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ORTHOSKIM: In silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding
Charles Pouchon1, Frédéric Boyer1, Cristina Roquet1,2
1LECA, Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, Grenoble, France.
Molecular Ecology Resources
|January 11, 2022
Summary
ORTHOSKIM is a new bioinformatics pipeline that efficiently extracts targeted organelle and nuclear DNA sequences from low-coverage genome skimming data. This method overcomes challenges in assembling complex genomes, aiding evolutionary studies in nonmodel organisms.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- Low-coverage whole genome shotgun sequencing (genome skimming) is cost-effective for nonmodel organisms.
- It yields data on chloroplast (cpDNA), mitochondrial (mtDNA), and nuclear ribosomal DNA (rDNA).
- Bioinformatic challenges hinder accurate data retrieval, especially for complex genomes like plant mtDNA and cpDNA.
Purpose of the Study:
- Introduce ORTHOSKIM, a novel pipeline for targeted sequence capture from genomic and transcriptomic libraries.
- Address challenges in obtaining organelle and nuclear DNA sequences from complex genomes.
- Facilitate accurate phylogenetic reconstructions using genome skimming data.
Main Methods:
- ORTHOSKIM employs a three-step process: global assembly, mapping to references, and target sequence extraction.
- Includes quality control tests and supports various capture modes for coding/noncoding regions.
- Generates aligned DNA matrices for phylogenetic analysis.
Main Results:
- Demonstrated high success rates in recovering cpDNA, mtDNA, and rDNA sequences.
- Successfully applied to challenging plant families (Primulaceae, Ericaceae) with complex cpDNA assemblies.
- Recovered sequences suitable for accurate evolutionary relationship inference.
Conclusions:
- ORTHOSKIM effectively overcomes bioinformatic hurdles in genome skimming data analysis.
- Provides a robust tool for extracting targeted genomic regions for phylogenetic studies.
- Enhances the utility of genome skimming for evolutionary genomics in diverse eukaryotes.
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