Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae)

Abstract In this study, we report the assembly and annotation of five reference transcriptomes for the European hexaploid Spartina species (S. maritima, S. alterniflora and their homoploid hybrids S. x townsendii and S. x neyrautii) and the allododecaploid invasive species S. anglica. These transcriptomes were constructed from various leaf and root cDNA libraries that were sequenced using both Roche-454 and Illumina technologies. Considering the high ploidy levels of the Spartina genomes under study, and considering the absence of diploid reference genome and the need of an appropriate analytical strategy, we developed generic bioinformatics tools to (1) detect different haplotypes of each gene within each species and (2) assign a parental origin to haplotypes detected in the hexaploid hybrids and the neo-allopolyploid. The approach described here allows the detection of putative homeologs from sets of short reads. Synonymous substitution rate (KS) comparisons between haplotypes from the hexaploid species revealed the presence of one KS peak (likely resulting from the tetraploid duplication event). The procedure developed in this study can be applied for future differential gene expression or genomics experiments to study the fate of duplicated genes in the invasive allododecaploid S. anglica.

• Publication year

  2016

• Venue

  Genome Biology and Evolution

• Publication date

  2016-08-18

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1093/gbe/evw209PMID 27614235PMCID 5633685
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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