Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology

Meng, Fanbo; Pan, Yuxin; Wang, Jinpeng; Yu, Jigao; Liu, Chao; Zhang, Zhikang; Wei, Chendan; Guo, He; Wang, Xiyin

doi:10.3389/fgene.2020.00239

Cited by 15 publications

(10 citation statements)

References 39 publications

(38 reference statements)

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“…Besides, it might continue to drive their evolution and functional innovation in that much increased mutations were observed in the duplicated genes, resulting in aberrant topology of gene trees ( Wang J. et al., 2019 ). At least 83.2% of phylogenetic trees constructed with collinear homologs, including grape, cotton, and cacao, did not conform to the expected topology, clearly due to elevated evolutionary rates of certain duplicated gene copies ( Meng et al., 2020 ).…”

Section: Polyploidization and Cotton Originationmentioning

confidence: 99%

Sequencing Multiple Cotton Genomes Reveals Complex Structures and Lays Foundation for Breeding

2020

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Cotton is a major fiber plant, which provides raw materials for clothing, protecting humans from the harsh environment of cold or hot weathers, enriching the culture and custom of human societies. Due to its importance, the diploid and tetraploid genomes of different cotton plants have been repeatedly sequenced to obtain their complete and fine genome sequences. These valuable genome data sets revealed the evolutionary past of the cotton plants, which were recursively affected by polyploidization, with a decaploidization contributing to the formation of the genus Gossypium, and a neo-tetraploidization contributing to the formation of nowadays widely cultivated cotton plants. Postpolyploidization genome instability resulted in numerous structural changes of the genomes, such as gene loss, DNA inversion and translocation, illegitimate recombination, and accumulation of repetitive sequences, and functional innovation accompanied by elevated evolutionary rates of genes. Many these changes have been asymmetric between subgnomes of the tetraploid cottons, rendering their divergent profiles of biological regulation and function. The availability of whole-genome sequences has now paved the way to identify and clone functional genes, e.g., those relating to fiber development, and to enhance breeding efforts to cultivate cottons to produce high-yield and high-quality fibers, and to resist environmental and biological stress.

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Section: Polyploidization and Cotton Originationmentioning

confidence: 99%

Sequencing Multiple Cotton Genomes Reveals Complex Structures and Lays Foundation for Breeding

2020

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“…Orthologous analysis suggested that the evolution of the MACPF genes was not balanced between the allotetraploid and diploid genomes and there were more genes in the Dt subgenomes (Figure 3 and Supplementary Figure 4). The imbalance transcript indicated that the donors of the Dt subgenomes and G. raimondii were important to the abiotic stresses in the allotetraploid cotton and in the Brassica napus allotetraploids (Wang et al, 2019;Meng et al, 2020;Zhang et al, 2020). In addition, Ka/Ks values showed that most gene pairs have undergone purification selection during evolution (Supplementary Table 6) and the purification selection in WRKY and plant homeodomain (PHD) gene family (Hurst, 2002;Gu et al, 2018;Wu et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic Analysis of the Membrane Attack Complex/Perforin Domain-Containing Proteins in Gossypium and the Role of GhMACPF26 in Cotton Under Cold Stress

et al. 2021

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The membrane attack complex/perforin (MACPF) domain-containing proteins are involved in the various developmental processes and in responding to diverse abiotic stress. The function and regulatory network of the MACPF genes are rarely reported in Gossypium spp. We study the detailed identification and partial functional verification of the members of the MACPF family. Totally, 100 putative MACPF proteins containing complete MACPF domain were identified from the four cotton species. They were classified into three phylogenetic groups and underwent multifold pressure indicating that selection produced new functional differentiation. Cotton MACPF gene family members expanded mainly through the whole-genome duplication (WGD)/segmental followed by the dispersed. Expression and cis-acting elements analysis revealed that MACPFs play a role in resistance to abiotic stresses, and some selected GhMACPFs were able to respond to the PEG and cold stresses. Co-expression analysis showed that GhMACPFs might interact with valine-glutamine (VQ), WRKY, and Apetala 2 (AP2)/ethylene responsive factor (ERF) domain-containing genes under cold stress. In addition, silencing endogenous GhMACPF26 in cotton by the virus-induced gene silencing (VIGS) method indicated that GhMACPF26 negatively regulates cold tolerance. Our data provided a comprehensive phylogenetic evolutionary view of Gossypium MACPFs. The MACPFs may work together with multiple transcriptional factors and play roles in acclimation to abiotic stress, especially cold stress in cotton.

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“…However, the credibility of the tree was well supported by known or expected phylogenetic relationship, paralogy between homeologs from subgenomes, or orthology between homeologs from different organisms. Actually, the known or expected relationship between homeologs was further supported by inferred gene colinearity, which is a good criteria to explore the real phylogeny, especially when it was disturbed by non-uniform evolutionary rates of plant genes ( Meng et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Illegitimate Recombination Between Homeologous Genes in Wheat Genome

et al. 2020

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Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology

Cited by 15 publications

References 39 publications

Sequencing Multiple Cotton Genomes Reveals Complex Structures and Lays Foundation for Breeding

Sequencing Multiple Cotton Genomes Reveals Complex Structures and Lays Foundation for Breeding

Phylogenetic Analysis of the Membrane Attack Complex/Perforin Domain-Containing Proteins in Gossypium and the Role of GhMACPF26 in Cotton Under Cold Stress

Illegitimate Recombination Between Homeologous Genes in Wheat Genome

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