Genome-Wide Analysis of the COBRA-Like Gene Family Supports Gene Expansion through Whole-Genome Duplication in Soybean (Glycine max)

The COBRA-like (COBL) gene family has been associated with the regulation of cell wall expansion and cellulose deposition. COBL mutants result in reduced levels and disorganized deposition of cellulose causing defects in the cell wall and inhibiting plant development. In this study, we report the identification of 24 COBL genes (GmCOBL) in the soybean genome. Phylogenetic analysis revealed that the COBL proteins are divided into two groups, which differ by about 170 amino acids in the N-terminal region. The GmCOBL genes were heterogeneously distributed in 14 of the 20 soybean chromosomes. This study showed that segmental duplication has contributed significantly to the expansion of the COBL family in soybean during all Glycine-specific whole-genome duplication events. The expression profile revealed that the expression of the paralogous genes is highly variable between organs and tissues of the plant. Only 20% of the paralogous gene pairs showed similar expression patterns. The high expression levels of some GmCOBLs suggest they are likely essential for regulating cell expansion during the whole soybean life cycle. Our comprehensive overview of the COBL gene family in soybean provides useful information for further understanding the evolution and diversification of COBL genes in soybean.

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Bioinformatic methods applied to the analysis of the genes retained after the whole genome duplication events in the sterlet genome (Acipenser ruthenus)

2020 Cognitive Sciences, Genomics and Bioinformatics (CSGB) ◽

10.1109/csgb51356.2020.9214587 ◽

2020 ◽

Author(s):

Mikhail Fofanov ◽

Tatyana Sheglova ◽

Vladimir Trifonov ◽

Manfred Schartl

Keyword(s):

Whole Genome Duplication ◽

Genome Duplication ◽

Whole Genome ◽

Acipenser Ruthenus ◽

Duplication Events

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Genome-Wide Analysis of Soybean JmjC Domain-Containing Proteins Suggests Evolutionary Conservation Following Whole-Genome Duplication

Frontiers in Plant Science ◽

10.3389/fpls.2016.01800 ◽

2016 ◽

Vol 7 ◽

Cited By ~ 10

Author(s):

Yapeng Han ◽

Xiangyong Li ◽

Lin Cheng ◽

Yanchun Liu ◽

Hui Wang ◽

...

Keyword(s):

Whole Genome Duplication ◽

Genome Duplication ◽

Evolutionary Conservation ◽

Whole Genome ◽

Genome Wide Analysis ◽

Genome Wide ◽

Jmjc Domain

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Gene-dosage issues: a recurrent theme in whole genome duplication events

Trends in Genetics ◽

10.1016/j.tig.2021.06.006 ◽

2021 ◽

Author(s):

Reiner A. Veitia ◽

James A. Birchler

Keyword(s):

Whole Genome Duplication ◽

Genome Duplication ◽

Gene Dosage ◽

Whole Genome ◽

Duplication Events ◽

Recurrent Theme

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Fine-scale ecological and transcriptomic data reveal niche differentiation of an allopolyploid from diploid parents in Cardamine

10.1101/600783 ◽

2019 ◽

Cited By ~ 2

Author(s):

Reiko Akiyama ◽

Jianqiang Sun ◽

Masaomi Hatakeyama ◽

Heidi E.L. Lischer ◽

Roman V. Briskine ◽

...

Keyword(s):

Water Availability ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Expression Patterns ◽

Niche Differentiation ◽

Gene Expression Patterns ◽

Whole Genome ◽

Fine Scale ◽

Transcriptomic Data ◽

Cardamine Flexuosa

AbstractPolyploidization, or whole genome duplication, is one of the major mechanisms of plant speciation. Allopolyploids (species that harbor polyploid genomes originating from hybridization of different diploid species) have been hypothesized to occupy a niche with intermediate, broader, or fluctuating environmental conditions compared with parental diploids. It remains unclear whether empirical data support this hypothesis and whether specialization of expression patterns of the homeologs (paralogous gene copies resulting from allopolyploidization) relates to habitat environments. Here, we studied the ecology and transcriptomics of a wild allopolyploid Cardamine flexuosa and its diploid parents C. hirsuta and C. amara at a fine geographical scale in their native area in Switzerland. We found that the diploid parents favored opposite extremes in terms of soil moisture, soil carbon-to-nitrogen ratios, and light availability. The habitat of the allopolyploid C. flexuosa was broader compared with those of its parental species and overlapped with those of the parents, but not at its extremes. In C. flexuosa, the genes related to water availability were overrepresented among those at both the expression level and the expression ratio of homeolog pairs, which varied among habitat environments. These findings provide empirical evidence for niche differentiation between an allopolyploid and its diploid parents at a fine scale, where both ecological and transcriptomic data indicated water availability to be the key environmental factor for niche differentiation.Significance statementPolyploidization, or whole genome duplication, is common in plants and may contribute to their ecological diversification. However, little is known about the niche differentiation of wild allopolyploids relative to their diploid parents and the gene expression patterns that may underlie such ecological divergence. We detected niche differentiation between the allopolyploid Cardamine flexuosa and its diploid parents C. amara and C. hirsuta along water availability gradient at a fine scale. The ecological differentiation was mirrored by the dynamic control of water availability-related gene expression patterns according to habitat environments. Thus, both ecological and transcriptomic data revealed niche differentiation between an allopolyploid species and its diploid parents.

