Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence

Abstract Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of endogenous viral elements. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for 1 generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identif..., Shrimp breeding and selection for sequencing:
A second-generation (G2) male Penaeus monodon that had undergone a single cycle of inbreeding was selected for genomic sequencing. The original wild-caught broodstock were collected from a Queensland east coast location (approximately 17.3°S, 146.0°E) in September 2013. In October 2013, 14 first-generation (G1) families were produced from the brood stock at Seafarm Flying Fish Point hatchery (approximately 17.5°S, 146.1°E). In February 2015, pleopod tissue was sampled from 50 female and 50 male G1 broodstock. These tissues were genotyped (using 2 x 60 SNP panels (Sellars et al. 2014) to identify the parental origin of each broodstock and to select related mating pairs to generate the inbred G2 progeny. In August 2015, groups of 50 juvenile males from 5 inbred G2 families were euthanized to collect muscle tissue from the first abdominal segment for sequencing and the second most anterior pair of pleopods for genotyping. These tissues, as well..., This file contains the genome annotation of the Australian Penaeus monodon genome deposited on NCBI.

Raw and assembled sequence data generated by this study have been deposited in GenBank BioProject PRJNA590309, BioSample SAMN13324362. PacBio and Illumina raw data can be found under accession numbers SRR10713990-SRR10714025. The final scaffolded assembly can be found under accession JAAFYK000000000. RNA-seq data used for annotation originated from an earlier study (Huerlimann et al. 2018).