Abstract
We present genome sequences of 7 species of sea slugs from 4 genera. Illumina sequencing was performed on tissue from wild-collected museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.
Methods
Tissues from single, wild-collected individuals were used for this study. Three specimens were obtained from the Western Australian Museum (WAM) Marine Mollusca collection (Western Australian Museum 2023), and four were collected live for this study (CPIC, AMNH, MNHN). Live specimens were collected by hand while SCUBA diving and preserved in 95-100% EtOH for DNA sequencing.
DNA extraction was performed using the Qiagen DNEasy genomic extraction kit using the standard process. Paired-end sequencing libraries were constructed using the Illumina TruSeq kit according to the manufacturer’s instructions. The libraries were sequenced on an Illumina Hi-Seq platform in paired-end, 2 × 150bp format. The resulting fastq files were trimmed of adapter/primer sequences and low-quality regions with Trimmomatic v0.33 (Bolger, Lohse, and Usadel 2014). The trimmed sequence was assembled by SPAdes v3.15.4 (Bankevich et al. 2012) followed by a final assembly finishing step using Zanfona (Kieras, O’Neill, and Pirro 2021).
Results and Data Availability
| Species | Locality | Date Collected | Accession | Specimen_voucher |
|---|---|---|---|---|
| Bornella anguilla | Beagle Bay, Kimberley, WA, Australia | 12 March 2008 | JBDGEK000000000 | WAMS:44513 |
| Lomanotus vermiformis | Bocas del Toro, Panama | 6 Aug 2004 | JBBPDF000000000 | CPIC:00556 |
| Melibe bucephala | Seringapatam Reef, WA, Australia | 27 Sept 2007 | JBCJKE000000000 | WAMS:31224 |
| Melibe viridis | South Mole, Fremantle, WA, Australia | 15 April 2019 | JBCIKM000000000 | WAMS:72630 |
| Plocamopherus ceylonicus | Kwinana Grain Terminal Jetty, Rockingham, WA, Australia | 21 June 2023 | JBCJKF000000000 | AMNH:IZC-00385163 |
| Plocamopherus imperialis | Koumac, New Caledonia | 7 Nov 2018 | JBCHJU000000000 | MHNH-IM-2019-26525 |
| Plocamopherus tilesii | Koumac New Caledonia | 21 Nov 2019 | JBBPCV000000000 | MNHN-IM-2019-26526 |
Acknowledgments
We are grateful for specimens and support from Lisa Kirkendale and Corey Whisson at the Western Australian Museum, and collecting assistance from Henry Carrick for Plocamopherus ceylonicus. We also thank Rachel Colin for supporting field work in Bocas del Toro, Panama and facilitating export and collecting permits and Philippe Bouchet for the invitation to participate in the specimens “Our Planet Reviewed”—New Caledonia expeditions (2018–2019), a joint project of MNHN and Conservatoire d’Espaces Naturels (CEN) de Nouvelle-Calédonie.
Funding
Funding was provided by Iridian Genomes grant# IRGEN_RG_2021-1345: Genomic Studies of Eukaryotic Taxa. Field work in Australia was funded by the American Museum of Natural History, and work in New Caledonia was funded by the Gouvernement de la Nouvelle-Calédonie, Province Nord, Agence Française de la Biodiversité (AFB), the Lounsbery Foundation, and Office des Postes et Télécommunications (OPT).
REFERENCES
- Bankevich Anton, Nurk Sergey, Antipov Dmitry, Gurevich Alexey A., Dvorkin Mikhail, Kulikov Alexander S., Lesin Valery M., et al. 2012. “SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.” Journal of Computational Biology 19 (5): 455–77. 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bolger Anthony M., Lohse Marc, and Usadel Bjoern. 2014. “Trimmomatic: A Flexible Trimmer for Illumina Sequence Data.” Bioinformatics 30 (15): 2114–20. 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kieras M, O’Neill K, and Pirro S. 2021. Zanfona, a genome assembly finishing tool for paired-end Illumina reads. https://github.com/zanfona734/zanfona. [Google Scholar]
- Western Australian Museum. 2023. “Western Australian Museum Provider for OZCAM.” 10.15468/5qt0dm. [DOI] [Google Scholar]