Abstract
Plant R2R3-MYBs comprise one of the largest transcription factor families; however, few R2R3-MYB genes in pecan have been functionally analyzed due to the limited genome information and potential functional redundancy caused by gene duplication. In this study, 153 R2R3-MYB genes were identified and subjected to comparative phylogenetic analysis with four other plant species. Then, the pecan R2R3-MYB gene family was divided into different clades, which were also supported by gene structure and motif composition results. Fifty-two duplication events including 77 R2R3-MYB genes were identified in this gene family, and Ka/Ks values showed that all of the duplication events were under the influence of negative selection. Expression levels of pecan R2R3-MYB genes during the graft union formation process were further investigated using RNA-seq with four different timepoints after grafting, namely, 0, 8, 15 and 30 d. Sixty-four differentially expressed R2R3-MYB genes were identified and showed different expression patterns after grafting. Co-expression networks were further constructed to discover the relationships between these genes. The co-expression networks contained 57 nodes (R2R3-MYB genes) and 219 edges (co-expression gene pairs) and CIL1528S0032 contained the maximum number of edges. Fifteen genes contained more than 10 edges; the majority of these were up-regulated during graft union formation and verified by qRT-PCR. This study provides a foundation for functional analysis to investigate the roles that R2R3-MYBs play in graft union formation in pecan and identify the key candidate genes.
Highlights
Transcription factors (TFs) regulate various developmental and physiological processes in plants via binding to promoters of target genes to activate or suppress gene expression
The putative MYB transcription factors in the pecan genome were identified by HMMER and confirmed by the existence of MYB domain
Sequence analyses of the members of this gene family revealed that the gene length of R2R3-MYBs in pecan varied from 624 to 38,366 base pairs, with proteins ranging in size from 161 to 1011 amino acids (Table S3)
Summary
Transcription factors (TFs) regulate various developmental and physiological processes in plants via binding to promoters of target genes to activate or suppress gene expression. The typical TFs commonly contain DNA-binding domains (DBDs), and can be classified into different families based on the sequence difference of DBDs [1]. Over 60 TF families with hundreds to thousands of members have been identified in higher plants, and only a few have been functionally analyzed [2]. The MYB transcription factor gene family is one of the largest TF families and is widely dispersed in plants. Members of the MYB gene family contain a N-terminal MYB DNA-binding domain, and the MYB domain frequently consists of one or more imperfect tandem repeats [3].
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
