A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas
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Abstract
Background
The Pacific oyster (Crassostrea gigas) is a bivalve mollusc with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. Herein we report the creation and annotation of a chromosome-level assembly for C. gigas.
Findings
High-coverage long- and short-read sequence data generated on Pacific Biosciences and Illumina platforms were used to generate an initial assembly, which was then scaffolded into 10 pseudo-chromosomes using both Hi-C sequencing and a high-density linkage map. The assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously published C. gigas assembly. Annotation based on Pacific Biosciences Iso-Seq and Illumina RNA-Seq resulted in identification of ∼30,000 putative protein-coding genes. Annotation of putative repeat elements highlighted an enrichment of Helitron rolling-circle transposable elements, suggesting their potential role in shaping the evolution of the C. gigas genome.
Conclusions
This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for selective breeding of C. gigas in aquaculture.
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Now published in GigaScience doi: 10.1093/gigascience/giab020
Carolina Peñaloza 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlejandro P. Gutierrez 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK2Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLel Eory 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this …
Now published in GigaScience doi: 10.1093/gigascience/giab020
Carolina Peñaloza 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlejandro P. Gutierrez 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK2Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLel Eory 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShan Wang 3Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiming Guo 3Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlan L. Archibald 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteTim P. Bean 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRoss D. Houston 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ross D. HoustonFor correspondence: ross.houston@roslin.ed.ac.uk
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab020 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102693 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102694
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