A chromosome-level genome assembly for the Pacific oyster ( Crassostrea gigas )
This article has been Reviewed by the following groups
Discuss this preprint
Start a discussion What are Sciety discussions?Listed in
- Evaluated articles (GigaScience)
Abstract
The Pacific oyster ( Crassostrea gigas ) is a marine bivalve species 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. In the current study, high coverage long and short read sequence data generated on Pacific Biosciences and Illumina platforms from a single female individual specimen was used to generate an initial assembly, which was then scaffolded into 10 pseudo chromosomes using both Hi-C sequencing and a high density SNP linkage map. The final 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. The new assembly was annotated using Pacific Biosciences Iso-Seq and Illumina RNA-Seq data, identifying 30K putative protein coding genes, with an average of 3.9 transcripts per gene. Annotation of putative repeat elements highlighted an inverse relationship with gene density, and identified putative centromeres of the metacentric chromosomes. An enrichment of Helitron rolling circle transponsable elements was observed, suggesting their potential role in shaping the evolution of the C. gigas genome. 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 genetic improvement of C. gigas in aquaculture breeding programmes.
Article activity feed
-
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
-
