Genome-wide identification and expression analyses of TCP transcription factor genes in Gossypium barbadense

Zheng, Kai; Ni, Zhongfu; Qu, Yanying; Cai, Yongsheng; Yang, Zhaoen; Sun, Guixin; Chen, Quanjia

doi:10.1038/s41598-018-32626-5

Cited by 44 publications

(37 citation statements)

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“…Most of the previous investigation in individual plant species [31,33,111,112] generally divided TCP family genes into Classes I and II, with Class II being further divided into CIN and CYC clades, but some studies [26,113,114] divided this gene family into nine to 11 subgroups. In our analyses, consistent with most of the previous studies, the topology of the phylogenetic tree of the 535 plant TCP proteins was preliminary divided into two major classes, namely Class I and II (Figure 2).…”

Section: Discussionmentioning

confidence: 99%

Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants

Liu

Wang

Yang

et al. 2019

IJMS

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The plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) transcription factor genes are involved in plants’ development, hormonal pathways, and stress response but their evolutionary history is uncertain. The genome-wide analysis performed here for 47 plant species revealed 535 TCP candidates in terrestrial plants and none in aquatic plants, and that TCP family genes originated early in the history of land plants. Phylogenetic analysis divided the candidate genes into Classes I and II, and Class II was further divided into CYCLOIDEA (CYC) and CINCINNATA (CIN) clades; CYC is more recent and originated from CIN in angiosperms. Protein architecture, intron pattern, and sequence characteristics were conserved in each class or clade supporting this classification. The two classes significantly expanded through whole-genome duplication during evolution. Expression analysis revealed the conserved expression of TCP genes from lower to higher plants. The expression patterns of Class I and CIN genes in different stages of the same tissue revealed their function in plant development and their opposite effects in the same biological process. Interaction network analysis showed that TCP proteins tend to form protein complexes, and their interaction networks were conserved during evolution. These results contribute to further functional studies on TCP family genes.

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Section: Discussionmentioning

confidence: 99%

Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants

Liu

Wang

Yang

et al. 2019

IJMS

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“…Xinhai21 is a hybrid of the Giza variety from Egypt and has been the major cultivar in Xinjiang over the years, and Ashmon is a resource material that was introduced from Syria. Our research team investigated the quality of these two sea-island cotton fibres over the three years under field conditions and found that Xinhai21 had a greater fibre length than Ashmon (Table 1) [32]. To understand the role of GbCYPs during different developmental stages of cotton fibre, we chose Ashmon as the control material and analysed the expression profiles of six GbCYPs ( GbCYP18-5 , GbCYP18-6 , GbCYP27-2 , GbCYP36 , GbCYP47-1 and GbCYP58 ) between Xinhai21 and Ashmon.…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Identification of Cyclophilin Gene Family in Cotton and Expression Analysis of the Fibre Development in Gossypium barbadense

Chen

Sun

et al. 2019

IJMS

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Cyclophilins (CYPs) are a member of the immunophilin superfamily (in addition to FKBPs and parvulins) and play a significant role in peptidyl-prolyl cis-trans isomerase (PPIase) activity. Previous studies have shown that CYPs have important functions in plants, but no genome-wide analysis of the cotton CYP gene family has been reported, and the specific biological function of this gene is still elusive. Based on the release of the cotton genome sequence, we identified 75, 78, 40 and 38 CYP gene sequences from G. barbadense, G. hirsutum, G. arboreum, and G. raimondii, respectively; 221 CYP genes were unequally located on chromosomes. Phylogenetic analysis showed that 231 CYP genes clustered into three major groups and eight subgroups. Collinearity analysis showed that segmental duplications played a significant role in the expansion of CYP members in cotton. There were light-responsiveness, abiotic-stress and hormone-response elements upstream of most of the CYPs. In addition, the motif composition analysis revealed that 49 cyclophilin proteins had extra domains, including TPR (tetratricopeptide repeat), coiled coil, U-box, RRM (RNA recognition motif), WD40 (RNA recognition motif) and zinc finger domains, along with the cyclophilin-like domain (CLD). The expression patterns based on qRT-PCR showed that six CYP expression levels showed greater differences between Xinhai21 (long fibres, G. barbadense) and Ashmon (short fibres, G. barbadense) at 10 and 20 days postanthesis (DPA). These results signified that CYP genes are involved in the elongation stage of cotton fibre development. This study provides a valuable resource for further investigations of CYP gene functions and molecular mechanisms in cotton.

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“…Plant-specific TCP TFs play various roles in plant growth and development. In many plants, the general organization of the TCP family is conserved, and there are more members in class I compared to class II (Du et al, 2017;Li et al, 2017;Liu et al, 2018b;Ma et al, 2014;Ma et al, 2016;Shi et al, 2016;Wang et al, 2018;Wang et al, 2019c;Zhao et al, 2018;Zheng et al, 2018). In B. juncea var.…”

Section: Discussionmentioning

confidence: 99%

“…The teosinte branched1/Cycloidea/proliferating cell factor (TCP) family is a group of plantspecific transcription factors (TFs) reportedly involved in embryonic growth (Takeda et al, 2003), leaf development (Bresso et al, 2018;Danisman et al, 2012;Du et al, 2017;Kieffer et al, 2011;Liu et al, 2018b;Ma et al, 2016;Uberti-Manassero et al, 2012; Citrullus lanatus s (Shi et al, 2016), 66 in Triticum aestivum (Zhao et al, 2018), 75 in Gossypium barbadense (Zheng et al, 2018), 31 in Solanum tuberosum (Wang et al, 2019c), 39 in Brassica rapa L. ssp. Pekinensis (Liu et al, 2018b), and 39 in B. rapa ssp.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and characterization of TCP family genes in Brassica juncea var. tumida

Chang

et al. 2020

PeerJ

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Background Teosinte branched1/Cycloidea/proliferating cell factors (TCPs) are plant-specific transcription factors widely involved in leaf development, flowering, shoot branching, the circadian rhythm, hormone signaling, and stress responses. However, the TCP function in Brassica juncea var. tumida, the tumorous stem mustard, has not yet been reported. This study identified and characterized the entire TCP family members in B. juncea var. tumida. Methods We identified 62 BjTCP genes from the B. juncea var. tumida genome and analyzed their phylogenetic relationship, gene structure, protein motifs, chromosome location, and expression profile in different tissues. Results Of the 62 BjTCP genes we identified in B. juncea var. tumida, containing 34 class I and 28 class II subfamily members, 61 were distributed on 18 chromosomes. Gene structure and conserved motif analysis showed that the same clade genes displayed a similar exon/intron gene structure and conserved motifs. Cis-acting element results showed that the same clade genes also had a similar cis-acting element; however, subtle differences implied a different regulatory pathway. The BjTCP18s members were low-expressed in Dayejie strains and the unswelling stage of Yonganxiaoye strains. Treatment with gibberellin (GA) and salicylic acid (SA) showed that GA and SA affect the expression levels of multiple TCP genes. Conclusion We performed the first genome-wide analysis of the TCP gene family of B. juncea var. tumida. Our results have provided valuable information for understanding the classification and functions of TCP genes in B. juncea var. tumida.

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Genome-wide identification and expression analyses of TCP transcription factor genes in Gossypium barbadense

Cited by 44 publications

References 50 publications

Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants

Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants

Genome-Wide Identification of Cyclophilin Gene Family in Cotton and Expression Analysis of the Fibre Development in Gossypium barbadense

Genome-wide identification and characterization of TCP family genes in Brassica juncea var. tumida

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