Abstract
Penaeid shrimp fishery and culture is a commercial enterprise contributing to employment, nutritional security and foreign exchange of developing countries. The genetic improvement programs being operated in shrimp benefit hugely from genomic resources. We report here a high-quality genome assembly for a penaeid shrimp, Penaeus indicus, which is the only Crustacean assembly to meet the reference standards of 1 and 10 Mb N50 lengths for contigs and scaffolds, respectively, among genomes of >1.5 Gb assembly length. The assembly is 1.93 Gb length (34.4 Mb scaffold N50) with 28,720 protein-coding genes and 49.31% repeat elements. The P. indicus assembly has 31.99% of simple sequence repeats, the highest among sequenced animal genomes. In comparison to other shrimp genomes having short contig lengths, the P. indicus assembly has 346 un-gapped contigs of over 1 Mb length and betters other shrimp genomes on sequence contiguity. This contiguous genome revealed 15,563 coding single nucleotide polymorphisms (SNPs) of which 2,572 are non-synonymous. The assembly and the SNP data resources have applications to genetic improvement programs, evolutionary studies and stock management.
Highlights
Farmed shrimp are important contributors of seafood, provide nutritional security, support employment opportunities and are an export commodity earning foreign exchange for many developing countries
We report 2,572 high quality, non-synonymous coding single nucleotide polymorphisms (SNPs) identified for the first time in a finished genome assembly of shrimp
The generated bam file was sorted using SAMtools v1.2 (Li et al, 2009) and processed in bcftools-1.3.1 (Li, 2011) to generate variant call format (VCF) file. Those SNPs with a raw read depth of ≥20 at SNP site, at least 10 reads each supporting the reference and alternative alleles and phred quality scores of ≥100 were extracted from VCF file as good quality SNPs
Summary
Farmed shrimp are important contributors of seafood, provide nutritional security, support employment opportunities and are an export commodity earning foreign exchange for many developing countries. About 83% of the 6.55 million tonnes of global farmed shrimp production in 2019 (FAO, 2020) is contributed by a single species, Penaeus vannamei. Though P. vannamei is not a native species, several shrimp producing countries are importing the broodstock of this species to breed locally and produce post-larvae required for commercial cultures. Availability of genetically improved and specific pathogen free stocks is the main reason in choosing P. vannamei for shrimp production. Such global dependence on a single species is not an ideal scenario for sustainability of shrimp farming industry. There is a need to develop and promote other shrimp species that have
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