Phylogenomische Analyse zur Systematik der Nereididae (Annelida)
Zusammenfassung der Projektergebnisse
Nereididae constitute a family of marine and freshwater-living worms within Annelida with over 770 species of nereidids described worldwide. Their overall abundance, wide distribution, and ease of culturing, makes some nereidids suitable as laboratory species. Notably, Platynereis dumerilii has continuously been bred in laboratories for more than 70 years and is now one of the most well-studied species within Lophotrochozoa. Despite this, interspecies relationships, and the relationships between currently accepted subfamilies, within this group are poorly resolved. Prior phylogenetic studies have limited taxonomic coverage and are based on morphological characters or a handful of mitochondrial markers. We conducted a phylogenomic study using low-coverage whole-genome sequencing data from more than 100 individuals Near-universal single-copy orthologs (USCOs) were obtained using a newly designed genome-skimming tool called Patchwork. This sowtware enables to mine phylogenetic markers from highly fragmented short-read assemblies as well as directly from sequence reads. Patchwork is an alignment-based tool that utilizes the sequence aligner DIAMOND. Homologous regions are obtained via sequence similarity search, followed by a “hit-stitching” phase, in which adjacent or overlapping regions are merged into a single unit. We additionally analysed mitochondrial genomes from 132 species by combining our own data with publicly available sequences. Phylogenetic analyses of 777 concatenated USCOs and complete mitochondrial genomes resulted in largely congruent and highly supported topologies. Our study implies that Gymnonereididae sensu Banse 1977 is the sister group to all other nereidids. Furthermore, larger genera such as Alitta, Nereis, and Neanthes are recovered as non-monophyletic. Analyses of mitochondrial genes and mitochondrial gene order in nereidids provide additional consistent support to our findings.
Projektbezogene Publikationen (Auswahl)
-
Robust phylogenomic inference through genome skimming as demonstrated by a systematic analysis of Nereididae. Dissertation Georg-August- Universität Göttingen
Thalén, F.
-
Patchwork: Alignment-Based Retrieval and Concatenation of Phylogenetic Markers from Genomic Data. Genome Biology and Evolution, 15(12).
Thalén, Felix; Köhne, Clara G. & Bleidorn, Christoph
