AUTHOR=Li Jing , Guo Shukuan , Min Htwe Yin , Sun Xiwei , Zhou Lixia , Wang Fangyuan , Zeng Chunru , Chen Shuangyan , Iqbal Amjad , Yang Yaodong 

TITLE=Genome-wide identification, classification and expression analysis of MYB gene family in coconut (Cocos nucifera L.)

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1263595

DOI=10.3389/fpls.2023.1263595

ISSN=1664-462X

ABSTRACT=<p>MYB transcription factors regulate the growth, development, and secondary metabolism of plant species. To investigate the origin of color variations in coconut pericarp, we identified and analyzed the <italic>MYB</italic> gene family present in coconut. According to the sequence of <italic>MYB</italic> genes in Arabidopsis thaliana, homologous <italic>MYB</italic> gene sequences were found in the whole genome database of coconut, the conserved sequence motifs within <italic>MYB</italic> proteins were analyzed by Motif Elicitation (MEME) tool, and the sequences without conservative structure were eliminated. Additionally, we employed RNA-seq technology to generate gene expression signatures of the R2R3-<italic>MYB</italic> genes across distinctive coconut parts exhibiting diverse colors. To validate these profiles, we conducted quantitative PCR (qPCR). Through comprehensive genome-wide screening, we successfully identified a collection of 179 <italic>MYB</italic> genes in coconut. Subsequent phylogenetic analysis categorized these 179 coconut <italic>MYB</italic> genes into 4-subfamilies: 124 R2R3-<italic>MYB</italic>, 4 3R-<italic>MYB</italic> types, 4 4R-<italic>MYB</italic> type, and 47 unknown types. Furthermore, these genes were further divided into 34 subgroups, with 28 of these subgroups successfully classified into known subfamilies found in Arabidopsis thaliana. By mapping the <italic>CnMYB</italic> genes onto the 16 chromosomes of the coconut genome, we unveiled a collinearity association between them. Moreover, a preservation of gene structure and motif distribution was observed across the <italic>CnMYB</italic> genes. Our research encompassed a thorough investigation of the R2R3-<italic>MYB</italic> genes present in the coconut genome, including the chromosomal localization, gene assembly, conserved regions, phylogenetic associations, and promoter cis-acting elements of the studied genes. Our findings revealed a collection of 12 R2R3-MYB candidate genes, namely <italic>CnMYB8</italic>, <italic>CnMYB15</italic>, <italic>CnMYB27</italic>, <italic>CnMYB28</italic>, <italic>CnMYB61</italic>, <italic>CnMYB63</italic>, <italic>CnMYB68</italic>, <italic>CnMYB94</italic>, <italic>CnMYB101</italic>, <italic>CnMYB150</italic>, <italic>CnMYB153</italic>, and <italic>CnMYB164</italic>. These genes showed differential expressions in diverse tissues and developmental stages of four coconut species, such as <italic>CnMYB68</italic>, <italic>CnMYB101</italic>, and <italic>CnMYB28</italic> exhibited high expression in majority of tissues and coconut species, while <italic>CnMYB94</italic> and <italic>CnMYB164</italic> showed lower expression. These findings shed light on the crucial functional divergence of <italic>CnMYB</italic> genes across various coconut tissues, suggesting these genes as promising candidate genes for facilitating color development in this important crop.</p>