Abstract
Myeloblastosis (MYB) transcription factors (TFs) form a large gene family involved in a variety of biological processes in plants. Little is known about their roles in the development of cotton pigment glands. In this study, 646 MYB members were identified in Gossypium hirsutum genome and phylogenetic classification was analyzed. Evolution analysis revealed assymetric evolution of GhMYBs during polyploidization and sequence divergence of MYBs in G. hirustum was preferentially happend in D sub-genome. WGCNA (weighted gene co-expression network analysis) showed that four modules had potential relationship with gland development or gossypol biosynthesis in cotton. Eight differentially expressed GhMYB genes were identified by screening transcriptome data of three pairs of glanded and glandless cotton lines. Of these, four were selected as candidate genes for cotton pigment gland formation or gossypol biosynthesis by qRT-PCR assay. Silencing of GH_A11G1361 (GhMYB4) downregulated expression of multiple genes in gossypol biosynthesis pathway, indicating it could be involved in gossypol biosynthesis. The potential protein interaction network suggests that several MYBs may have indirect interaction with GhMYC2-like, a key regulator of pigment gland formation. Our study was the systematic analysis of MYB genes in cotton pigment gland development, providing candidate genes for further study on the roles of cotton MYB genes in pigment gland formation, gossypol biosynthesis and future crop plant improvement.
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Data availability
The transcriptome data in current study are available in the NCBI repository (SRR1652399, SRR1652403, SRR1652393, SRR1652392, SRR1652340, SRR1652395, SRR1652396, SRR1652406, SRR1652486, SRR1649571).
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Acknowledgements
We are grateful to the State Key Laboratory of Cotton Biology, Institute of Cotton research, Chinese Academy of Agricultural Sciences for providing the seeds of G. hirsutum. This research is supported by the National Key R and D Plan of China (No. 2018YFD0100402), National Natural Science Foundation of China (No. 31621005 and No. 31901581), Central Public-interest Scientific Institution Basic Research Fund (No.1610162021013), Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences, and the United States Department of Agriculture-Agricultural Research Service (USDA-ARS Project No. 3091-210000-44-00D).
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YLD, HLC, JZY, and GLS conceived and designed the research, interpreted the results, and wrote the manuscript; YLD prepared the materials and conducted the experiments; SL contributed to the data analysis and preparations of figures; DYZ, QLW, LML and YPZ provided technical assistance and research input. All authors read and approved the final manuscript.
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Communicated by Bing Yang.
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Supplementary file2 (XLSX 28 KB) Table S2 MYB members in five tetraploids (AD1–AD5) and their two putative donors (A1 and A2 for A sub-genome)
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Supplementary file3 (XLSX 27 KB) Table S3 MYB members in five tetraploids (AD1–AD5) and their putative donor (D5 for D sub-genome)
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Supplementary file4 (XLSX 71 KB) Table S4 Features of the G. hirsutum MYB genes and their corresponding proteins. The basic properties including transcript length, amino acid lengths, molecular weight, isoelectric point, charge, grand average of hydropathy, exon numbers and mean exon length of the 646 GhMYBs
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Supplementary file5 (XLSX 32 KB) Table S5 Cis-elements in the promoter region of the 74 MYBs which transcription abundance was higher in samples with gland
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Supplementary file6 (JPG 391 KB) Fig. S1 Species trees based on sequences of MYBs in A and D sub-genomes, respectively. (a) Species trees based on sequences of MYBs in A sub-genome. (b) Species trees based on sequences of MYBs in D sub-genome
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Supplementary file7 (PNG 214 KB) Fig. S2 Heatmap of nine genes which were validated to be involved in development of cotton gland
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Dai, Y., Liu, S., Zuo, D. et al. Identification of MYB gene family and functional analysis of GhMYB4 in cotton (Gossypium spp.). Mol Genet Genomics 298, 755–766 (2023). https://doi.org/10.1007/s00438-023-02005-5
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DOI: https://doi.org/10.1007/s00438-023-02005-5