Genome-wide Identification and Comparative Evolutionary Analysis of the R2R3-MYB Transcription Factor Gene Family in Pepper

doi:10.11983/CBB20143

Abstract

Abstract: As one of the largest transcription factor (TF) families in plants, MYB TFs are involved in various physiological and biochemical processes, such as plant growth, metabolism, and response to various biotic and abiotic stresses. R2R3-MYB is the main form of MYB TFs in higher plants. Pepper is a vegetable crop with important economic value, but the R2R3-MYB TF family has not been systematically studied in pepper. In this study, 94 CaMYB, 92 CbMYB, and 94 CcMYB TFs genes were identified with comparative genomic analysis in Capsicum annuum, C. baccatum, and C. chinense, respectively. These genes were categorized into 28 subfamilies. Collinearity analysis indicated that there were 73 groups of orthologous R2R3-MYB genes among three pepper species. There were five, four, and two unique R2R3-MYB genes in C. annuum, C. baccatum, and C. chinense, respectively. In addition, we identified 12 pairs of duplicated genes, and eight of which are tandemly repeated genes, which already existed before the divergence of three pepper species. Comparative genomics analysis suggested that the homologous R2R3-MYB TFs underwent functionally divergence during the evolution of pepper. Analysis on the expression profile showed that R2R3-MYB genes were expressed in three major patterns: high expression in roots, leaves, stems, and flowers, such as CaMYB13/CbMYB12/- CcMYB13; high expression in flowers, such as CaMYB93/CbMYB86/CcMYB12; high expression in roots, such as CaMYB48/CbMYB47/CcMYB51. These results lay a foundation for further study on the biological functions of R2R3-MYB TFs in the growth and development of pepper.

Key words: Capsicum annuum, C. baccatum, C. chinense, R2R3-MYB transcription factor, orthologous gene

Kaicheng Kang, Xiqiang Niu, Xianzhong Huang, Nengbing Hu, Yihu Sui, Kaijing Zhang, Hao Ai. Genome-wide Identification and Comparative Evolutionary Analysis of the R2R3-MYB Transcription Factor Gene Family in Pepper[J]. Chinese Bulletin of Botany, 2021, 56(3): 315-329.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB20143

https://www.chinbullbotany.com/EN/Y2021/V56/I3/315

Figures/Tables 9

Table 1 Primer sequences used in this study

Gene name	Primer sequences (5′→3′)	Use
CaMYB62	ATCGCAGCGTATGAACACAC	qRT-PCR
CaMYB62	TTGTTACCGTGTTTGGCCTG	qRT-PCR
CaMYB35	GGCGGTGAATGTGATGATCC	qRT-PCR
CaMYB35	GGAAACCCCGTAGAAGCAAC	qRT-PCR
CaMYB92	TGATCCAACAACACACAGGC	qRT-PCR
CaMYB92	TTGTTCTCGAAATGGGCTGC	qRT-PCR
CaMYB39	TGGGGCAATCGTTGGTCTAA	qRT-PCR
CaMYB39	TGGATGTAAGTGGTGGTGGG	qRT-PCR
CaMYB25	AACCACCTACCTCGGCATTT	qRT-PCR
CaMYB25	TCACTTTTGTTTGAGCCTGCA	qRT-PCR
CaMYB2	CATCATCACCAGCAGTCACA	qRT-PCR
CaMYB2	GATCGACTTGCCAGCAGAAC	qRT-PCR
CaMYB8	CAGATCCTAGGGCTCTCGTG	qRT-PCR
CaMYB8	GGCCCGACTAATCCTGAGAT	qRT-PCR
CaMYB80	TCTTGGCAATAGGTGGTCGA	qRT-PCR
CaMYB80	TGCTGCTCTCGTGGATAATCT	qRT-PCR
CaMYB19	GGACACAACATGGACAGCAG	qRT-PCR
CaMYB19	CTGAATCAGATGGGGAAGGA	qRT-PCR
CaUBI-3	TGTCCATCTGCTCTCTGTTG	Internal reference gene
CaUBI-3	CACCCCAAGCACAATAAGAC	Internal reference gene

Figure 1 Sequence logos of the R2 (A) and R3 (B) MYB domains from three Capsicum species The score of an amino acid (Bits) indicates the frequency of its occurrence at this site.

Figure 2 Phylogenetic tree of the R2R3-MYB transcription factor family from three Capsicum species and Arabidopsis thaliana S1-S30 represent 30 subgroups.

Figure 3 Phylogenetic tree, gene exon-intron structure and motif analysis of R2R3-MYB transcription factor family in three Capsicum species (A) Phylogenetic tree of the 27 subfamilies; (B) Exon-intron structure of the 27 subfamilies (Black boxes indicate exons and black lines indicate introns); (C) The motif distribution of the 27 subfamilies (The boxes with different colors indicate different motifs)

Figure 4 The number of R2R3-MYB transcription factor orthologous genes in Capsicum annuum, C. baccatum, and C. chinense

Figure 5 Homologous R2R3-MYB transcription factor gene pairs in Capsicum annuum (Ca), C. baccatum (Cb), and C. chinense (Cc) Tracks from outside to inside are the number of chromosomes, number of R2R3-MYB genes (0-5) (20 Mb windows), and homologous gene pairs among three Capsicum species. The gray lines connect the homologous gene pairs that exist in three Capsicum species; the red lines connect the homologous gene pairs in two species; the green lines connect the replicated genes; and the blue lines connect the tandem repeated genes.

Figure 6 The Ka/Ks ratios for the orthologous and duplicated gene pairs of R2R3-MYB transcription factor in Capsicum annuum, C. baccatum, and C. chinense The black dots represent gene pairs with non-synonymous substitution rate (Ka)/synonymous substitution rate (Ks)>1.

Figure 7 Expression profile of R2R3-MYB genes in different tissues from Capsicum annuum (Ca), C. baccatum (Cb), and C. chinense (Cc) The color bars indicate the variation range of log10(FPKM+1) values of R2R3-MYB genes in different tissues. The expression of the genes in red was verified by qRT-PCR.

Figure 8 Tissue expression profile of nine R2R3-MYB genes by qRT-PCR

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