期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 34, 期 6, 页码 1479-1491出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msx099
关键词
gene-body methylation; Arabidopsis; gene length; gene expression
资金
- Japan Society for the Promotion of Science (JSPS) [15K18585]
- National Science Foundation (NSF) Plant Genome Research Program [1609024]
- National Science Foundation (NSF) [IOS-1542703]
- Albert and Elaine Borchard Foundation
- Division Of Integrative Organismal Systems
- Direct For Biological Sciences [1609024, 1542703] Funding Source: National Science Foundation
- Grants-in-Aid for Scientific Research [15K18585] Funding Source: KAKEN
DNA methylation labels a specific subset of genes in plant genomes. Recent work has shown that this gene-body methylation (gbM) is a conserved feature of orthologs, because highly methylated genes in one species tend to be highly methylated in another. In this study, we examined the exceptions to that rule by identifying genes that differ in gbM status between two plant species-Arabidopsis thaliana and Arabidopsis lyrata. Using Capsella grandiflora as an out-group, we polarized the loss and gain of gbM for orthologs in the Arabidopsis lineage. Our survey identified a few hundred genes that differed between ingroup species, out of similar to 9,000 orthologs. The estimated rate of gbM gain was similar to 2 x 10(-9) per gene per year for both ingroup taxa and was similar to the loss rate in A. lyrata. In contrast, A. thaliana had a similar to 3-fold higher estimated rate of gbM loss per gene, consistent with a recent diminishment of genome size. As in previous studies, we found that body-methylated genes were expressed broadly across tissues and were also longer than other genic sets. Genes that differed in gbM status exhibited higher variance in expression between species than genes that were body-methylated in both species. Moreover, the gain of gbM in one lineage tended to be associated with an increase of expression in that lineage. The genes that varied in gbM status between species varied more significantly in length between species than other sets of genes; we hypothesize that length is a key feature in the transition between body-methylated and nonmethylated genes.
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