Abstract
WRKY transcription factors play key roles in stress responses, growth, and development. We previously reported on the evolution of WRKYs from unicellular green algae to land plants. To address recent evolution events, we studied three domesticated and eight wild species in the genus Oryza, an ideal model due to its long history of domestication, economic importance, and central role as a model system. We have identified prevalence of Group III WRKYs despite differences in breeding of cultivated and wild species. Same groups of WRKY genes tend to cluster together, suggesting recent, multiple duplication events. Duplications followed by divergence may result in neofunctionalizations of co-expressed WRKY genes that finely tune the regulation of target genes in a same metabolic or response pathway. WRKY genes have undergone recent rearrangements to form novel genes. Group Ib WRKYs, unique to AA genome type Oryza species, are derived from Group III genes dated back to 6.76 million years ago. Gene tree reconciliation analysis with the species tree revealed details of duplication and loss events in the 11 genomes. Selection analysis on single copy orthologs reveals the highly conserved nature of the WRKY domain and clusters of fast evolving sites under strong positive selection pressure. Also, the numbers of single copy orthologs under positive or negative selection almost evenly split. Our results provide valuable insights into the preservation and diversification of an important gene family under strong selective pressure for biotechnological improvements of the world’s most valued food crop.
Highlights
WRKY transcription factors play key roles in stress responses, growth, and development
Analysis of the 11 Oryza genomes reveal a total of 1,018 WRKY genes (Table 1 and Supplementary Table S1)
Genes are distributed across the 12 chromosomes of these diploid Oryza species, with chromosome 1 having the greatest number of WRKYs (24%), followed by chromosome 5 (17%) and chromosome 3 (10%; Fig. 1)
Summary
WRKY transcription factors play key roles in stress responses, growth, and development. One of the most prominent gene families encodes WRKY transcription factors[1] They play key roles in plant immune responses[2,3], responses to abiotic stresses such as salt and d rought[4], and hormones such as abscisic a cid[5]. WRKY genes are only present in green plants, fungi, Amoebozoa, and fornicate[6,7] Their high specificity to and rapid expansions in plants hint at their key roles in evolution from single cellular aquatic algae, gradually developing varied defense strategies to combat biotic and abiotic stress agents, and becoming multicellular flowering organisms. E.g., in a genus, helps address gene family evolution within the genus This can provide insights that may be more valuable than genomic comparison studies among different genera. Domesticated Asian rice (Oryza sativa), which is the most widely exploited member of the genus, Scientific Reports | (2021) 11:14887
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