ArticleBMC bioinformatics2013
Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Modern Approaches for Transcriptome Analyses in Plants.Advances in experimental medicine and biology · 2021Article
- Multiple origins of green coloration in frogs mediated by a novel biliverdin-binding serpin.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm.BMC genomics · 2019Article
- Article
- Epistatic determinism of durum wheat resistance to the wheat spindle streak mosaic virus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
- A Developmental Transcriptome Map for AllotetraploidFrontiers in plant science · 2016Article
- Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat.PloS one · 2016Article
- Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci.Systematic biology · 2015Article
- Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana.PloS one · 2014Article
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Authors and funding
8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundUsing Next Generation Sequencing, SNP discovery is relatively easy on diploid species and still hampered in polyploid species by the confusion due to homeology. We develop HomeoSplitter; a fast and effective solution to split original contigs obtained by RNAseq into two homeologous sequences. It uses the differential expression of the two homeologous genes in the RNA. We verify that the new sequences are closer to the diploid progenitors of the allopolyploid species than the original contig. By remapping original reads on these new sequences, we also verify that the number of valuable detected SNPs has significantly increased.
resultsHomeoSplitter is a fast and effective solution to disentangle homeologous sequences based on a maximum likelihood optimization. On a benchmark set of 2,505 clusters containing homologous sequences of urartu, speltoides and durum, HomeoSplitter was efficient to build sequences closer to the diploid references and increased the number of valuable SNPs from 188 out of 1,360 SNPs detected when mapping the reads on the de novo durum assembly to 762 out of 1,620 SNPs when mapping on HomeoSplitter contigs.
conclusionsThe HomeoSplitter program is freely available at http://bioweb.supagro.inra.fr/homeoSplitter/. This work provides a practical solution to the complex problem of disentangling homeologous transcripts in allo-tetraploids, which further allows an improved SNP detection.
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