Dataset Information

Identification, Characterization, and Expression Patterns of TCP Genes and microRNA319 in Cotton.

ABSTRACT: The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (TCP) gene family is a group of plant-specific transcription factors that have versatile functions in developmental processes and stress responses. In this study, a total of 73 TCP genes in upland cotton were identified and characterizated. Phylogenetic analysis classified them into three subgroups: 50 belonged to PCF, 16 to CIN, and 7 to CYC/TB1. GhTCP genes are randomly distributed in 22 of the 26 chromosomes in cotton. Expression patterns of GhTCPs were analyzed in 10 tissues, including different developmental stages of ovule and fiber, as well as under heat, salt, and drought stresses. Transcriptome analysis showed that 44 GhTCP genes exhibited varied transcript accumulation patterns in the tested tissues and 41 GhTCP genes were differentially expressed in response to heat, salt, and drought stresses. Furthermore, three GhTCP genes of the CIN clade were found to contain miR319-binding sites. An anti-correlation expression of GhTCP21 and GhTCP54 was analyzed with miR319 under salt and drought stress. Our results lay the foundation for understanding the complex mechanisms of GhTCP-mediated developmental processes and abiotic stress-signaling transduction pathways in cotton.

SUBMITTER: Yin Z

PROVIDER: S-EPMC6274894 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Identification, Characterization, and Expression Patterns of TCP Genes and microRNA319 in Cotton.

Yin Zujun Z Li Yan Y Zhu Weidong W Fu Xiaoqiong X Han Xiulan X Wang Junjuan J Lin Huan H Ye Wuwei W

International journal of molecular sciences 20181120 11

The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (TCP) gene family is a group of plant-specific transcription factors that have versatile functions in developmental processes and stress responses. In this study, a total of 73 <i>TCP</i> genes in upland cotton were identified and characterizated. Phylogenetic analysis classified them into three subgroups: 50 belonged to PCF, 16 to CIN, and 7 to CYC/TB1. <i>GhTCP</i> genes are randomly distributed in 22 of the 26 chromosomes in c ...[more]

PMID: 30463287

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Project description:BACKGROUND:The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stresses, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and a necessity when studying the mechanisms of stress- tolerance in cotton. RESULTS:In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely localized in cells, but primarily in the nucleus. The PUBs in cotton were classified into six subfamilies (A-F) on the basis of phylogenetic analysis, which was testified by the analysis of conserved motifs and exon-intron structures. Chromosomal localization analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment analysis, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs in A2 and D5 were found; however no tandem duplications in A2 or D5 were found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, At sub-genome and Dt sub-genome of G. hirsutum, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum. CONCLUSIONS:This study reported the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in the response to abiotic stresses (including salt, drought, hot and cold) to varying degrees.

Dataset Information

Identification, Characterization, and Expression Patterns of TCP Genes and microRNA319 in Cotton.

Publications

Identification, Characterization, and Expression Patterns of TCP Genes and microRNA319 in Cotton.

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