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

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...

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Published in:	Molecular ecology resources Vol. 22; no. 5; pp. 2018 - 2037
Main Authors:	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
Format:	Journal Article
Language:	English
Published:	England Wiley Subscription Services, Inc 01-07-2022 Wiley/Blackwell
Subjects:	Assembling Biochemistry, Molecular Biology bioinformatics Chloroplasts Coverage Data acquisition DNA, Chloroplast - genetics DNA, Mitochondrial - genetics DNA, Ribosomal - genetics Ericales Gene mapping Gene sequencing genome skimming Genome, Chloroplast Genomes Genomics Genomics - methods Libraries Life Sciences Mitochondria Mitochondrial DNA mitochondrion Nucleotide sequence nucleus phylogenomic Phylogeny plastome Quality control Sequence Analysis, DNA - methods Skimming Transcriptome Transcriptomics phylogenomic plastome Ericales transcriptome bioinformatics nucleus genome skimming mitochondrion
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Summary:	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.
Bibliography:	Members of the PhyloAlps and PhyloNorway consortia are co‐authors of this article and can be found under the heading Collaborators. ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1755-098X 1755-0998
DOI:	10.1111/1755-0998.13584