Comparative Genome Analyses Highlight Transposon-Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton

Wang, Maojun; Li, Jianying; Wang, Pengcheng; Liu, Fang; Liu, Zhenping; Zhao, Guannan; Xu, Zhongping; Pei, Liuling; Grover, Corrinne E.; Wendel, Jonathan F.; Wang, Kunbo; Zhang, Xianlong

doi:10.1093/molbev/msab128

Cited by 57 publications

(40 citation statements)

References 92 publications

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“…While the presence of lineage-specific genes is not surprising, their relative contribution to the gene space of each species is exceptionally large, reaching 20-30%. In comparison, gene space difference between highly contiguous angiosperm genomes with similar depth of divergence is less pronounced (17,80,(82)(83)(84)(85)(86)(87)(88)(89). For instance, the proportion of species-specific genes usually remains below 3-10% in most studies.…”

Section: Discussionmentioning

confidence: 99%

Genome dynamics in mosses: Extensive synteny coexists with a highly dynamic gene space

Kirbis¹,

Rahmatpour

Dong

et al. 2022

Preprint

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Background: While genome evolutionary processes of seed plants are intensively investigated, very little is known about seed-free plants in this respect. Here, we use one of the largest groups of seed-free plants, the mosses, and newly generated chromosome-scale genome assemblies to investigate three poorly known aspects of genome dynamics and their underlying processes in seed-free plants: (i) genome size variation, (ii) genomic collinearity/synteny, and (iii) gene set differentiation. Results: Comparative genomic analyses on the model moss Physcomitrium (Physcomitrella) patens and two genomes of Funaria hygrometrica reveal that, like in seed plants, genome size change (approx. 140 Mbp) is primarily due to transposable element expansion/contraction. Despite 60 million years of divergence, the genomes of P. patens and F. hygrometrica show remarkable chromosomal stability with the majority of homologous genes located in conserved collinear blocks. In addition, both genomes contain a relatively large set of lineage-specific genes with no detectible homologs in the other speciesʼ genome, suggesting a highly dynamic gene space fueled by the process of de novo gene birth and loss rather than by gene family diversification/duplication. Conclusions: These, combined with previous observations suggest that genome dynamics in mosses involves the coexistence of a collinear homologous and a highly dynamic species-specific gene sets. Besides its significance for understanding genome evolution, the presented chromosome-scale genome assemblies will provide a foundation for comparative genomic and functional studies in the Funariaceae, a family holding historical and contemporary model taxa in the evolutionary biology of mosses.

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Section: Discussionmentioning

confidence: 99%

Genome dynamics in mosses: Extensive synteny coexists with a highly dynamic gene space

Kirbis¹,

Rahmatpour

Dong

et al. 2022

Preprint

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“…As sequencing technology develops, the economic value of cotton fibers increases and the genomes of Gossypium hirsutum L. (AADD, 2n = 4X = 52) ( Paterson et al, 2012 ; Li et al, 2015 ; Hu et al, 2019 ; Wang et al, 2019 ), G. anomalum (BB, 2n = 2X = 26) ( Grover et al, 2021a ), G. stocksii (EE, 2n = 2X = 26) ( Grover et al, 2021b ), G. longicalyx (FF, 2 n = 2 X = 26) ( Grover et al, 2020 ), and G. rotundifolium (KK, 2n = 2X = 26) ( Wang et al, 2021 ), etc. have all been sequenced.…”

Section: Introductionmentioning

confidence: 99%

The hexokinase Gene Family in Cotton: Genome-Wide Characterization and Bioinformatics Analysis

Liu

Wang

et al. 2022

Front. Plant Sci.

