A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas
Carolina Peñaloza,Alejandro P. Gutierrez,Lel Eory,Shan Wang,Ximing Guo,Alan Archibald,Tim P. Bean,Ross D. Houston +7 more
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TLDR
In this paper, the authors report the creation and annotation of a chromosome-level assembly for C. gigas, which was then scaffolded into 10 pseudo-chromosomes using both Hi-C sequencing and a high-density linkage map.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.read more
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Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity
Ao Li,He Dai,Ximing Guo,Ziyan Zhang,Kexin Zhang,Chaogang Wang,Xinxing Wang,Wei Wang,Hongju Chen,Xumin Li,Hongkun Zheng,Li Li,Guofan Zhang +12 more
TL;DR: In this article, a chromosome-level assembly and resequencing of individuals across wide latitude distribution in the estuarine oyster (Crassostrea ariakensis) revealed unexpectedly low genomic diversity and population structures shaped by historical glaciation, geological events and oceanographic forces.
Journal ArticleDOI
Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks
Sarah Farhat,Eric Bonnivard,Emmanuelle Pales Espinosa,Arnaud Tanguy,Isabelle Boutet,Nadège Guiglielmoni,Jean-François Flot,Bassem Allam +7 more
TL;DR: A 1.86 Gb chromosome-level assembly of the hard clam Mercenaria mercenaria was generated using a combination of long and short-read sequencing technologies, with an N50 of 83 Mb as discussed by the authors .
Journal ArticleDOI
Chromosome‐level reference genome for European flat oyster (Ostrea edulis L.)
Manu Kumar Gundappa,Carolina Peñaloza,Tim Regan,Isabelle Boutet,Arnaud Tanguy,Ross D. Houston,Tim P. Bean,Daniel J. Macqueen +7 more
TL;DR: A chromosome-level assembly and annotation for the European Flat oyster genome is reported, generated using Oxford Nanopore, Illumina, Dovetail OmniC™ proximity ligation and RNA sequencing, and improves the understanding of bivalve genome evolution.
Journal ArticleDOI
Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks
Sarah Farhat,Eric Bonnivard,Emmanuelle Pales Espinosa,Arnaud Tanguy,Isabelle Boutet,Nadège Guiglielmoni,Jean-François Flot,Bassem Allam +7 more
TL;DR: A 1.86 Gb chromosome-level assembly of the hard clam Mercenaria mercenaria was generated using a combination of long and short-read sequencing technologies, with an N50 of 83 Mb as mentioned in this paper .
Journal ArticleDOI
Genome-wide association study toward efficient selection breeding of resistance to Vibrio alginolyticus in Pacific oyster, Crassostrea gigas
TL;DR: A genome wide association study in the Pacific oyster to identify genetic loci underlying resistance to bacterial Vibrios, a major group of pathogens in the ocean, revealed polygenic architecture of resistance traits, and identified 178 genes involved in various processes of immune response.
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