Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms

Ren Ren, Haifeng Wang, Chunce Guo, Ning Zhang, Liping Zeng, Yamao Chen, Hong Ma, Ji Qi

Research output: Contribution to journalArticle

51 Scopus citations

Abstract

Gene duplications provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication (WGD) doubles the chromosomes initially and results in hundreds to thousands of retained duplicates. WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes, and thus are considered as a major driving force in species diversification. We performed comparative genomic and phylogenomic analyses of 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms to detect large-scale gene duplication events by surveying tens of thousands of gene family trees. These analyses confirmed most of the previously reported WGDs and provided strong evidence for novel ones in many lineages. The detected WGDs supported a model of exponential gene loss during evolution with an estimated half-life of approximately 21.6 million years, and were correlated with both the emergence of lineages with high degrees of diversification and periods of global climate changes. The new datasets and analyses detected many novel WGDs widely spread during angiosperm evolution, uncovered preferential retention of gene functions in essential cellular metabolisms, and provided clues for the roles of WGD in promoting angiosperm radiation and enhancing their adaptation to environmental changes. Novel WGDs were detected for many lineages by comparative genomic and phylogenomic analysis of 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes. A model of exponential gene loss rate was proposed for WGDs from different angiosperm lineages. Most WGDs detected were associated with lineages with greater species abundance, suggesting their contribution to species radiation.

Original languageEnglish (US)
Pages (from-to)414-428
Number of pages15
JournalMolecular plant
Volume11
Issue number3
DOIs
StatePublished - Mar 5 2018

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Plant Science

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