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Hexokinase (HXK) is involved in hexose phosphorylation, sugar sensing, and signal transduction, all of which regulate plant growth and adaptation to stresses. Gossypium hirsutum L. is one of the most important fiber crops in the world, however, little is known about the HXKs gene family in G. hirsutum L. We identified 17 GhHXKs from the allotetraploid G. hirsutum L. genome (AADD). G. raimondii (DD) and G. arboreum (AA) are the diploid progenitors of G. hirsutum L. and contributed equally to the At_genome and Dt_genome GhHXKs genes. The chromosomal locations and exon-intron structures of GhHXK genes among cotton species are conservative. Phylogenetic analysis grouped the HXK proteins into four and three groups based on whether they were monocotyledons and dicotyledons, respectively. Duplication event analysis demonstrated that HXKs in G. hirsutum L. primarily originated from segmental duplication, which prior to diploid hybridization. Experiments of qRT-PCR, transcriptome and promoter cis-elements demonstrated that GhHXKs’ promoters have auxin and GA responsive elements that are highly expressed in the fiber initiation and elongation stages, while the promoters contain ABA-, MeJA-, and SA-responsive elements that are highly expressed during the synthesis of the secondary cell wall. We performed a comprehensive analysis of the GhHXK gene family is a vital fiber crop, which lays the foundation for future studies assessing its role in fiber development.

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“…Forty-four more assemblies have been added in CottonGen (Tables 2 and 3). They are twenty-eight from diploid species: three new versions of G. raimondii [16][17][18]; four versions of G. arboreum [18][19][20][21]; one for the other cultivated diploid species G. herbaceum; [21], twenty versions of eighteen wild diploid species [17,18,[22][23][24][25][26][27] (details in Table 2); and sixteen from tetraploid species-nine versions of G. hirsutum [21,[28][29][30][31][32][33][34], four versions of G. barbadense [31,32,34,35], and one for each of three wild tetraploid species: G. tomentosum [34], G. mustelinum [34], and G. darwinii [34] (Table 3). The predicted genes from these assemblies have been further annotated by the CottonGen team to include homology to cotton proteins from UniProtKB/Swiss-Prot [36,37] and NCBI [38,39] and the proteins of other well annotated or closely related species.…”

Section: Whole Genome Sequence Datamentioning

confidence: 99%

CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research

Jung

Cheng

et al. 2021

Plants

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Over the last eight years, the volume of whole genome, gene expression, SNP genotyping, and phenotype data generated by the cotton research community has exponentially increased. The efficient utilization/re-utilization of these complex and large datasets for knowledge discovery, translation, and application in crop improvement requires them to be curated, integrated with other types of data, and made available for access and analysis through efficient online search tools. Initiated in 2012, CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data, and analysis tools. Used by cotton researchers worldwide, and managed by experts with crop-specific knowledge, it continuous to be the logical choice to integrate new data and provide necessary interfaces for information retrieval. The repository in CottonGen contains colleague, gene, genome, genotype, germplasm, map, marker, metabolite, phenotype, publication, QTL, species, transcriptome, and trait data curated by the CottonGen team. The number of data entries housed in CottonGen has increased dramatically, for example, since 2014 there has been an 18-fold increase in genes/mRNAs, a 23-fold increase in whole genomes, and a 372-fold increase in genotype data. New tools include a genetic map viewer, a genome browser, a synteny viewer, a metabolite pathways browser, sequence retrieval, BLAST, and a breeding information management system (BIMS), as well as various search pages for new data types. CottonGen serves as the home to the International Cotton Genome Initiative, managing its elections and serving as a communication and coordination hub for the community. With its extensive curation and integration of data and online tools, CottonGen will continue to facilitate utilization of its critical resources to empower research for cotton crop improvement.

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Comparative Genome Analyses Highlight Transposon-Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton

Cited by 57 publications

References 92 publications

Genome dynamics in mosses: Extensive synteny coexists with a highly dynamic gene space

Genome dynamics in mosses: Extensive synteny coexists with a highly dynamic gene space

The hexokinase Gene Family in Cotton: Genome-Wide Characterization and Bioinformatics Analysis

CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research

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