Nuclear genomes of Birgus latro, Paralithodes camtschaticus, and Panulirus ornatus

Veldsman, Werner Pieter; Yan, Ke; Hui, Jerome H.L.; Chan, Ting Fung; Baeza, Antonio J.; Qin, Jing; Chu, Ka Hou

doi:10.5281/zenodo.4589425

Cited by 1 publication

(4 citation statements)

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“…Raw and trimmed data were inspected using FastQC [63] and MultiQC [64]. Reads were aligned to the draft Red king crab (Paralithodes camtschaticus) genome (Genbank accession GCA_018397895.1) [65,66] using Bowtie2 v2.4.2 with the preset option-sensitive [67,68]. The number of fragments aligning to gene coding regions of the P. camtschaticus genome was quantified using featureCounts v2.0.3 [69] with settings -p-countReadPairs to count paired-end fragments and -C and -B to exclude chimeras and singletons, respectively.…”

Section: Bioinformaticsmentioning

confidence: 99%

“…The number of fragments aligning to gene coding regions of the P. camtschaticus genome was quantified using featureCounts v2.0.3 [69] with settings -p-countReadPairs to count paired-end fragments and -C and -B to exclude chimeras and singletons, respectively. Gene functions were identified by querying coding sequences of the P. camtschaticus genome, derived from gene annotations published along with the P. camtschaticus genome [66], against the Uniprot/Swissprot database [70] using blastx from blast v2.11.0 (e-value < 1 −10 ) [71].…”

Section: Bioinformaticsmentioning

confidence: 99%

“…A total of ~2.65B paired-end reads (henceforth "fragments") remained after discarding ~4.55M (0.17%) during initial quality-filtering, with a per-sample mean of 61.7M +/-10.7M fragments. Across all samples ~2.14B reads were aligned to the P. camtschaticus draft genome [65,66], for a total alignment rate of 80.47%. The average per-sample alignment rate was 80.43%±2.15%, which included 43.19%±1.50% and 24.52%±0.89% of concordantly mapped fragments that mapped uniquely and multiple times, respectively.…”

Section: Rna-seq Pre-processing For Gene Expression Analysismentioning

confidence: 99%

“…Initial examination of the gene counts using PCA identified one sample from the ambient pH treatment as an outlier, which was removed from the dataset and resulted in 14, 13, and 15 samples for the ambient, moderate, and severe OA treatments, respectively (Table 1). In total, we detected all 162,611 gene features that are in the draft P. camtschaticus genome [66], but after removing low frequency genes (totaling 0.75% of fragments), 74,778 genes remained for analysis, 32,435 of which mapped to genes in the Uniprot/Swissprot database. The high number of genes to which reads mapped reflects the large P. camtschaticus draft genome, which includes a high degree of repeat elements characteristic of crustacean genomes [65].…”

Section: Plos Climatementioning

confidence: 99%

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Narrowed gene functions and enhanced transposon activity are associated with high tolerance to ocean acidification in a juvenile subarctic crustacean

Spencer,

Long,

Spies

et al. 2024

PLOS Clim

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Ocean acidification (OA) threatens marine crustaceans, particularly those at high latitudes where conditions are rapidly changing. Red king crab (RKC) support important fisheries in Alaskan waters. RKC early life stages are sensitive to OA when exposure occurs as embryos and juveniles. However, in a supporting study, RKC were surprisingly tolerant of varying OA conditions (pH 7.5, 7.8, & 8.0) when reared long-term from larval hatching to the first crab stage (C1). Here, we examined gene expression in the C1 juveniles to characterize transcriptional activity of these OA-tolerant crabs. Expression of nearly half of all genes (44%) correlated with OA treatment, suggesting a strong molecular response to OA, contrary to the phenotypic results. Downregulated functions were numerous in response to OA, and included reduced energy production, biosynthesis, immune function, and notably lipid and carbohydrate metabolic processes, which suggest a shift in metabolic strategy to protein catabolism, possibly to reduce CO2 production and facilitate acid/base regulation. Only a handful of functions were enriched in OA-induced genes, which were related to transcription regulation, control of growth and cell death, and signaling activity. Transposon activity was high in OA-reared crab, many of which were upregulated at consistent levels, suggesting that transposon mobilization may be a component of the RKC OA-response system. Genetic composition did not differ among OA treatments indicating that transcriptional differences in OA-reared crab were more likely attributed to phenotypic plasticity than selective mortality. Our results suggest that OA-reared RKC have a narrowed, possibly optimized, set of gene functions that enables OA-tolerance through the early juvenile stage. OA-exposure from hatch may benefit RKC and related species by “hardening” them against OA through physiological reprogramming. Future studies should test OA-hardened crabs in additional challenges, as metabolic and immune limitations may ultimately make them more vulnerable to infection or secondary stressors.

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