Improved genomic resources for the black tiger prawn (Penaeus monodon)

First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes

“…We assessed the contiguity of the three de novo ostracod genome assemblies by the number of scaffolds and their N50. Both features are comparable to those of the copepod Apocylops royi ( Jørgensen et al 2019 ) and the amphipod Parhyale hawaiensis ( Kao et al 2016 ) ( Table 1 ) and better than for crustaceans with larger genomes such as the decapods Cherax quadricarinatus ( Tan et al 2020 ), Palaeomon carinicauda ( Li et al 2019 ), Penaeus mondon ( Van Quyen et al 2020 ), Marsupenaeus japonicus ( Yuan et al 2018 ), and Procamburus virginalis ( Gutekunst et al 2018 ; Table 1 ). Genome assemblies of several other crustaceans, however, have smaller scaffold numbers and higher N50 and thus better contiguities than the assemblies obtained here for nonmarine ostracods.…”

A Giant Genome for a Giant Crayfish (Cherax quadricarinatus) With Insights Into cox1 Pseudogenes in Decapod Genomes

“…This assembly is available on NCBI (BioProject: PRJNA559771, WGS: VSFE00000000). It is noteworthy that this study has incorporated the largest dataset of long Nanopore reads to date for a decapod genome assembly (36 Gbp, ∼7×), the other being the recent updated assembly of the black tiger prawn genome that incorporated the use of 2.5 Gbp of long Nanopore reads (∼1.25×) (Van Quyen et al, 2020). The only other study to use long reads in decapod whole genome research is by Zhang et al (2019) who utilized PacBio reads to support the assembly of the genome for the Pacific white shrimp L. vannamei.…”

“…The genetics of C. quadricarinatus has been well studied using PCR-based approaches and recently, next generation sequencing has been used for mitogenomic and transcriptomic studies (Baker et al, 2008;Gan et al, 2016;Tan et al, 2016). In this paper, we present the first genome assembly for a southern hemisphere crayfish using a hybrid assembly approach utilizing long Nanopore reads and short Illumina reads, which has proven to be an efficient and effective approach for the assembly and annotation of species with large and repetitive genomes (Austin et al, 2017;Tan et al, 2018;Gan et al, 2019;Sánchez-Herrero et al, 2019), but has only been minimally explored to support decapod assemblies (Van Quyen et al, 2020).…”

Gonadulins, the fourth type of Insulin-related peptides in Decapods

“…A list of all SRAs used can be found in the supplementary data. Draft genome assembliess for the following species have been used : Penaeus vannamei (Zhang et al, 2019), P. monodon (Van Quyen et al, 2020), Palaemon carinicauda (Yuan et al, 2017), Procambarus virginalis (Gutekunst et al, 2018), Cherax quadricarinatus (unpublished, but available at https://www.ncbi.nlm.nih.gov/assembly/GCA_009761615.1/), and two assemblies each for Eriocheir sinensis (Song et al, 2016;Tang et al, 2020b) and Portunus trituberculataus (https://www.ncbi.nlm.nih.gov/assembly/GCA_008373055.1/; Tang et al, 2020a).…”