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 (EVEs) 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 EVEs 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 EVEs. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for one 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 identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific EVEs identified an element comprised of a 9,045 bp stretch of repeated, inverted and jumbled genome fragments of Infectious hypodermal and hematopoietic necrosis virus (IHHNV) bounded by a repeated 591/590 bp host sequence. As only near complete linear ∼4 kb IHHNV genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear EVE types. The existence of joined inverted IHHNV genome fragments also provides a means by which hairpin dsRNAs could be expressed and processed by the shrimp RNA interference (RNAi) machinery.

Shrimp genome sequence contains independent clusters of ancient and current Endogenous Viral Elements (EVE) of the parvovirus IHHNV

“…Huerlimann et al [ 15 ] give a detailed analyses of the EVE cluster found on SG97 of their Australian P. monodon specimen plus a detailed comparison of it to the two EVE clusters that they (like us) discovered in PC35 of the Thai P. monodon WGS. Thus, those interested the detailed comparison should consult the Australian publication.…”

“…A recent publication [ 15 ] using DNA extracted from an Australian P. monodon specimen for genome analysis revealed one EVE cluster in their Scaffold group 97 (SG97) with high identity to GenBank EU675312 (i.e., the Australian version of IHHNV-A with 99% sequence identity to DQ228358). Given the information from our earlier publication and from the work reported herein and from the Australian publication, it is likely that the continuous sequence records for DQ228358 and EU675312 at GenBank are assembly artifacts, and that they were obtained from fragmented and scrambled target sequences that had sufficient overlap to result in their assembly into single linear sequences when using the sequence of infectious IHHNV (GenBank record AF218266) as a reference [ 3 , 12 ].…”

White spot syndrome virus endogenous viral elements (EVE) revealed by circular viral copy DNA (cvcDNA) in shrimp

“…We now know that the sequences of the WSSV contigs are very likely an artificial result of the sequence assembly process that uses overlapping small-read sequences assembled against a reference sequence, rather than an actual contiguous sequence in the target genome. This was clearly revealed for EVE of the shrimp virus IHHNV in full shrimp genome sequences developed using long-read technology (Huerlimann et al, 2022; Taengchaiyaphum et al, 2022). The EVE fragments of the IHHNV genome occurred in clusters scrambled (in location and reading direction), some with overlapping sequences that resulted in a cumulative sum of IHHNV-EVE sequence lengths that exceeded the whole IHHNV genome length.…”

“…It has recently been revealed that shrimp EVE may also give rise to cvcDNA that can be selectively isolated and sequenced as a means of screening for EVE in shrimp breeding stocks (Taengchaiyaphum et al, 2021). Based on data from whole genome sequencing of the giant tiger shrimp Penaeus monodon , it has been shown that EVE occur as fragments together with host transposable element sequences in host shrimp piRNA-gene-like clusters bracketed by linear repeats (Huerlimann et al, 2022; Taengchaiyaphum et al, 2022). The viral genome fragments in these clusters are scrambled in terms of reading direction and original genome position and may also redundantly overlap when mapped to the target virus genome.…”

Penaeid Shrimp Chromosome Studies Entering the Post-Genomic Era

“…The high percentage of repetitive sequences and the difficulty of DNA manipulation due to the large amount of mucopolysaccharides and phosphatases were the main reasons for the delay in sequencing and assembling the shrimp genome until 2019 [73,74]. Before the application of third-generation long-reads sequencing technology, many attempts to assemble the shrimp genome with short sequencing reads resulted in highly fragmented assemblies, illustrating the repeatability and complexity of the shrimp genome [1,[74][75][76]. Long-reads sequencing using the PacBio or Nanopore platforms to sequence shrimp DNA has effectively solved the problem of fragmented genome assembly.…”