A new probe set to target ultraconserved elements for Malacostraca

Since its introduction about a decade ago, target enrichment sequencing of ultraconserved elements (UCEs) has proven to be an invaluable tool for studies across temporal and evolutionary scales, and thus employed from population genetics, to historical biogeography and deep phylogenetics. UCE probe sets are available for an increasing range of major taxonomic groups, including cnidarians, vertebrates, terrestrial arthropods, and mollusks. Here, we present the first probe set targeting UCEs in crustaceans, specifically designed for decapods and other malacostracan lineages. Probes were designed using published genomes of nine decapod and one peracarid species, as well as raw Nanopore long reads of one additional brachyuran species. The final probe set consists of about 20,000 probes, targeting 1,348 unique UCE loci. Preliminary analyses of UCE data obtained from an intertidal mangrove crab, and from deep-sea squat lobsters indicate high UCE recovery rates (regularly about 1,000 loci per sample) in evolutionarily shallow datasets. To test the probe set at deeper phylogenetic levels, we additionally compiled a dataset across Malacostraca (including representatives of Decapoda, Peracarida, Euphausiacea, Stomatopoda, and Phyllocarida), and were able to recover hundreds of UCEs for the non-decapod species, expanding the targeted use of this UCE probeset to all Malacostraca. Additionally, we recovered similar numbers of UCEs from historical museum specimens up to > 150 years old, that were included in all three datasets, showing once more that UCEs are a fruitful technique for leveraging museum specimens for genomic studies. Overall, our results highlight the versatility of this UCE probe set and its high potential for crustacean evolutionary studies.

Identifier
Source https://data.blue-cloud.org/search-details?step=~0121E1CE987C1A2AE2BC1AC2F438032BAE0F46FB73B
Metadata Access https://data.blue-cloud.org/api/collections/1E1CE987C1A2AE2BC1AC2F438032BAE0F46FB73B
Provenance
Instrument Illumina NovaSeq 6000; PromethION; ILLUMINA; OXFORD_NANOPORE
Publisher Blue-Cloud Data Discovery & Access service; ELIXIR-ENA
Publication Year 2024
OpenAccess true
Contact blue-cloud-support(at)maris.nl
Representation
Discipline Marine Science
Spatial Coverage (-159.965W, -13.051S, 133.017E, 45.886N)
Temporal Coverage Begin 1901-01-01T00:00:00Z
Temporal Coverage End 2023-07-15T00:00:00Z