ORTHOSKIM: In silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications

Autor: Pouchon, Charles, Boyer, Frédéric, Roquet, Cristina, Denoeud, France, Chave, Jérome, Coissac, Eric, Alsos, Inger Greve, Lavergne, Sébastien, Smyčka, J, Boleda, M, Thuiller, W, Gielly, L, Taberlet, P, Rioux, D, Hombiat, A, Bzeznick, B, Alberti, A, Wincker, P, Orvain, C, Perrier, C, Douzet, R, Rome, M, Valay, Jg, Aubert, S, Zimmermann, N, Wüest, Ro, Latzin, S, Wipf, S, van Es, J, Garraud, L, Villaret, Jc, Abdulhak, S, Bonnet, V, Huc, S, Fort, N, Legland, T, Sanz, T, Pache, G, Mikolajczak, A, Noble, V, Michaud, H, Offerhaus, B, Pires, M, Morvant, Y, Dentant, C, Salomez, P, Bonet, R, Delahaye, T, Leccia, Mf, Perfus, M, Eggenberg, S, Möhl, A, Hurdu, B, Pușcaș, M, Slovák, M, Alsos, Ig, Merkel, F, Lammers, Y, Coissac, E, Pouchon, C, Denoeud, F
Přispěvatelé: Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Université Paris Cité (UPCité), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), National Centre for Biosystematics [Oslo], Natural History Museum [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Cellule Terroirs Viticoles, Partenaires INRAE, Istituto per la Microelettronica e Microsistemi [Catania] (IMM), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université d'Angers (UA), Centre National de la Propriété Forestière (CNPF-IDF), ANR-16-CE93-0004,Origin-Alps,Origins, assembly and conservation of plant diversity in the European Alps(2016)
Jazyk: angličtina
Rok vydání: 2022
Předmět:
Zdroj: Molecular Ecology Resources
Molecular Ecology Resources, 2022, 22 (5), pp.2018-2037. ⟨10.1111/1755-0998.13584⟩
ISSN: 1755-098X
1755-0998
DOI: 10.1111/1755-0998.13584⟩
Popis: Low-coverage whole genome shotgun sequencing (or genome skimming) has emerged as a cost-effective method for acquiring genomic data in nonmodel organisms. This method provides sequence information on chloroplast genome (cpDNA), mitochondrial genome (mtDNA) and nuclear ribosomal regions (rDNA), which are over-represented within cells. However, numerous bioinformatic challenges remain to accurately and rapidly obtain such data in organisms with complex genomic structures and rearrangements, in particular for mtDNA in plants or for cpDNA in some plant families. Here we introduce the pipeline ORTHOSKIM, which performs in silico capture of targeted sequences from genomic and transcriptomic libraries without assembling whole organelle genomes. ORTHOSKIM proceeds in three steps: (i) global sequence assembly, (ii) mapping against reference sequences and (iii) target sequence extraction; importantly it also includes a range of quality control tests. Different modes are implemented to capture both coding and noncoding regions of cpDNA, mtDNA and rDNA sequences, along with predefined nuclear sequences (e.g., ultraconserved elements) or collections of single-copy orthologue genes. Moreover, aligned DNA matrices are produced for phylogenetic reconstructions, by performing multiple alignments of the captured sequences. While ORTHOSKIM is suitable for any eukaryote, a case study is presented here, using 114 genome-skimming libraries and four RNA sequencing libraries obtained for two plant families, Primulaceae and Ericaceae, the latter being a well-known problematic family for cpDNA assemblies. ORTHOSKIM recovered with high success rates cpDNA, mtDNA and rDNA sequences, well suited to accurately infer evolutionary relationships within these families. ORTHOSKIM is released under a GPL-3 licence and is available at: https://github.com/cpouchon/ORTHOSKIM.
Databáze: OpenAIRE
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