Genome-wide identification and expression profiling of the COBRA-like genes reveal likely roles in stem strength in rapeseed (Brassica napus L.)

Yang, Qian; Wang, Shan; Chen, Hao; You, Liang; Liu, Fangying; Liu, Zhongsong

doi:10.1371/journal.pone.0260268

Cited by 4 publications

(12 citation statements)

References 56 publications

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“…COBL genes play a vital role in cell growth, wood fiber, and cellulose synthesis. The function and biological significance of the COBL proteins in a wide variety of plants, Arabidopsis , brassica, soyabean, rice, cotton, wheat, L. Chinense , and Populus , have been the subject of study ( Dai et al., 2009 ; Ye et al., 2009 ; Niu et al., 2015 ; Sangi et al., 2021 ; Yang et al., 2021 ; Zaheer et al., 2021 ; Qiu et al., 2023 ). There has not been a methodical and comprehensive study of COBL genes in poplar.…”

Section: Discussionmentioning

confidence: 99%

“…Whole genome duplication (WGD) occurrences were analyzed using MCScanX. The synteny and collinearity analyses were visualized between poplar and five other plant species ( Arabidopsis , eucalyptus , cotton, T. cacao , and V. vinifera ) using TBtools with default settings ( Chen et al., 2020 ; Yang et al., 2021 ).…”

Section: Methodsmentioning

confidence: 99%

“…The Ka/Ks ratios for PtrCOBL12-PtrCOBL3 and PtrCOBL8-PtrCOBL10 were the lowest among the paralogous genes, indicating these genes were able to keep their original roles despite their shorter divergence dates. The highest Ka/Ks value and very divergent expression patterns were found for the paralog pair PtrCOBL13-PtrCOBL14, providing strong evidence for their functional divergence after duplication (Sangi et al, 2021;Yang et al, 2021).…”

Section: Wgd Collaborated To Cobl Gene Family Expansionmentioning

confidence: 99%

“…But there has not been enough research done on COBRA-Like genes in tree species like poplar to draw any firm conclusions. COBRA belong to a plants p e c i fi c m u l t i g e n e ( C O B -l i k e ) f a m i l y a n d e n c o d e glycosylphosphatidylinositol (GPI)-anchored proteins embodying the hydrophilic region at the C-terminal, typically having an wattachment site for GPI modification accompanying an N-terminal secretion signal (Liu et al, 2013;Yang et al, 2021). COB protein is localized in vesicles, in the Golgi apparatus, and lastly at the cell surface, conforming to a classic GPI secretion pathway.…”

Section: Introductionmentioning

confidence: 99%

“…The COBL family members have been identified to intercede in several developmental and physiological processes, including stem strength, pollen tube growth, pathogen resistance, and root-hair growth ( Ko et al., 2006 ; Li et al., 2013 ; Yang et al., 2021 ; Li et al., 2022 ). Many mutants with aberrant cell expansion and cellulose deposition have been investigated to learn about the molecular processes that govern the direction and process of cell expansion during plant development ( Ko et al., 2006 ; Hochholdinger et al., 2008 ).…”

Section: Introductionmentioning

confidence: 99%

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Recent genome resequencing paraded COBRA-Like gene family roles in abiotic stress and wood formation in Poplar

Sajjad,

Ahmad,

Riaz

et al. 2023

Front. Plant Sci.

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A cell wall determines the mechanical properties of a cell, serves as a barrier against plant stresses, and allows cell division and growth processes. The COBRA-Like (COBL) gene family encodes a putative glycosylphosphatidylinositol (GPI)-anchored protein that controls cellulose deposition and cell progression in plants by contributing to the microfibril orientation of a cell wall. Despite being studied in different plant species, there is a dearth of the comprehensive global analysis of COBL genes in poplar. Poplar is employed as a model woody plant to study abiotic stresses and biomass production in tree research. Improved genome resequencing has enabled the comprehensive exploration of the evolution and functional capacities of PtrCOBLs (Poplar COBRA-Like genes) in poplar. Phylogeny analysis has discerned and classified PtrCOBLs into two groups resembling the Arabidopsis COBL family, and group I genes possess longer proteins but have fewer exons than group II. Analysis of gene structure and motifs revealed PtrCOBLs maintained a rather stable motif and exon–intron pattern across members of the same group. Synteny and collinearity analyses exhibited that the evolution of the COBL gene family was heavily influenced by gene duplication events. PtrCOBL genes have undergone both segmental duplication and tandem duplication, followed by purifying selection. Promotor analysis flaunted various phytohormone-, growth- and stress-related cis-elements (e.g., MYB, ABA, MeJA, SA, AuxR, and ATBP1). Likewise, 29 Ptr-miRNAs of 20 families were found targeting 11 PtrCOBL genes. PtrCOBLs were found localized at the plasma membrane and extracellular matrix, while gene ontology analysis showed their involvement in plant development, plant growth, stress response, cellulose biosynthesis, and cell wall biogenesis. RNA-seq datasets depicted the bulk of PtrCOBL genes expression being found in plant stem tissues and leaves, rendering mechanical strength and rejoinders to environmental cues. PtrCOBL2, 3, 10, and 11 manifested the highest expression in vasculature and abiotic stress, and resemblant expression trends were upheld by qRT-PCR. Co-expression network analysis identified PtrCOBL2 and PtrCOBL3 as hub genes across all abiotic stresses and wood developing tissues. The current study reports regulating roles of PtrCOBLs in xylem differentiating tissues, tension wood formation, and abiotic stress latency that lay the groundwork for future functional studies of the PtrCOBL genes in poplar breeding.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Wgd Collaborated To Cobl Gene Family Expansionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Recent genome resequencing paraded COBRA-Like gene family roles in abiotic stress and wood formation in Poplar

