RT Journal Article SR Electronic T1 Enhanced functional divergence of duplicate genes several million years after gene duplication in the Arabidopsis lineage JF bioRxiv FD Cold Spring Harbor Laboratory SP 047639 DO 10.1101/047639 A1 Kousuke Hanada A1 Ayumi Tezuka A1 Masafumi Nozawa A1 Yutaka Suzuki A1 Sumio Sugano A1 Atsushi J. Nagano A1 Motomi Ito A1 Shi-Ichi Morinaga YR 2016 UL http://biorxiv.org/content/early/2016/04/07/047639.abstract AB Lineage-specifically duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selective pressures immediately after gene duplication is clear in the speciation process. Plants have substantially higher gene duplication rates than most other eukaryotes. Here, using Illumina short reads from Arabidopsis halleri, which has highly qualified plant genomes in close species (Brassica rapa, A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups among B. rapa, A. thaliana, A. lyrata and A. halleri. The frequency of duplication events in the Arabidopsis lineage was approximately 10 times higher than the frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss. Of the currently retained genes in A. halleri, 11–24% had undergone gene duplication in the Arabidopsis lineage. To examine the degree of selective pressure for duplicated genes, we calculated the ratios of nonsynonymous to synonymous substitution rates (KA/KS) in the A. halleri-lyrata and A. halleri lineages. Using a maximum-likelihood framework, we examined positive (KA/KS > 1) and purifying selection (KA/KS < 1) at a significant level (P < 0.01). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. More interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication at a higher proportion than immediately after gene duplication.