NGS-Indel Coder: A pipeline to code indel characters in phylogenomic data with an example of its application in milkweeds (Asclepias)
| Autor: | Aaron Liston, Mark Fishbein, Shannon C. K. Straub, Julien Boutte |
|---|---|
| Přispěvatelé: | Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Hobart and William Smith Colleges [Geneva, NY], Oklahoma State University [Stillwater] (OSU), Oregon State University (OSU), 1457510/1457473, National Sleep Foundation, 0919583/0919389, MF and SCKS, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Oklahoma State University [Stillwater] |
| Rok vydání: | 2019 |
| Předmět: |
0106 biological sciences
0301 basic medicine Nuclear gene [SDV]Life Sciences [q-bio] Biology Genes Plant 010603 evolutionary biology 01 natural sciences Coalescent theory 03 medical and health sciences Monophyly INDEL Mutation Phylogenetics Genetics Animals Clade Indel Molecular Biology Ecology Evolution Behavior and Systematics Asclepias Phylogeny Phylogenetic tree Base Sequence High-Throughput Nucleotide Sequencing Sub-sampling Evolutionary radiation Introns Incomplete lineage sorting Apocynaceae 030104 developmental biology Character coding Evolutionary biology Genetic Loci SNP detection [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] Gene tree filtering |
| Zdroj: | Molecular Phylogenetics and Evolution Molecular Phylogenetics and Evolution, 2019, 139, pp.106534. ⟨10.1016/j.ympev.2019.106534⟩ Molecular Phylogenetics and Evolution, Elsevier, 2019, 139, pp.106534. ⟨10.1016/j.ympev.2019.106534⟩ |
| ISSN: | 1095-9513 1055-7903 |
| Popis: | International audience; Targeted genome sequencing approaches allow characterization of evolutionary relationships using a considerable number of nuclear genes and informative characters. However, most phylogenomic analyses only utilize single nucleotide polymorphisms (SNPs). Studies at the species level, especially in groups that have recently radiated, often recover low amounts of phylogenetically informative variation in coding regions, and require non-coding sequences, which are richer in indels, to resolve gene trees. Here, NGS-Indel Coder, a pipeline to detect and omit false positive indels inferred from assemblies of short read sequence data, was developed to resolve the relationships among and within major clades of the American milkweeds (Asclepias), which are the result of a rapid and recent evolutionary radiation, and whose phylogeny has been difficult to resolve. This pipeline was applied to a Hyb-Seq data set of 768 loci including targeted exons and flanking intron regions from 33 milkweed species. Robust species tree inference was improved by excluding small alignment partitions ( |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full Text from ScienceDirect