Genome survey sequencing of the Caribbean spiny lobsterPanulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery

Abstract

Background Panulirus argus is an ecologically relevant species in shallow water hard-bottom environments and coral reefs and target of the most lucrative fishery in the greater Caribbean region. Methods This study reports, for the first time, the genome size and nuclear repetitive elements, including the 45S ribosomal DNA operon, 5S unit, and microsatellites, of P. argus. Results Using a k-mer approach, the average haploid genome size estimated for P. argus was 2.17 Gbp. Repetitive elements comprised 69.02% of the nuclear genome. In turn, 30.98% of the genome represented low- or single-copy sequences. A considerable proportion of repetitive sequences could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to Class I-LINE which were noticeably more abundant than Class I-LTR-Ty- 3/Gypsy, Class I-LTR-Penelope, and Class I-LTR-Ty-3/Bel-Pao elements. Satellite DNA was also abundant. The ribosomal operon in P. argus comprises, in the following order, a 5′ ETS (length = 707 bp), ssrDNA (1,875 bp), ITS1 (736 bp), 5.8S rDNA (162 bp), ITS2 (1,314 bp), lsrDNA (5,387 bp), and 3′ ETS (287 bp). A total of 1,281 SSRs were identified.

A first genome survey sequencing of alvinocaridid shrimp Shinkaicaris leurokolos in deep-sea hydrothermal vent environment

“…Long interspersed nuclear elements (LINEs) were the most common among the TEs, accounting for 10.45%, followed by DNA transposons (6.09%) and long-terminal repeat elements (LTRs) (4.79%) (Table 4). These repetitive elements, including LINEs, DNA and LTRs, also take up a large proportion of genomes in many other decapod crustaceans (Baeza, 2020; Tang et al ., 2020; Chak et al ., 2021; Uengwetwanit et al ., 2021). However, it has been suggested that the ‘unclassified’ TEs with a large proportion may contain species-specific variants of known repetitive elements, and we should be cautious when comparing these datasets directly with those of other species (Murgarella et al ., 2016).…”

“…Genome survey sequencing (GSS) using next-generation sequencing is currently an important and cost-effective approach to evaluate genome information such as genome size, GC content, heterozygosity and repeat content, as well as developing molecular markers (Li et al, 2019;Baeza, 2020Baeza, , 2021Baeza et al, 2022;Choi et al, 2021). In the present study, we aimed to estimate the genomic characteristics of S. leurokolos through GSS, identify repetitive elements in the nuclear genome and assemble a complete mitochondrial genome.…”

Complete genome of Vibrio harveyi isolate K2014767 from the hepatopancreas of captive Caribbean spiny lobster ( Panulirus argus )

“…The Caribbean spiny lobster ( Panulirus argus ) inhabits the Atlantic Ocean from North Carolina, USA to Brazil. The largest of the spiny lobsters, P. argus comprises the second-largest lobster fishery in the United States ( 1 – 5 ). Vibrio harveyi is autochthonous to marine habitats and a pathogen of wild and captive marine fish and invertebrates ( 6 – 8 ), with reports of V. harveyi -associated disease in shrimp, crabs, and lobster ( 9 , 10 ).…”