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. 2022 Apr 2;22(1):167.
doi: 10.1186/s12870-022-03554-4.

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

Yu-Meng Nie  1 , Fang-Xu Han  1 , Jing-Jing Ma  1 , Xi Chen  1 , Yi-Tong Song  1 , Shi-Hui Niu  2 , Harry X Wu  3
Affiliations

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

Yu-Meng Nie et al. BMC Plant Biol. .

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

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Conflict of interest statement

The authors declare no financial or commercial conflict of interest.

Figures

Fig. 1
Fig. 1
Phylogenetic analysis of TCP genes between P. tabuliformis, Chlamydomonas reinhardtii, Marchantia polymorpha, Selaginella moellendorffii, Physcomitrella patens, Oryza sativa, Populus trichocarpa and Arabidopsis. Different subfamilies were indicated in a specific colour. Genes of P. tabuliformis were marked with small red squares
Fig. 2
Fig. 2
Multiple alignments of TCP family members in P. tabuliformis. Overall conserved amino acids were shaded in blue. The Basic, Helix I, Loop and Helix II regions were indicated
Fig. 3
Fig. 3
Phylogenetic relationships, domain, gene structure, and architecture of conserved protein motifs in PtTCP family. A. Estimated phylogeny of PtTCP genes. B. Different motifs were represented by different colors. The black lines represented the non-conserved sequences. Lengths of motifs for each PtTCP protein were displayed proportionally. C. TCP domains were represented by green, TCP superfamily were represented by yellow. D. UTR were represented by green, CDS were represented by yellow. Nucleic acid lengths are indicated by the scale at the bottom
Fig. 4
Fig. 4
Schematic representations for the chromosomal distribution of TCP genes in P. tabuliformis. A total of 43 TCP family genes were anchored onto 12 chromosomes of P. tabuliformis. The scale on the left represented the physical length of the chromosomes; Mb = million base pair. The clade I genes were shown in red, clade II in blue, clade III in yellow, and clade IV in green
Fig. 5
Fig. 5
Estimated gene network including PtTCPs and core clock genes in annual cycle (A) and diurnal cycle (B). The clock genes of P. tabuliformis were in the blue box, the TCP family genes were in the red box. The red lines indicate a positive relationship between two genes, and the blue lines indicate a negative relationship between two genes
Fig. 6
Fig. 6
The expression of PtTCP2, PtTCP12, PtTCP36, PtTCP37, PtTCP38, PtTCP41 and PtTCP43. Monitoring lasts for two years, from July 1, 2017 to July 1, 2019. Error bars represented variability of three independent replicates
Fig. 7
Fig. 7
The expression of PtTCP42 at 8:00, 12:00, 16:00, 20:00, 24:00 and 4:00 in March 25, June 25, July 25, August 25, September 25 and December 25. Error bars represented variability of three independent replicates
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