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Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms
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  • Claudia Ortiz-Sepulveda,
  • Mathieu Genete,
  • Christelle Blassiau,
  • Cécile Godé,
  • Christian Albrecht,
  • Xavier Vekemans,
  • Bert Van Bocxlaer
Claudia Ortiz-Sepulveda
Université de Lille
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Mathieu Genete
CNRS
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Christelle Blassiau
Université de Lille
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Cécile Godé
CNRS
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Christian Albrecht
Justus Liebig Universitat Giessen
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Xavier Vekemans
Universite de Lille
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Bert Van Bocxlaer
CNRS
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Abstract

Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful, but nevertheless produced a substantial dataset. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (>515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (>11,000 informative sites), although some branches lack support in the latter case. Variant calling on the exome of Coelaturini from the Malawi Basin produced ~2,000 SNPs per population pair. Nucleotide diversity and population differentiation was low compared to previous estimates in mollusks, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming non-specific sequence data obtained for Coelaturini of the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays an identical gene order to that of the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for the development of integrative genomic studies on micro- and macroevolutionary dynamics in non-model organisms.