcriptome, metabolome and comparative genomic efforts provide valuable insights into the genome evolution and spice trait biology of Apiaceae and other related plants, and facilitated further research into important gene functions and crop improvement.1444

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Section: Methodsmentioning

confidence: 99%

Deciphering the high‐quality genome sequence of coriander that causes controversial feelings

Song

Wang

et al. 2020

Plant Biotechnology Journal

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“…2). Using a hierarchical and eventrelated approach by which we deciphered gene collinearity in many other genomes 28,29 , we identified colinear genes produced by each of the WGD/T events. CRGs were significantly increased in colinear regions in all species except for S. moellendorffii.…”

Section: Hierarchical Analyses Of Recursive Polyploidies and Crg Expamentioning

confidence: 99%

Preferential gene retention increases the robustness of cold regulation in Brassicaceae and other plants after polyploidization

et al. 2020

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Cold stress profoundly affects plant growth and development and is a key factor affecting the geographic distribution and evolution of plants. Plants have evolved adaptive mechanisms to cope with cold stress. Here, through the genomic analysis of Arabidopsis, three Brassica species and 17 other representative species, we found that both cold-related genes (CRGs) and their collinearity were preferentially retained after polyploidization followed by genome instability, while genome-wide gene sets exhibited a variety of other expansion mechanisms. The coldrelated regulatory network was increased in Brassicaceae genomes, which were recursively affected by polyploidization. By combining our findings regarding the selective retention of CRGs from this ecological genomics study with the available knowledge of cold-induced chromosome doubling, we hypothesize that cold stress may have contributed to the success of polyploid plants through both increasing polyploidization and selectively maintaining CRGs during evolution. This hypothesis requires further biological and ecological exploration to obtain solid supporting evidence, which will potentially contribute to understanding the generation of polyploids and to the field of ecological genomics.

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“…The phylogeny of angiosperm species and the associated paleopolyploidy events were redrawn based on a tree reported earlier by Van de Peer et al. (Van de Peer et al , 2017) and the APG IV system(Byng et al , 2016) with minor modifications: the hexapolyploidy event in cucurbitaceae(Wang et al , 2018), the fern genome duplications(Li et al , 2018), the ancestral duplication events mosses(Devos et al , 2016, Lang et al , 2018) and in Caryophyllales(Yang et al , 2018), were included in the tree.…”

Section: Methodsmentioning

confidence: 99%

Evolution of Auxin Response Factors in plants characterized by phylogenomic synteny network analyses

Gao

Rui

Oliver

et al. 2019

Preprint

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16Auxin response factors (ARFs) have long been a research focus and represent a class of key regulators of plant growth 17 and development. Previous studies focusing genes from limited number of species were unable to uncover the 18 evolutionary trajectory of this family. Here, more than 3,500 ARFs collected from plant genomes and transcriptomes 19 covering major streptophyte lineages were used to reconstruct the broad-scale family phylogeny, where the early origin 20 and diversification of ARF in charophytes was delineated. Based on the family phylogeny, we proposed a unified six-21 group classification system for angiosperm ARFs. Phylogenomic synteny network analyses revealed the deeply 22 conserved genomic syntenies within each of the six ARF groups and the interlocking syntenic relationships connecting 23 distinct groups. Recurrent duplication events, such as those that occurred in seed plant, angiosperms, core eudicots and 24 grasses contributed the expansion of ARF genes which facilitated functional diversification. Ancestral transposition 25 activities in important plant families, including crucifers, legumes and grasses, were unveiled by synteny network 26 analyses. Ancestral gene duplications along with transpositions have profound evolutionary significance which may 27 have accelerated the functional diversification process of paralogues. Our study provides insights into the evolution of 28 ARFs which will enhance our current understandings for this important transcription factor family. 29 30

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An Overlooked Paleotetraploidization in Cucurbitaceae

Cited by 100 publications

References 33 publications

Deciphering the high‐quality genome sequence of coriander that causes controversial feelings

Deciphering the high‐quality genome sequence of coriander that causes controversial feelings

Preferential gene retention increases the robustness of cold regulation in Brassicaceae and other plants after polyploidization

Evolution of Auxin Response Factors in plants characterized by phylogenomic synteny network analyses

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