Abstract
The WRKY gene family, which encodes proteins in the regulation processes of diverse developmental stages, is one of the largest families of transcription factors in higher plants. In this study, by searching for interspecies gene colinearity (microsynteny) and dating the age distributions of duplicated genes, we found 35 chromosomal segments of subgroup I genes of WRKY family (WRKY I) in four Gramineae species (Brachypodium, rice, sorghum, and maize) formed eight orthologous groups. After a stepwise gene-by-gene reciprocal comparison of all the protein sequences in the WRKY I gene flanking areas, highly conserved regions of microsynteny were found in the four Gramineae species. Most gene pairs showed conserved orientation within syntenic genome regions. Furthermore, tandem duplication events played the leading role in gene expansion. Eventually, environmental selection pressure analysis indicated strong purifying selection for the WRKY I genes in Gramineae, which may have been followed by gene loss and rearrangement. The results presented in this study provide basic information of Gramineae WRKY I genes and form the foundation for future functional studies of these genes. High level of microsynteny in the four grass species provides further evidence that a large-scale genome duplication event predated speciation.
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Acknowledgments
We thank the members of the Key Laboratory of Crop Biology of Anhui province for their assistance in this study. This work was supported by the Natural Science Foundation of China (91435110,31301324,). We extend our thanks to the reviewers for their careful reading and helpful comments on this manuscript.
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Communicated by Sureshkumar Balasubramanian
Jing Jin and Jingjing Kong contributed equally to this work.
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Supplementary Fig. S1
Distribution of synonymous distances (Ks) between paralogous genes flanking duplicated WRKY I genes in the four Gramineae species. The histogram depicts the number of duplicated gene pairs (y-axis) versus synonymous distances between pairs (x-axis). (PDF 717 kb)
Supplementary Fig. S2
Phylogenetic tree based on sequences of WRKY I proteins from Arabidopsis, Brachypodium, rice, sorghum, and maize. (PDF 17 kb)
Supplementary Table S1
Gene names, identifiers, and predicted lengths, molecular weights, and isoelectric points for WRKY I proteins from Brachypodium, rice, sorghum, and maize. (XLS 33 kb)
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Jin, J., Kong, J., Qiu, J. et al. High level of microsynteny and purifying selection affect the evolution of WRKY family in Gramineae. Dev Genes Evol 226, 15–25 (2016). https://doi.org/10.1007/s00427-015-0523-2
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DOI: https://doi.org/10.1007/s00427-015-0523-2