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[italic]R2R3-MYB[/italic] Gene Evolution in Plants, Incorporating Ferns into the Story
International Journal of Plant Sciences ( IF 2.3 ) Pub Date : 2021-01-01 , DOI: 10.1086/710579
Brenda Hernández-Hernández , Rosalinda Tapia-López , Barbara A. Ambrose , Alejandra Vasco

Premise of research. MYB transcription factors are one of the largest families of genes in land plants. They are involved in many regulatory processes, such as primary and secondary metabolism, cell fate and identity, developmental processes, and responses to biotic and abiotic stresses. Phylogenetic studies have mainly focused on R2R3-MYB evolution in seed plants; however, a comprehensive sampling across land plants is lacking, as none have included ferns. Methodology. To better understand the evolution of R2R3-MYB genes in land plants, we surveyed the R2R3-MYB gene sequences from six genomes belonging to the main lineages of land plants (bryophytes, lycophytes, ferns, angiosperms, and gymnosperms). In addition, we searched transcriptome sequences of selected fern and lycophyte transcriptomes. We assembled a nucleotide matrix of the MYB domain and conducted maximum likelihood analyses to infer phylogenetic relationships and gene-tree reconciliation analyses to infer gene duplications. We labeled the main clades with the known MYB functions onto the resulting tree. To detect reported as well as new conserved motifs, we ran protein motif analyses through MEME. Pivotal results. Our results support previous studies indicating that R2R3-MYBs in seed plants are more diverse than in any other lineage of vascular plants. Most of the well-supported clades recovered are inferred to be already present in the ancestor of land plants. We found that ferns have numerous copies of R2R3-MYBs, although not as many as seed plants. Protein motif analyses revealed that R2R3-MYB motifs are highly conserved across land plants, suggesting that most R2R3-MYB orthologues, including those of ferns, might have DNA-binding capabilities and could be involved in regulatory processes that are similar to those of their angiosperm homologues. Our analyses showed that there are no fern orthologues of the angiosperm MYB leaf developmental genes ARP, raising interesting questions about the evolution and origin of leaves in ferns and seed plants. Conclusions. Our results provide the phylogenetic context for research on the genetic and functional evolution of an important gene family of developmental and metabolic regulators across the plant tree of life.

中文翻译:

[italic]R2R3-MYB[/italic] 植物基因进化,将蕨类植物融入故事

研究的前提。MYB 转录因子是陆地植物中最大的基因家族之一。它们参与许多调节过程,例如初级和次级代谢、细胞命运和身份、发育过程以及对生物和非生物胁迫的反应。系统发育研究主要集中在种子植物的 R2R3-MYB 进化上;然而,缺乏对陆地植物的全面抽样,因为没有一个包括蕨类植物。方法。为了更好地了解陆生植物中 R2R3-MYB 基因的进化,我们调查了属于陆生植物主要谱系(苔藓植物、石松植物、蕨类植物、被子植物和裸子植物)的六个基因组的 R2R3-MYB 基因序列。此外,我们搜索了选定的蕨类植物和石松植物转录组的转录组序列。我们组装了 MYB 结构域的核苷酸矩阵,并进行了最大似然分析以推断系统发育关系和基因树协调分析以推断基因重复。我们用已知的 MYB 函数将主要进化枝标记到结果树上。为了检测报告的以及新的保守基序,我们通过 MEME 进行了蛋白质基序分析。关键结果。我们的结果支持先前的研究,表明种子植物中的 R2R3-MYB 比维管植物的任何其他谱系更加多样化。据推测,大多数得到良好支持的进化枝已经存在于陆生植物的祖先中。我们发现蕨类植物有许多 R2R3-MYB 的副本,尽管不如种子植物多。蛋白质基序分析表明,R2R3-MYB 基序在陆地植物中高度保守,这表明大多数 R2R3-MYB 直向同源物,包括蕨类植物的直向同源物,可能具有 DNA 结合能力,并且可能参与与其被子植物同源物相似的调节过程。我们的分析表明,被子植物 MYB 叶发育基因 ARP 没有蕨类直向同源物,这引发了有关蕨类植物和种子植物叶子进化和起源的有趣问题。结论。我们的结果为研究整个植物生命树中发育和代谢调节剂的重要基因家族的遗传和功能进化提供了系统发育背景。我们的分析表明,被子植物 MYB 叶发育基因 ARP 没有蕨类直向同源物,这引发了有关蕨类植物和种子植物叶子进化和起源的有趣问题。结论。我们的结果为研究整个植物生命树中发育和代谢调节剂的重要基因家族的遗传和功能进化提供了系统发育背景。我们的分析表明,被子植物 MYB 叶发育基因 ARP 没有蕨类直向同源物,这引发了有关蕨类植物和种子植物叶子进化和起源的有趣问题。结论。我们的结果为研究整个植物生命树中发育和代谢调节剂的重要基因家族的遗传和功能进化提供了系统发育背景。
更新日期:2021-01-01
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