ArticleBMC bioinformatics2015
A composite genome approach to identify phylogenetically informative data from next-generation sequencing.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- WASTER: Practical de novo Phylogenomics from Low-coverage Short Reads.Molecular biology and evolution · 2026Article
- Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Extensive transcriptome data providing great efficacy in genetic research and adaptive gene discovery: a case study ofFrontiers in plant science · 2024Article
- Parallel evolution of opsin visual pigments in hawkmoths by tuning of spectral sensitivities during transition from a nocturnal to a diurnal ecology.The Journal of experimental biology · 2022Article
- Screening the PRISM Library againstACS omega · 2022Article
- Utilizing Big Data to Identify Tiny Toxic Components:Foods (Basel, Switzerland) · 2021Article
- Genome-Scale Profiling Reveals Noncoding Loci Carry Higher Proportions of Concordant Data.Molecular biology and evolution · 2021Article
- Into the wild: new yeast genomes from natural environments and new tools for their analysis.FEMS yeast research · 2020Review
- sppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing.Molecular biology and evolution · 2018Article
- A Primer on Infectious Disease Bacterial Genomics.Clinical microbiology reviews · 2016Review
- Transcriptomic resources and marker validation for diploid and polyploidApplications in plant sciences · 2016Article
- Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny.PloS one · 2016Article
- Article
- Reference-free discovery of nuclear SNPs permits accurate, sensitive identification ofApplications in plant sciencesArticle
- From WGS to gels: Development and testing of PCR primers targeting toxicApplications in plant sciencesArticle
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundImprovements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.
resultsFor simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.
conclusionsSISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.