Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)

Autor: Jérémy Clotault, Fabrice Foucher, Jordan Marie-Magdelaine, Tom Ruttink, Valéry Malécot, Kevin Debray
Přispěvatelé: Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-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), Research Institute for Agricultural, Fisheries and Food (ILVO), French Pays de la Loire region, Angers Loire Metropole, European Regional Development Fund, French Ministry of Higher Education and Research, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Flanders Research Institute for Agriculture, Fisheries and Food (ILVO)
Jazyk: angličtina
Rok vydání: 2019
Předmět:
0106 biological sciences
0301 basic medicine
Lineage (evolution)
Gene Dosage
01 natural sciences
Coalescent theory
Phylogenomics
Species-level phylogenomics
Taxonomic rank
Plastids
[SDV.SA.HORT]Life Sciences [q-bio]/Agricultural sciences/Horticulture
Phylogeny
UTILITY
Likelihood Functions
Vegetal Biology
Phylogenetic tree
Methodology Article
Genomics
Phylogenetic informativeness
Agricultural sciences
Botanique
GENOME
CONGRUENCE
TREES
Genome
Plant
Autre (Sciences du Vivant)
Botanics
Nuclear gene
GENES
Evolution
Biology
Rosa
010603 evolutionary biology
03 medical and health sciences
Conflicting topologies
Nuclear single-copy orthologs
Phylogenetics
PHYLOGENETIC-RELATIONSHIPS
QH359-425
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology
ALGORITHM
Ecology
Evolution
Behavior and Systematics
DNA Primers
Cell Nucleus
CHLOROPLAST DNA-SEQUENCES
WILD ROSES
030104 developmental biology
Evolutionary biology
Genetic Loci
EVOLUTIONARY
Biologie végétale
Sciences agricoles
Zdroj: BMC Evolutionary Biology, Vol 19, Iss 1, Pp 1-19 (2019)
BMC Evolutionary Biology
BMC Evolutionary Biology, BioMed Central, 2019, 19 (1), 19 p. ⟨10.1186/s12862-019-1479-z⟩
BMC Evolutionary Biology, BioMed Central, 2019, 19 (1), ⟨10.1186/s12862-019-1479-z⟩
BMC Evolutionary Biology 1 (19), 19 p.. (2019)
ISSN: 1471-2148
DOI: 10.1186/s12862-019-1479-z
Popis: Background With an ever-growing number of published genomes, many low levels of the Tree of Life now contain several species with enough molecular data to perform shallow-scale phylogenomic studies. Moving away from using just a few universal phylogenetic markers, we can now target thousands of other loci to decipher taxa relationships. Making the best possible selection of informative sequences regarding the taxa studied has emerged as a new issue. Here, we developed a general procedure to mine genomic data, looking for orthologous single-copy loci capable of deciphering phylogenetic relationships below the generic rank. To develop our strategy, we chose the genus Rosa, a rapid-evolving lineage of the Rosaceae family in which several species genomes have recently been sequenced. We also compared our loci to conventional plastid markers, commonly used for phylogenetic inference in this genus. Results We generated 1856 sequence tags in putative single-copy orthologous nuclear loci. Associated in silico primer pairs can potentially amplify fragments able to resolve a wide range of speciation events within the genus Rosa. Analysis of parsimony-informative site content showed the value of non-coding genomic regions to obtain variable sequences despite the fact that they may be more difficult to target in less related species. Dozens of nuclear loci outperform the conventional plastid phylogenetic markers in terms of phylogenetic informativeness, for both recent and ancient evolutionary divergences. However, conflicting phylogenetic signals were found between nuclear gene tree topologies and the species-tree topology, shedding light on the many patterns of hybridization and/or incomplete lineage sorting that occur in the genus Rosa. Conclusions With recently published genome sequence data, we developed a set of single-copy orthologous nuclear loci to resolve species-level phylogenomics in the genus Rosa. This genome-wide scale dataset contains hundreds of highly variable loci which phylogenetic interest was assessed in terms of phylogenetic informativeness and topological conflict. Our target identification procedure can easily be reproduced to identify new highly informative loci for other taxonomic groups and ranks. Electronic supplementary material The online version of this article (10.1186/s12862-019-1479-z) contains supplementary material, which is available to authorized users.
Databáze: OpenAIRE
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