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Research article - Peer-reviewed, 2022

Genome-wide TCP transcription factors analysis provides insight into their new functions in seasonal and diurnal growth rhythm in Pinus tabuliformis

Nie, Yu-Meng; Han, Fang-Xu; Ma, Jing-Jing; Chen, Xi; Song, Yi-Tong; Niu, Shi-Hui; Wu, Harry X.;

Abstract

Background Pinus tabuliformis adapts to cold climate with dry winter in northern China, serving as important commercial tree species. The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTOR family(TCP)transcription factors were found to play a role in the circadian clock system in Arabidopsis. However, the role of TCP transcription factors in P. tabuliformis remains little understood. Results In the present study, 43 TCP genes were identified from P. tabuliformis genome database. Based on the phylogeny tree and sequence similarity, the 43 TCP genes were classified into four groups. The motif results showed that different subfamilies indeed contained different motifs. Clade II genes contain motif 1, clade I genes contain motif 1, 8, 10 and clade III and IV contain more motifs, which is consistent with our grouping results. The structural analysis of PtTCP genes showed that most PtTCPs lacked introns. The distribution of clade I and clade II on the chromosome is relatively scattered, while clade III and clade IV is relatively concentrated. Co-expression network indicated that PtTCP2, PtTCP12, PtTCP36, PtTCP37, PtTCP38, PtTCP41 and PtTCP43 were co-expressed with clock genes in annual cycle and their annual cycle expression profiles both showed obvious seasonal oscillations. PtTCP2, PtTCP12, PtTCP37, PtTCP38, PtTCP40, PtTCP41, PtTCP42 and PtTCP43 were co-expressed with clock genes in diurnal cycle. Only the expression of PtTCP42 showed diurnal oscillation. Conclusions The TCP gene family, especially clade II, may play an important role in the regulation of the season and circadian rhythm of P. tabuliformis. In addition, the low temperature in winter may affect the diurnal oscillations.

Keywords

TCP; Gene family; Pinus tabuliformis; Seasonal; Diurnal; Oscillation

Published in

BMC Plant Biology

2022, volume: 22, number: 1, article number: 167
Publisher: BMC

Authors' information

Nie, Yu-Meng
Beijing Forestry University
Han, Fang-Xu
Beijing Forestry University
Ma, Jing-Jing
Beijing Forestry University
Chen, Xi
Beijing Forestry University
Song, Yi-Tong
Beijing Forestry University
Niu, Shi-Hui
Beijing Forestry University
Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology

UKÄ Subject classification

Genetics
Botany

Publication Identifiers

DOI: https://doi.org/10.1186/s12870-022-03554-4

URI (permanent link to this page)

https://res.slu.se/id/publ/116763