DNA sequence baits targeting ultra-conserved elements in marine invertebrates

Petersen, Haidi; Knott, Emily; Banta, Gary; Winding Hansen, Benni. (2022). DNA sequence baits targeting ultra-conserved elements in marine invertebrates . V. 1.10.2021. University of Jyväskylä. https://doi.org/10.17011/jyx/dataset/80617.

JYU authors:
  • Contact person (yes/no): No
  • Contact person (yes/no): Yes

All authors: Petersen, Haidi; Knott, Emily; Banta, Gary; Winding Hansen, Benni

Funders: Department of Biological and Environmental Science; Department of Mathematics and Statistics


Availability and identifiers

Availability: Direct download

Publication year: 2022

URN identifier in original repository: http://urn.fi/URN:NBN:fi:jyu-202204202301

DOI identifier in original repository: https://doi.org/10.17011/jyx/dataset/80617

URN identifier in JYX: http://urn.fi/URN:NBN:fi:jyu-202204202301

DOI identifier in JYX: https://doi.org/10.17011/jyx/dataset/80617

Description of the dataset

Description: This dataset includes four files of DNA sequence baits targeted to ultra-conserved elements (UCEs) identified from four different taxonomic groups of marine invertebrates: Annelida, Bivalvia, Gastropoda and Crustacea. UCE loci are genomic regions of high conservation that can be found throughout the genomes that can be extracted from the genome and sequenced for use in phylogenetic, phylogeographic and population genetic analyses. The UCE loci were located by aligning a minimum of five species’ genomes to a base genome in each taxonomic group and searching for overlapping highly conserved areas. The UCE baits were designed with screening coverage of 4X using the pipeline phyluce v. 1.6.6 (https://github.com/faircloth-lab/phyluce; Faircloth 2015). The analysis generated 3316 baits for 590 conserved loci in annelids, 4110 baits for 519 loci in bivalves, 25547 baits for 4367 loci in gastropods and 27545 baits for 3755 conserved loci in crustaceans. A final set of 3000 baits per taxonomic group (12000 baits in total) was created by Arbor Biosciences (Ann Arbor, MI, USA, arborbiosci.com) using their myBaits probe design support. For more detailed documentation, see the downloadable dataset description file.

Language: English

Free keywords: population genetics, biogeography, Baltic Sea, benthic invertebrates, ultra-conserved elements, DNA probes, DNA hybridization

Keywords (YSO): animal populations; DNA; hybridisation; genome

Fields of science: 1181 Ecology, evolutionary biology; 1184 Genetics, developmental biology, physiology; 1172 Environmental sciences

Do you deal with data concerning special categories of personal data in your research?: No

Last updated on 2023-07-08 at 11:10