title: Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences.
abstract: The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework. Here we compare ten de novo-assembled transcriptomes representing the major lineages of the angiosperm genus Cornus (dogwood) and relevant outgroups using a customized pipeline for analyses. Using three distinct approaches, molecular dating of orthologous genes, analyses of the distribution of synonymous substitutions between paralogous genes, and examination of substitution rates through time, we detected a shared WGD event in the late Cretaceous across all taxa sampled. The inferred doubling event coincides temporally with the paleoclimatic changes associated with the initial divergence of the genus into three major lineages. Analyses also showed an acceleration of rates of molecular evolution after WGD. The highest rates of molecular evolution were observed in the transcriptome of the herbaceous lineage, C. canadensis, a species commonly found at higher latitudes, including the Arctic. Our study demonstrates the value of transcriptome data for understanding genome evolution in closely related species. The results suggest dramatic increase in sea surface temperature in the late Cretaceous may have contributed to the evolution and diversification of flowering plants.
authors.affiliation: Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America.|Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, PR China.|Department of Biology, Duke University, 130 Science Drive, Durham, NC, United States of America.
authors.forename: Yan
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America.
authors.forename: Qiuyun
authors.initials: Q
authors.lastname: Xiang
authors.affiliation: Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, PR China.
authors.forename: Paul S
authors.initials: PS
authors.lastname: Manos
authors.affiliation: Florida Natural History Museum, University of Florida, Gainesville, FL, United States of America.|Department of Biology, University of Florida, Gainesville, FL, United States of America.
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Soltis
authors.affiliation: Florida Natural History Museum, University of Florida, Gainesville, FL, United States of America.|Department of Biology, University of Florida, Gainesville, FL, United States of America.
authors.forename: Pamela S
authors.initials: PS
authors.lastname: Soltis
authors.affiliation: Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, United States of America.
authors.forename: Bao-Hua
authors.initials: BH
authors.lastname: Song
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Shifeng
authors.initials: S
authors.lastname: Cheng
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
authors.forename: Gane
authors.initials: G
authors.lastname: Wong
mesh_terms: D029768:Cornus / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D059467:Transcriptome