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      Population Level Purifying Selection and Gene Expression Shape Subgenome Evolution in Maize.

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          Abstract

          The maize ancestor experienced a recent whole-genome duplication (WGD) followed by gene erosion which generated two subgenomes, the dominant subgenome (maize1) experiencing fewer deletions than maize2. We take advantage of available extensive polymorphism and gene expression data in maize to study purifying selection and gene expression divergence between WGD retained paralog pairs. We first report a strong correlation in nucleotide diversity between duplicate pairs, except for upstream regions. We then show that maize1 genes are under stronger purifying selection than maize2. WGD retained genes have higher gene dosage and biased Gene Ontologies consistent with previous studies. The relative gene expression of paralogs across tissues demonstrates that 98% of duplicate pairs have either subfunctionalized in a tissuewise manner or have diverged consistently in their expression thereby preventing functional complementation. Tissuewise subfunctionalization seems to be a hallmark of transcription factors, whereas consistent repression occurs for macromolecular complexes. We show that dominant gene expression is a strong determinant of the strength of purifying selection, explaining the inferred stronger negative selection on maize1 genes. We propose a novel expression-based classification of duplicates which is more robust to explain observed polymorphism patterns than the subgenome location. Finally, upstream regions of repressed genes exhibit an enrichment in transposable elements which indicates a possible mechanism for expression divergence.

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          Author and article information

          Journal
          Mol. Biol. Evol.
          Molecular biology and evolution
          Oxford University Press (OUP)
          1537-1719
          0737-4038
          Dec 2015
          : 32
          : 12
          Affiliations
          [1 ] Section of Population Genetics, School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany pophaly@wzw.tum.de.
          [2 ] Section of Population Genetics, School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany.
          Article
          msv191
          10.1093/molbev/msv191
          26374232
          e3e53ef3-e00c-41d9-93cc-c2e35ef2b1ea
          History

          DoFE,gene expression,purifying selection,whole-genome duplication

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