Genome-wide identification and characterization of TCP transcription factor genes in upland cotton (Gossypium hirsutum)

Li, Wen; Li, Deng-Di; Han, Lihong; Tao, Miao; Hu, Qianqian; Wang, Wenying; Zhang, Jingbo; Li, Xuebao; Huang, Geng-Qing

doi:10.1038/s41598-017-10609-2

Cited by 51 publications

(38 citation statements)

References 57 publications

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“…arboreum 21 , and three fewer than G . hirsutum 22 . This discrepancy may contribute to the more desirable fiber of the sea-island cotton compared to that from other cotton genera.…”

Section: Discussionmentioning

confidence: 99%

“…6A ), show expression characteristics consistent with expression levels reported in G . hirsutum 22 . However, in the present study, these genes sustained expression in fiber on days 5–20, peaking on day 15.…”

Section: Discussionmentioning

confidence: 99%

“…arboreum 21 , and G . hirsutum 22 . TCP family members are involved in plant growth and development, seed germination, jasmonic acid synthesis, and the regulation of leaf senescence 23 , 24 .…”

Section: Introductionmentioning

confidence: 99%

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

Zheng

et al. 2018

Sci Rep

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Sea-island cotton (Gossypium barbadense) has drawn great attention in the textile industry for its comprehensive resistance and superior fiber properties. However, the mechanisms involved in fiber growth and development are unclear. As TCP transcription factors play important roles in plant growth and development, this study investigated the TCP family genes in G. barbadense (GbTCP). We identified 75 GbTCP genes, of which 68 had no introns. Phylogenetic analyses categorized the GbTCP transcription factors into 11 groups. Genomic analyses showed that 66 genes are located on 21 chromosomes. Phylogenetic analyses of G. arboreum, G. raimondii, G. hirsutum, G. barbadense, Theobroma cacao, Arabidopsis thaliana, Oryza sativa, Sorghum bicolor, and Zea mays, Picea abies, Sphagnum fallax and Physcomitrella patens, categorized 373 TCP genes into two classes (Classes I and II). By studying the structures of TCP genes in sea-island cotton, we identified genes from the same evolutionary branches that showed similar motif patterns. qRT-PCR results suggested that the GbTCPs had different expression patterns in fibers at various developmental stages of cotton, with several showing specific expression patterns during development. This report helps lay the foundation for future investigations of TCP functions and molecular mechanisms in sea-island cotton fiber development.

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“…arboreum 21 , and three fewer than G . hirsutum 22 . This discrepancy may contribute to the more desirable fiber of the sea-island cotton compared to that from other cotton genera.…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

Zheng

et al. 2018

Sci Rep

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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%

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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“…TCP domain was named after the initial characters from the four identified proteins encoded by apparently unrelated genes: teosinte branched 1 ( tb1 ), cycloidea ( cyc ), and proliferating cell factors 1 & 2 ( pcf1 and pcf2 ) ,. So far, probably more than a thousand TCP sequences are available from various plant species and a large quantity of functional studies has come to light . TCP proteins play important roles in various physiological processes including cell proliferation and differentiation, branching, leaf development, floral morphology, circadian clock regulation, seed germination, mitochondrial biogenesis and hormone signaling .…”

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confidence: 99%

The crystal structure of the TCP domain of PCF6 in Oryza sativa L. reveals an RHH‐like fold

et al. 2020

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The Teosinte branched 1/Cycloidea/Proliferating cell factor (TCP) domain is an evolutionarily conserved DNA binding domain unique to the plant kingdom. To date, the functions of TCPs have been well studied, but the threedimensional structure of the TCP domain is lacking. Here, we have determined the crystal structure of the TCP domain from OsPCF6. The structure reveals that the TCP domain adopts three short b-strands followed by a helix-loop-helix structure, distinct from the canonical basic helix-loop-helix structure. This folded domain shows high structural similarity to the ribbonhelix-helix (RHH) transcriptional repressors, a family of DNA binding proteins with a conserved 3D structural motif (RHH fold), indicating that TCPs could be reclassified as RHH proteins. Our work will provide insight toward a better understanding of the mechanisms underlying TCP protein function.

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Genome-wide identification and characterization of TCP transcription factor genes in upland cotton (Gossypium hirsutum)

Cited by 51 publications

References 57 publications

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

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

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

The crystal structure of the TCP domain of PCF6 in Oryza sativa L. reveals an RHH‐like fold

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