scholarly journals High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas

2020 ◽  
Vol 10 (12) ◽  
pp. 4691-4705
Author(s):  
Xiaoshen Yin ◽  
Alberto Arias-Pérez ◽  
Tevfik Hamdi Kitapci ◽  
Dennis Hedgecock
Keyword(s):  
Genome Assembly ◽  
Crassostrea Gigas ◽  
Pacific Oyster ◽  
Genotyping By Sequencing ◽  
Biological Knowledge ◽  
Linkage Maps ◽  
Nucleotide Polymorphisms ◽  
Linkage Groups ◽  
The Pacific ◽  
Chromosome Level

Studies of linkage and linkage mapping have advanced genetic and biological knowledge for over 100 years. In addition to their growing role, today, in mapping phenotypes to genotypes, dense linkage maps can help to validate genome assemblies. Previously, we showed that 40% of scaffolds in the first genome assembly for the Pacific oyster Crassostrea gigas were chimeric, containing single nucleotide polymorphisms (SNPs) mapping to different linkage groups. Here, we merge 14 linkage maps constructed of SNPs generated from genotyping-by-sequencing (GBS) methods with five, previously constructed linkage maps, to create a compendium of nearly 69 thousand SNPs mapped with high confidence. We use this compendium to assess a recently available, chromosome-level assembly of the C. gigas genome, mapping SNPs in 275 of 301 contigs and comparing the ordering of these contigs, by linkage, to their assembly by Hi-C sequencing methods. We find that, while 26% of contigs contain chimeric blocks of SNPs, i.e., adjacent SNPs mapping to different linkage groups than the majority of SNPs in their contig, these apparent misassemblies amount to only 0.08% of the genome sequence. Furthermore, nearly 90% of 275 contigs mapped by linkage and sequencing are assembled identically; inconsistencies between the two assemblies for the remaining 10% of contigs appear to result from insufficient linkage information. Thus, our compilation of linkage maps strongly supports this chromosome-level assembly of the oyster genome. Finally, we use this assembly to estimate, for the first time in a Lophotrochozoan, genome-wide recombination rates and causes of variation in this fundamental process.

scholarly journals A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas

GigaScience ◽  
2021 ◽  
Vol 10 (3) ◽  
Author(s):  
Carolina Peñaloza ◽  
Alejandro P Gutierrez ◽  
Lél Eöry ◽  
Shan Wang ◽  
Ximing Guo ◽  
...  
Keyword(s):  
Crassostrea Gigas ◽  
Pacific Oyster ◽  
Sequence Data ◽  
High Coverage ◽  
Protein Coding ◽  
Rolling Circle ◽  
Repeat Elements ◽  
Pacific Biosciences ◽  
The Pacific ◽  
Chromosome Level

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.

scholarly journals A chromosome-level genome assembly for the Pacific oyster (Crassostrea gigas)

2020 ◽  
Author(s):  
Carolina Peñaloza ◽  
Alejandro P. Gutierrez ◽  
Lel Eory ◽  
Shan Wang ◽  
Ximing Guo ◽  
...  
Keyword(s):  
Crassostrea Gigas ◽  
Pacific Oyster ◽  
Sequence Data ◽  
Gene Annotation ◽  
Marine Bivalve ◽  
High Coverage ◽  
Rolling Circle ◽  
Pacific Biosciences ◽  
The Pacific ◽  
Chromosome Level

AbstractThe 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.

scholarly journals Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds

2015 ◽  
Vol 5 (10) ◽  
pp. 2007-2019 ◽  
Author(s):  
Dennis Hedgecock ◽  
Grace Shin ◽  
Andrew Y. Gracey ◽  
David Van Den Berg ◽  
Manoj P. Samanta
Keyword(s):  
Crassostrea Gigas ◽  
Second Generation ◽  
Pacific Oyster ◽  
Linkage Maps ◽  
The Pacific

scholarly journals Fixation, Segregation and Linkage of Allozyme Loci in Inbred Families of the Pacific Oyster Crassostrea gigas (Thunberg): Implications for the Causes of Inbreeding Depression

Genetics ◽  
1997 ◽  
Vol 146 (1) ◽  
pp. 321-334 ◽  
Author(s):  
Daniel J McGoldrick ◽  
Dennis Hedgecock
Keyword(s):  
Crassostrea Gigas ◽  
Pacific Oyster ◽  
Segregation Ratio ◽  
Significant Heterogeneity ◽  
Linkage Groups ◽  
Likelihood Ratios ◽  
The Pacific ◽  
Log Likelihood ◽  
Segregation Ratios ◽  
Allozyme Loci

The effect that inbreeding has on the fixation and segregation of genes has rarely been confirmed by direct observation. Here, fixation, segregation, and linkage of allozymes is investigated in the progeny of self-fertilized hermaphrodites of the normally outcrossing Pacific oyster Crassostrea gigas. The estimate of fixation pooled over loci, individuals, and families, F = 0.462, is significantly lower than the expected value of 0.5. Log-likelihood ratios reveal significant heterogeneity in fixation among individuals, among families, and among loci. In addition, the grand pooled segregation ratio, 127:243:54, deviates significantly from 1:2:1, with a bias against homozygotes for alleles of lesser frequency in the natural population. Segregation ratios for 11 of 14 loci are significantly heterogeneous among families, and exact tests for segregation within families reveal 16 significant results out of 51 tests. Thus, fixation and segregation of allozyme markers in inbred oyster families deviates from the expectations of neutral inbreeding theory. Di-genic disequilibria are significant for four of 74 di-locus pairs revealing two linkage groups. Strong viability selection is apparently conditional on the genotype of the hermaphrodite-founders and is largely focused on these two linkage groups. These genetic effects are explained by interaction between cis-linked factors and polymorphic regulatory backgrounds.

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