ArticleInternational journal of plant genomics2013
SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species.
Article in International journal of plant genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids.Plant methods · 2025Article
- Homoploid hybridization adds clarity to the origins of octoploid strawberries.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Review
- Polyploidy and hybridization in the Mediterranean: unravelling the evolutionary history of Centaurium (Gentianaceae).Annals of botany · 2024Article
- Picks in the Fabric of a Polyploidy Complex: Integrative Species Delimitation in the TetraploidBiology · 2023Article
- Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids.Plants (Basel, Switzerland) · 2022Review
- Subgenome evolution in allotetraploid plants.The Plant journal : for cell and molecular biology · 2021Article
- Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids.Briefings in bioinformatics · 2021Review
- Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data.Frontiers in plant science · 2020Article
- Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae).Genome biology and evolution · 2016Article
- De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia.BMC genomics · 2016Article
- Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers.Molecular ecology · 2016Article
- Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima.G3 (Bethesda, Md.) · 2015Article
- Methods for mapping and categorization of DNA sequence reads from allopolyploid organisms.BMC genetics · 2015Article
- A roadmap of phylogenomic methods for studying polyploid plant genera.Applications in plant sciencesArticle
- Variant calling in polyploids for population and quantitative genetics.Applications in plant sciencesArticle
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing is a common approach to discover SNP variants, especially in plant species. However, methods to analyze predicted SNPs are often optimized for diploid plant species whereas many crop species are allopolyploids and combine related but divergent subgenomes (homoeologous chromosome sets). We created a software tool, SNiPloid, that exploits and interprets putative SNPs in the context of allopolyploidy by comparing SNPs from an allopolyploid with those obtained in its modern-day diploid progenitors. SNiPloid can compare SNPs obtained from a sample to estimate the subgenome contribution to the transcriptome or SNPs obtained from two polyploid accessions to search for SNP divergence.
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Registered trials
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