Biased Gene Fractionation and Dominant Gene Expression among the Subgenomes of Brassica rapa

F. Cheng, J. Wu, L. Fang, S. Sun, B. Liu, K. Lin, A.B. Bonnema, Xiaowu Wang

Research output: Contribution to journalArticleAcademicpeer-review

167 Citations (Scopus)

Abstract

Polyploidization, both ancient and recent, is frequent among plants. A ‘‘two-step theory’’ was proposed to explain the meso-triplication of the Brassica ‘‘A’’ genome: Brassica rapa. By accurately partitioning of this genome, we observed that genes in the less fractioned subgenome (LF) were dominantly expressed over the genes in more fractioned subgenomes (MFs: MF1 and MF2), while the genes in MF1 were slightly dominantly expressed over the genes in MF2. The results indicated that the dominantly expressed genes tended to be resistant against gene fractionation. By re-sequencing two B. rapa accessions: a vegetable turnip (VT117) and a Rapid Cycling line (L144), we found that genes in LF had less nonsynonymous or frameshift mutations than genes in MFs; however mutation rates were not significantly different between MF1 and MF2. The differences in gene expression patterns and on-going gene death among the three subgenomes suggest that ‘‘two-step’’ genome triplication and differential subgenome methylation played important roles in the genome evolution of B. rapa.
Original languageEnglish
Article numbere36442
JournalPLoS ONE
Volume7
Issue number5
DOIs
Publication statusPublished - 2012

Keywords

  • short read alignment
  • arabidopsis-thaliana
  • dna methylation
  • genome sequence
  • duplication
  • evolution
  • polyploids
  • plants

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