RT Journal Article
SR Electronic
T1 A chromosome-level genome assembly for the Pacific oyster (<em>Crassostrea gigas</em>)
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.09.25.313494
DO 10.1101/2020.09.25.313494
A1 Carolina Peñaloza
A1 Alejandro P. Gutierrez
A1 Lel Eory
A1 Shan Wang
A1 Ximing Guo
A1 Alan L. Archibald
A1 Tim P. Bean
A1 Ross D. Houston
YR 2020
UL http://biorxiv.org/content/early/2020/09/25/2020.09.25.313494.abstract
AB 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.Competing Interest StatementThe authors have declared no competing interest.bpbase pairsBQbase qualityBUSCOBenchmarking Universal Single-Copy OrthologscMcentimorgancDNAcoding DNADNAdeoxyribonucleic acidGbgiga base pairsGCguanine-cytosineGbgigabase pairskbkilobase pairsKEGGKyoto encyclopedia of genes and genomesMAPQmapping qualityMbmegabase pairsN50median sizePacBioPacific BiosciencesRNAribonucleic acidRNA-SeqRNA-sequencingSMRTsingle-molecule real-time