Chromosome-level genome assembly of the blue crab,Callinectes sapidus

Abstract

The blue crab, Callinectes sapidus (Rathbun, 1896) is an economically, culturally, and ecologically important species found across the temperate and tropical North and South American Atlantic coast. A reference genome will enable research for this high-value species. Initial assembly combined 200x coverage Illumina paired-end reads, a 60x 8 kb mate-paired library, and 50x PacBio data using the MaSuRCA assembler resulting in a 985 Mb assembly with a scaffold N50 of 153 kb. Dovetail Chicago and HiC sequencing with the 3d DNA assembler and Juicebox assembly tools were then used for chromosome scaffolding. The fifty largest scaffolds span 810 Mb are 1.5 to 37 Mb long and have a repeat content of 36%. The 190 Mb unplaced sequence is in 3921 sequences over 10kb with a repeat content of 68%. The final assembly N50 is 18.9 Mb for scaffolds and 9317 bases for contigs. Of arthropod BUSCO, ∼88% (888/1,013) were complete and single copies. Using 309 million RNAseq read pairs from 12 different tissues and developmental stages, 25,249 protein-coding genes were predicted. Between C. sapidus and Portunus trituberculatus genomes, 41 of 50 large scaffolds had high nucleotide identity and protein-coding synteny, but nine scaffolds in both assemblies were not clear matches. The protein-coding genes included 9423 one-to-one putative orthologs, of which 7165 were syntenic between the two crab species. Overall, the two crab genome assemblies show strong similarities at the nucleotide, protein, and chromosome level and verify the blue crab genome as an excellent reference for this important seafood species.

A Haplotype-resolved, Chromosome-scale Genome for Malus domestica 'WA 38'

“…As expected, in the CROG gene count clustermap (Supplemental Figure S6), ‘WA 38’ clustered closely with ‘Honeycrisp’. The ‘WA 38’ + ‘Honeycrisp’ group is clustered with other apple genomes, including a recently published ‘Antonovka’ genome (Švara et al 2023) and the ‘Gala’ genome (Sun et al 2020), indicating similar gene counts in a vast majority of orthogroups among M. domestica cultivars. The CROG gene count z -score box plot shows (Supplemental Figure S7) that the average z -score of ‘WA 38’ gene counts are slightly higher than expected (with 0 as the perfect score), indicating that there are a number of CROGs containing more genes from the ‘WA 38’ annotations compared to other apples.…”

“…Gene family analysis is performed using PlantTribes2 and the pre-constructed 26Gv2-scaffold orthogroup database (Wafula et al 2022). Out of the 18,110 pre-constructed orthogroups, proteins from all apple annotations [5 published genomes (‘Honeycrisp’ (Khan et al 2022), ‘Gala’ (Sun et al 2020), ‘Hanfu’ (L. Zhang et al 2019), ‘Antonovka’ (Švara et al 2023), and the GDDH13 ‘Golden Delicious’ (Daccord et al 2017) genomes) and the ‘WA 38’ genome from this work] are found in 11,671 orthogroups. ‘Golden Delicious’ Genome v1.0 (Velasco et al 2010) was omitted from this analysis due to poor annotation quality.…”

Genomic Analyses Implicate the Amazon–Orinoco Plume as the Driver of Cryptic Speciation in a Swimming Crab

“…Raw sequence files were demultiplexed (--inline-index), cleaned (-c), quality-filtered (q), and rescued (-r), allowing two mismatches using the process_radtags program in STACKS v.2.3d [ 50 ]. Short reads were indexed and aligned to the blue crab ( Callinectes sapidus ) reference genome (Csap_IMET_V1, [ 51 ]) using Burrow–Wheller Aligner (BWA-MEM) v. 0.7.17 [ 52 , 53 , 54 ] with default settings. Generated SAM files were converted to BAM files using SAMtools v.1.9 [ 55 ].…”

Recent advances in crustacean genomics and their potential application in aquaculture

“…With the development of sequencing platforms and assembly algorithms, the newly upgraded genomes will solve many problems in chromosome Shrimp, crayfish and crabs are the most economically relevant crustaceans. However, most of their genomes still have short contig N50 lengths, e.g., Penaeus vannamei (57.65 Kb), 13 Penaeus monodon (45.08 Kb), 173,174 Procambarus virginalis (745 bp), 84 Cherax quadricarinatus (3.29 Kb), 122 Homarus americanus (133.31 Kb), 67 P. carinicauda (816 bp), 54 Eriocheir sinensis (26.05 Kb), 31 Callinectes sapidus (14.31 Kb), 175 and Paralithodes platypus (147.47 Kb). 56 Although the N50 contig length does not represent the overall quality of the genome, a long contig N50 not only indicates high continuity but also high genome integrity.…”