Polyploidy Index and Its Implications for the Evolution of Polyploids

Wang, Jinpeng; Qin, Jun; Sun, Pengchuan; Ma, Xuelian; Yu, Jigao; Li, Yuxian; Sun, Shiqun; Lei, Tianyu; Meng, Fanbo; Wei, Chendan; Li, Xinyu; Guo, He; Liu, Xiaojian; Xia, Ruiyan; Wang, Li; Ge, Weina; Song, Xiaoming; Zhang, Lan; Guo, Di; Wang, Jinyu; Bao, Shoutong; Jiang, Shan; Feng, Yishan; Li, Xueping; Paterson, Andrew H.; Wang, Xiyin

doi:10.3389/fgene.2019.00807

Cited by 28 publications

(45 citation statements)

References 48 publications

(61 reference statements)

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“…Many extant diploid species possess duplicated chromosomal regions as relics of ancient polyploidization events (Gaut, 2002). More specifically, it has been suggested that most of these have been allopolyploidizations and that more than 99.7% of angiosperms are directly derived from allopolyploidization (Wang et al, 2019). Therefore, one may speculate that the panicoid DNA could have been transferred into a (presumably) polyploid progenitor of Triticeae and further distributed vertically.…”

Section: Discussionmentioning

confidence: 99%

A Panicum‐derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress‐related genes

et al. 2021

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Intra-specific variability is a cornerstone of evolutionary success of species. Acquiring genetic material from distant sources is an important adaptive mechanism in bacteria, but it can also play a role in eukaryotes. In this paper, we investigate the nature and evolution of a chromosomal segment of panicoid (Poaceae, Panicoideae) origin occurring in the nuclear genomes of species of the barley genus Hordeum (Pooideae). The segment, spanning over 440 kb in the Asian Hordeum bogdanii and 219 kb in the South American Hordeum pubiflorum, resides on a pair of nucleolar organizer region (NOR)-bearing chromosomes. Conserved synteny and microcollinearity of the segment in both species indicate a common origin of the segment, which was acquired before the split of the respective barley lineages 5-1.7 million years ago. A major part of the foreign DNA consists of several approximately 68 kb long repeated blocks containing five stress-related protein-coding genes and transposable elements (TEs). Whereas outside these repeats, the locus was invaded by multiple TEs from the host genome, the repeated blocks are rather intact and appear to be preserved. The protein-coding genes remained partly functional, as indicated by conserved reading frames, a low amount of non-synonymous mutations, and expression of mRNA. A screen across Hordeum species targeting the panicoid protein-coding genes revealed the presence of the genes in all species of the section Stenostachys. In summary, our study shows that grass genomes can contain large genomic segments obtained from distantly related species. These segments usually remain undetected, but they may play an important role in the evolution and adaptation of species.

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Section: Discussionmentioning

confidence: 99%

A Panicum‐derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress‐related genes

et al. 2021

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“…2020 ), many important plant radiations were preceded by ancient allopolyploidization events (e.g., Estep et al. 2014 ; Aköz and Nordborg 2019 ; Wang et al. 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Linked by Ancestral Bonds: Multiple Whole-Genome Duplications and Reticulate Evolution in a Brassicaceae Tribe

Guo

Mandáková

Trachtová

et al. 2020

Molecular Biology and Evolution

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Pervasive hybridization and whole-genome duplications (WGDs) influenced genome evolution in several eukaryotic lineages. Although frequent and recurrent hybridizations may result in reticulate phylogenies, the evolutionary events underlying these reticulations, including detailed structure of the ancestral diploid and polyploid genomes, were only rarely reconstructed. Here, we elucidate the complex genomic history of a monophyletic clade from the mustard family (Brassicaceae), showing contentious relationships to the early-diverging clades of this model plant family. Genome evolution in the crucifer tribe Biscutelleae (∼60 species, 5 genera) was dominated by pervasive hybridizations and subsequent genome duplications. Diversification of an ancestral diploid genome into several divergent but crossable genomes was followed by hybridizations between these genomes. Whereas a single genus (Megadenia) remained diploid, the four remaining genera originated by allopolyploidy (Biscutella, Lunaria, Ricotia) or autopolyploidy (Heldreichia). The contentious relationships among the Biscutelleae genera, and between the tribe and other early diverged crucifer lineages, are best explained by close genomic relatedness among the recurrently hybridizing ancestral genomes. By using complementary cytogenomics and phylogenomics approaches, we demonstrate that the origin of a monophyletic plant clade can be more complex than a parsimonious assumption of a single WGD spurring postpolyploid cladogenesis. Instead, recurrent hybridization among the same and/or closely related parental genomes may phylogenetically interlink diploid and polyploid genomes despite the incidence of multiple independent WGDs. Our results provide new insights into evolution of early-diverging Brassicaceae lineages and elucidate challenges in resolving the contentious relationships within and between land plant lineages with pervasive hybridization and WGDs.

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“…These duplicated genes provide enormous opportunities for biological innovation [37][38][39]. It has been more and more evident that whole-genome duplications have contributed to the origination, fast divergence [40], establishment of major plant taxa [41,42], such as seed and flowering plants [43], and furthermore the subsets of the latter monocots and dicots [44][45][46][47].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification, phylogenetic and expressional analysis of the UXS gene family in cotton

Pan¹,

Wang²,

Wang³

et al. 2020

Preprint

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Background: UDP-glucuronate decarboxylase (UXS) is an enzyme in plants and participates in cell wall noncellulose. Previous research suggested that cotton GhUXS gene regulated the conversion of non-cellulosic polysaccharides and modulates their composition in plant cell walls, showing its possible cellular function determining the quality of cotton fibers. Here, we performed evolutionary, phylogenetic, and expressional analysis of UXS genes from cottons and other selected plants. Results: By exploring the sequenced cotton genomes, we identified 10, 10, 18, and 20 UXSs genes in Gossypium raimondii , Gossypium arboretum , Gossypium hirsutum and Gossypium barbadense , and retrieved their homologs from other representative plants, including 5 dicots, 1 monocot, 5 green alga, 1 moss, and 1 lycophyte. Phylogenetic analysis suggested that UXS genes could be divided into four subgroups and members within each subgroup shared similar exon-intron structures, motif and subcellular location. Notably, gene colinearity information indicates 100% constructed trees to have aberrant topology, and helps determine and use corrected phylogeny. In spite of conservative nature of UXS, during the evolution of Gossypium , UXS genes were subjected to significant positive selection on key evolutionary nodes. Expression profiles derived from RNA-seq data showed distinct expression patterns of GhUXS genes in various tissues and different development. Most of GhUXS gene expressed highly at 10, 20 and 25 DPA (day post anthesis) of fibers. Real-time quantitative PCR analysis GhUXS genes expressed highly at 20 DPA or 25 DPA. Conclusions: UXS is relatively conserved in plants and significant positive selection affects cotton UXS evolution. The comparative genome-wide identification and expression profiling would lay an important foundation to understanding the biological functions of UXS gene family in cotton species and other plants.

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Polyploidy Index and Its Implications for the Evolution of Polyploids

Cited by 28 publications

References 48 publications

A Panicum‐derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress‐related genes

A Panicum‐derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress‐related genes

Linked by Ancestral Bonds: Multiple Whole-Genome Duplications and Reticulate Evolution in a Brassicaceae Tribe

Genome-wide identification, phylogenetic and expressional analysis of the UXS gene family in cotton

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