ArticleGenome biology and evolution2016
Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae).
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Recurrent polyploidy and descending dysploidy as plant genome shapers: Insights from Sporobolus (Chloridoideae, Poaceae) genomes.PloS one · 2026Article
- On the way to diploidization and unexpected ploidy in the grass Sporobolus section Spartina mesopolyploids.Nature communications · 2025Article
- Recent allopolyploidy alters Spartina microRNA expression in response to xenobiotic-induced stress.Plant molecular biology · 2023Article
- Gene and Transposable Element Expression Evolution Following Recent and Past Polyploidy Events inFrontiers in genetics · 2021Article
- Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb-Seq.Applications in plant sciences · 2020Article
- Evolution of small RNA expression following hybridization and allopolyploidization: insights from Spartina species (Poaceae, Chloridoideae).Plant molecular biology · 2020Article
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Authors and funding
8 authors.
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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 (K
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