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Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences.

Publication ,  Journal Article
Yu, Y; Xiang, Q; Manos, PS; Soltis, DE; Soltis, PS; Song, B-H; Cheng, S; Liu, X; Wong, G
Published in: PloS one
January 2017

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.

Duke Scholars

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Published In

PloS one

DOI

EISSN

1932-6203

ISSN

1932-6203

Publication Date

January 2017

Volume

12

Issue

2

Start / End Page

e0171361

Related Subject Headings

  • Transcriptome
  • High-Throughput Nucleotide Sequencing
  • Genome, Plant
  • General Science & Technology
  • Gene Duplication
  • Evolution, Molecular
  • Cornus
 

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Yu, Y., Xiang, Q., Manos, P. S., Soltis, D. E., Soltis, P. S., Song, B.-H., … Wong, G. (2017). Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences. PloS One, 12(2), e0171361. https://doi.org/10.1371/journal.pone.0171361
Yu, Yan, Qiuyun Xiang, Paul S. Manos, Douglas E. Soltis, Pamela S. Soltis, Bao-Hua Song, Shifeng Cheng, Xin Liu, and Gane Wong. “Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences.PloS One 12, no. 2 (January 2017): e0171361. https://doi.org/10.1371/journal.pone.0171361.
Yu Y, Xiang Q, Manos PS, Soltis DE, Soltis PS, Song B-H, et al. Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences. PloS one. 2017 Jan;12(2):e0171361.
Yu, Yan, et al. “Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences.PloS One, vol. 12, no. 2, Jan. 2017, p. e0171361. Epmc, doi:10.1371/journal.pone.0171361.
Yu Y, Xiang Q, Manos PS, Soltis DE, Soltis PS, Song B-H, Cheng S, Liu X, Wong G. Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences. PloS one. 2017 Jan;12(2):e0171361.

Published In

PloS one

DOI

EISSN

1932-6203

ISSN

1932-6203

Publication Date

January 2017

Volume

12

Issue

2

Start / End Page

e0171361

Related Subject Headings

  • Transcriptome
  • High-Throughput Nucleotide Sequencing
  • Genome, Plant
  • General Science & Technology
  • Gene Duplication
  • Evolution, Molecular
  • Cornus