Sajjad,

Ahmad,

Riaz

et al. 2023

Front. Plant Sci.

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Self S-RNase reduces the expression of two pollen-specific COBRA genes to inhibit pollen tube growth in pear

Wu,

Xu,

et al. 2023

Mol Horticulture

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Due to self-incompatibility (SI) prevents self-fertilization, natural or artificial cross-pollination has been conducted in many orchards to stabilize fruit yield. However, it is still puzzled which routes of self S-RNase arresting pollen tube growth. Herein, 17 COBRA genes were isolated from pear genome. Of these genes, the pollen-specifically expressed PbCOB.A.1 and PbCOB.A.2 positively mediates pollen tube growth. The promoters of PbCOB.A.1 and/or PbCOB.A.2 were bound and activated by PbABF.E.2 (an ABRE-binding factor) and PbC2H2.K16.2 (a C2H2-type zinc finger protein). Notably, the expressions of PbCOB.A.1, PbCOB.A.2, and PbC2H2.K16.2 were repressed by self S-RNase, suggesting that self S-RNase reduces the expression of PbCOB.A.1 and PbCOB.A.2 by decreasing the expression of their upstream factors, such as PbC2H2.K16.2, to arrest pollen tube growth. PbCOB.A.1 or PbCOB.A.2 accelerates the growth of pollen tubes treated by self S-RNase, but can hardly affect level of reactive oxygen species and deploymerization of actin cytoskeleton in pollen tubes and cannot physically interact with any reported proteins involved in SI. These results indicate that PbCOB.A.1 and PbCOB.A.2 may not relieve S-RNase toxicity in incompatible pollen tube. The information provides a new route to elucidate the arresting pollen tube growth during SI reaction. Graphical Abstract

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Genome-Wide Identification and Hormone Response Analysis of the COBL Gene Family in Barley

Ren,

Ma,

Bao

et al. 2024

Genes

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Barley (Hordeum vulgare L.), a diverse cereal crop, exhibits remarkable versatility in its applications, ranging from food and fodder to industrial uses. The content of cellulose in barley is significantly influenced by the COBRA genes, which encode the plant glycosylphosphatidylinositol (GPI)-anchored protein (GAP) that plays a pivotal role in the deposition of cellulose within the cell wall. The COBL (COBRA-Like) gene family has been discovered across numerous species, yet the specific members of this family in barley remain undetermined. In this study, we discovered 13 COBL genes within the barley genome using bioinformatics methods, subcellular localization, and protein structure analysis, finding that most of the barley COBL proteins have a signal peptide structure and are localized on the plasma membrane. Simultaneously, we constructed a phylogenetic tree and undertook a comprehensive analysis of the evolutionary relationships. Other characteristics of HvCOBL family members, including intraspecific collinearity, gene structure, conserved motifs, and cis-acting elements, were thoroughly characterized in detail. The assessment of HvCOBL gene expression in barley under various hormone treatments was conducted through qRT-PCR analysis, revealing jasmonic acid (JA) as the predominant hormonal regulator of HvCOBL gene expression. In summary, this study comprehensively identified and analyzed the barley COBL gene family, aiming to provide basic information for exploring the members of the HvCOBL gene family and to propose directions for further research.

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Genome-wide identification and expression profiling of the COBRA-like genes reveal likely roles in stem strength in rapeseed (Brassica napus L.)

Cited by 4 publications

References 56 publications

Recent genome resequencing paraded COBRA-Like gene family roles in abiotic stress and wood formation in Poplar

Recent genome resequencing paraded COBRA-Like gene family roles in abiotic stress and wood formation in Poplar

Self S-RNase reduces the expression of two pollen-specific COBRA genes to inhibit pollen tube growth in pear

Genome-Wide Identification and Hormone Response Analysis of the COBL Gene Family in Barley

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