title: The Evolutionary History of R2R3-MYB Proteins Across 50 Eukaryotes: New Insights Into Subfamily Classification and Expansion.
abstract: R2R3-MYB proteins (2R-MYBs) are one of the main transcription factor families in higher plants. Since the evolutionary history of this gene family across the eukaryotic kingdom remains unknown, we performed a comparative analysis of 2R-MYBs from 50 major eukaryotic lineages, with particular emphasis on land plants. A total of 1548 candidates were identified among diverse taxonomic groups, which allowed for an updated classification of 73 highly conserved subfamilies, including many newly identified subfamilies. Our results revealed that the protein architectures, intron patterns, and sequence characteristics were remarkably conserved in each subfamily. At least four subfamilies were derived from early land plants, 10 evolved from spermatophytes, and 19 from angiosperms, demonstrating the diversity and preferential expansion of this gene family in land plants. Moreover, we determined that their remarkable expansion was mainly attributed to whole genome and segmental duplication, where duplicates were preferentially retained within certain subfamilies that shared three homologous intron patterns (a, b, and c) even though up to 12 types of patterns existed. Through our integrated distributions, sequence characteristics, and phylogenetic tree analyses, we confirm that 2R-MYBs are old and postulate that 3R-MYBs may be evolutionarily derived from 2R-MYBs via intragenic domain duplication.
authors.affiliation: College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
authors.forename: Hai
authors.initials: H
authors.lastname: Du
authors.affiliation: Department of Biological Sciences, National University of Singapore, 117543, Singapore.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Liang
authors.affiliation: 1] Department of Cancer Prevention, Institute for Cancer Research, Norwegian Radium Hospital-Oslo University Hospital, Oslo, Norway [2] Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
authors.forename: Sen
authors.initials: S
authors.lastname: Zhao
authors.affiliation: College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
authors.forename: Ming-Ge
authors.initials: MG
authors.lastname: Nan
authors.affiliation: Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045 Japan.
authors.forename: Lam-Son Phan
authors.initials: LS
authors.lastname: Tran
authors.affiliation: College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
authors.forename: Kun
authors.initials: K
authors.lastname: Lu
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute of Sichuan Agricultural University, Ministry of Agriculture, Chengdu Sichuan, China.
authors.forename: Yu-Bi
authors.initials: YB
authors.lastname: Huang
authors.affiliation: College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
authors.forename: Jia-Na
authors.initials: JN
authors.lastname: Li
mesh_terms: D000595:Amino Acid Sequence; D016208:Databases, Factual; D056890:Eukaryota / Q000235:genetics / Q000378:metabolism*; D019143:Evolution, Molecular; D007438:Introns; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000145:classification / Q000235:genetics / Q000378:metabolism*
chemical_list: D014157:Transcription Factors