title: The Utility of Genome Skimming for Phylogenomic Analyses as Demonstrated for Glycerid Relationships (Annelida, Glyceridae).
abstract: Glyceridae (Annelida) are a group of venomous annelids distributed worldwide from intertidal to abyssal depths. To trace the evolutionary history and complexity of glycerid venom cocktails, a solid backbone phylogeny of this group is essential. We therefore aimed to reconstruct the phylogenetic relationships of these annelids using Illumina sequencing technology. We constructed whole-genome shotgun libraries for 19 glycerid specimens and 1 outgroup species (Glycinde armigera). The chosen target genes comprise 13 mitochondrial proteins, 2 ribosomal mitochondrial genes, and 4 nuclear loci (18SrRNA, 28SrRNA, ITS1, and ITS2). Based on partitioned maximum likelihood as well as Bayesian analyses of the resulting supermatrix, we were finally able to resolve a robust glycerid phylogeny and identified three clades comprising the majority of taxa. Furthermore, we detected group II introns inside the cox1 gene of two analyzed glycerid specimens, with two different insertions in one of these species. Moreover, we generated reduced data sets comprising 10 million, 4 million, and 1 million reads from the original data sets to test the influence of the sequencing depth on assembling complete mitochondrial genomes from low coverage genome data. We estimated the coverage of mitochondrial genome sequences in each data set size by mapping the filtered Illumina reads against the respective mitochondrial contigs. By comparing the contig coverage calculated in all data set sizes, we got a hint for the scalability of our genome skimming approach. This allows estimating more precisely the number of reads that are at least necessary to reconstruct complete mitochondrial genomes in Glyceridae and probably non-model organisms in general.
authors.affiliation: Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Germany sandy.richter@uni-leipzig.de bleidorn@uni-leipzig.de.
authors.forename: Sandy
authors.initials: S
authors.lastname: Richter
authors.affiliation: Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Germany.
authors.forename: Francine
authors.initials: F
authors.lastname: Schwarz
authors.affiliation: Animal Evolution & Development, Institute of Biology, University of Leipzig, Germany Department of Zoology, Institute of Biology, University of Kassel, Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Hering
authors.affiliation: Fach Biologie, University of Vechta, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Böggemann
authors.affiliation: Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany sandy.richter@uni-leipzig.de bleidorn@uni-leipzig.de.
authors.forename: Christoph
authors.initials: C
authors.lastname: Bleidorn
mesh_terms: D000818:Animals; D000845:Annelida / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D049751:Genome, Helminth; D054629:Genome, Mitochondrial; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics
chemical_list: D012335:RNA, Ribosomal
keywords: Glyceridae; group II introns; mitogenomics; sequencing coverage; venomous annelids; whole-genome shotgun sequencing