Evolution And Expression Analysis Of Seven Subfamilies In R2R3-MYB Gene Family In Grapevine

Comparative genomics and gene expression analyses were combined in this study to explore the evolution and function of7subfamilies of the R2R3-MYB gene family. The7subfamilies are in the same evolution branch (Branch I) of R2R3-MYB gene family and they are enriched with genes related to abiotic stresses.Fourteen species were analyzed in this study, including Arabidopsis thaliana, Arabidopsis lyrata, Vitis vinifera, Populus trichocarpa, Glycine max, Fragaria vesca, Carica papaya, Sorghum bicolor, Zea mays, Setaria italica, Panicum virgatum, Oryza sativa, Brachypodium distachyon and Physcomitrella patens. The R2R3-MYB genes of the14species were screened and identified in the whole genome level, and we focused on the453Branch I genes. The branch I genes were divided into7subfamilies, named as S1to S7. R2R3-MYB gene family Branch I genes exist extensively in dicotyledon, monocotyledon and bryophyta. Bryophyta genes are only in S1and S2. S3only exist Arabidopsis thaliana, Arabidopsis lyrata and Carica papaya, or the eurasid II. n each of7subfamily in Branch I, the largest gene number usually goes to Glycine max, followed by Populus trichocarpa and Zea mays. Gene number in each subfamily in some degree represented the whole genome duplication events. Phylogenetic tree of Branch I showed that the topology within each subfamily is relatively robust; however, the topology between each subfamily is erratic and poorly supported. It indicated that the evolution history of plant R2R3-MYB is very complex. BLAST searchwas used to explore the sequence similarity between the7subfamilies. S6and S7, and S1to S5, have high sequence similarity in BLAST search. S1is in the central place, which has high sequence similarity with every other subfamily. Domain analysis supported the division of the subfamilies. Each subfamily has the specific and conserved motifs besides the R2R3domain. Based on the the nearby sequence of R2R3domain, the7subfamilies could be divided into2groups. One is consisted of S6and S7subfamilies, and the other is composed by S1to S5subfamilies. It agreed with the results of BLAST search. Notably, S6and S7subfamilies are enriched with genes related with abiotic stresses. In the combination of domain analysis and gene structure analysis, genes in Branch I could be divided into4categories. Typical category I genes have three exons; the category II and III genes have two exons; whereas the category IV genes have only one exon. Combined with domain position in gene sequence, conservatism is observed not only in the position of domain and motif in protein sequence, but also the position of domain and motif in gene sequence. Based on the observation, the difference of category I and II and the difference between category I and III gene structures are the presence or absence of insertion of the first intron or second intron in category I gene structure.Based on the published database of various microarray experiments, genes of grapevine and Arabidopsis in Branch I of R2R3-MYB gene family are analyzed for their expression patterns under different abiotic stresses. The analysis showed that besides genes in well-known abiotic-stress-related subfamilies S5, S6and S7, genes in S1-S4subfamilies also respond to abiotic stresses. However, the difference between S1-S4subfamilies and those in S5-S7subfamilies is that genes in S1-S4subfamilies usually respond to only one abiotic stress, such as drought, or salt stress, or cold stress, but genes in S5-S7subfamilies usually respond to more than two kinds of abiotic stresses in this detailed analysis. The expression of most of the differentially expressed genes was up-regulated, and few genes were down-regulated. The expression intensity, duration and up-or down-regulation of the genes are different under various abiotic stresses. For genes that have significantly different expression pattern under more than two abiotic stresses, they seem to play an important role in abiotic stresses regulation. These genes include Arabidopsis genes AtMYB74, AtMYB102, AtMYB15, AtMYB63, AtMYB60, AtMYB94, AtMYB96and grapevine genes GSVIVT01027811001, GSVIVT01011417001, GSVIVT01008005001. Besides, Arabidopsis genes AtMYB40, AtMYB43, AtMYB76, AtMYB29and AtMYB13are significantly regulated under only one abiotic stress. These genes may have specific role in responding to a certain kind of abiotic stress. Interestingly, AtMYB40and AtMYB43belong to the S2subfamily, which is known to function in lignin deposition; AtMYB76and AtMYB29belong to the S3subfamily, which is known for function in glucosinolate biosynthesis. Therefore, the two subfamilies may also function in abiotic stress regulation.In this study, we used molecular evolution approaches, including phylogenetic tree, domain analysis and gene structure analysis, to study the classification and evolution for the branch I of R2R3-MYB gene family. Combined with gene expression analysis, it helps us better understand the evolution history and function division of this gene family. In general, results in this research showed that the evolution history of R2R3-MYB gene family is complex based on the phylogenetic analysis. Genes in each subfamily have conserved gene structure and motifs. Genes in the well-known abiotic-stress-related subfamilies S5-S7are involved in regulating response to more than one abiotic stresses, however, some of the genes in other subfamilies seemed to also function in regulating responses to a certain kind of abiotic stress.