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Genome-wide analysis suggests high level of microsynteny and purifying selection affect the evolution of EIN3/EIL family in Rosaceae

PeerJ ◽

10.7717/peerj.3400 ◽

2017 ◽

Vol 5 ◽

pp. e3400 ◽

Cited By ~ 7

Author(s):

Yunpeng Cao ◽

Yahui Han ◽

Dandan Meng ◽

Dahui Li ◽

Qing Jin ◽

...

Keyword(s):

Gene Family ◽

Whole Genome Duplication ◽

Large Scale ◽

Prunus Persica ◽

Genome Duplication ◽

Purifying Selection ◽

Whole Genome ◽

Environmental Selection ◽

Rosaceae Species ◽

High Level

The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) proteins are a type of nuclear-localized protein with DNA-binding activity in plants. Although the EIN3/EIL gene family has been studied in several plant species, little is known about comprehensive study of the EIN3/EIL gene family in Rosaceae. In this study, ten, five, four, and five EIN3/EIL genes were identified in the genomes of pear (Pyrus bretschneideri), mei (Prunus mume), peach (Prunus persica) and strawberry (Fragaria vesca), respectively. Twenty-eight chromosomal segments of EIL/EIN3 gene family were found in four Rosaceae species, and these segments could form seven orthologous or paralogous groups based on interspecies or intraspecies gene colinearity (microsynteny) analysis. Moreover, the highly conserved regions of microsynteny were found in four Rosaceae species. Subsequently it was found that both whole genome duplication and tandem duplication events significantly contributed to the EIL/EIN3 gene family expansion. Gene expression analysis of the EIL/EIN3 genes in the pear revealed subfunctionalization for several PbEIL genes derived from whole genome duplication. It is noteworthy that according to environmental selection pressure analysis, the strong purifying selection should dominate the maintenance of the EIL/EIN3 gene family in four Rosaceae species. These results provided useful information on Rosaceae EIL/EIN3 genes, as well as insights into the evolution of this gene family in four Rosaceae species. Furthermore, high level of microsynteny in the four Rosaceae plants suggested that a large-scale genome duplication event in the EIL/EIN3 gene family was predated to speciation.

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Artificial whole genome duplication in paleopolyploid sturgeons yields highest documented chromosome number in vertebrates

Scientific Reports ◽

10.1038/s41598-020-76680-4 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Ievgen Lebeda ◽

Petr Ráb ◽

Zuzana Majtánová ◽

Martin Flajšhans

Keyword(s):

Chromosome Numbers ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Mitotic Division ◽

Chromosome Count ◽

Whole Genome ◽

Acipenser Baerii ◽

Ploidy Levels ◽

Duplication Events ◽

C Value

AbstractCritically endangered sturgeons, having undergone three whole genome duplication events, represent an exceptional example of ploidy plasticity in vertebrates. Three extant ploidy groups, combined with autopolyploidization, interspecific hybridization and the fertility of hybrids are important issues in sturgeon conservation and aquaculture. Here we demonstrate that the sturgeon genome can undergo numerous alterations of ploidy without severe physiological consequences, producing progeny with a range of ploidy levels and extremely high chromosome numbers. Artificial suppression of the first mitotic division alone, or in combination with suppression of the second meiotic division of functionally tetraploid zygotes (4n, C-value = 4.15) of Siberian sturgeon Acipenser baerii and Russian sturgeon A. gueldenstaedtii resulted in progeny of various ploidy levels—diploid/hexaploid (2n/6n) mosaics, hexaploid, octoploid juveniles (8n), and dodecaploid (12n) larvae. Counts between 477 to 520 chromosomes in octoploid juveniles of both sturgeons confirmed the modal chromosome numbers of parental species had been doubled. This exceeds the highest previously documented chromosome count among vertebrates 2n ~ 446 in the cyprinid fish Ptychobarbus dipogon.

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