Abstract Coleoids are part of the Cephalopoda class, which occupy an important position in most oceans both at an ecological level and at a commercial level. Nevertheless, some coleoid species are difficult to distinguish with traditional morphological identification in cases when specimens are heavily damaged during collection or when closely related taxa are existent. As a useful tool for rapid species assignment, DNA barcoding may offer significant potential for coleoid identification. Here, we used two mitochondrial fragments, cytochrome c oxidase I and the large ribosomal subunit (16S rRNA), to assess whether 34 coleoids accounting for about one‐third of the Chinese coleoid fauna could be identified by DNA barcoding technique. The pairwise intra‐ and interspecific distances were assessed, and relationships among species were estimated by NJ and Bayesian analyses. High levels of genetic differentiation within Loliolus beka led to an overlap between intra‐ and interspecific distances. All remaining species forming well‐differentiated clades in the NJ and Bayesian trees were identical for both fragments. Loliolus beka possessed two mitochondrial lineages with high levels of intraspecific distances, suggesting the occurrence of cryptic species. This study confirms the efficacy of DNA barcoding for identifying species as well as discovering cryptic diversity of Chinese coleoids. It also lays a foundation for other ecological and biological studies of Coleoidea.
Abstract Background DNA methylation in mammals and insects is influenced by both genetic factors and sex. However, the extent to which these variables affect DNA methylation in molluscs has not been fully explored. Results In this study, we examined the genomic DNA methylation patterns in two genetically distinct oyster strains using whole-genome bisulfite sequencing (WGBS). Our analysis revealed a sex-associated difference in methylation, with females exhibiting more hypo-methylation than males in somatic tissues. Among the two strains, approximately 20,000 differential methylation regions (DMRs) were identified, with half of these DMRs being conserved in the offspring. Moreover, regions with differential methylation in parents typically displayed intermediate methylation levels in their progeny. This observation aligns with the notion that DNA methylation levels in the F1 progeny were consistent with their parents in the consistently methylated regions, suggesting a heritable stability in these epigenetic marks. Conclusions The findings indicate that genome-wide DNA methylation is preserved through generations in oysters, hinting at its potential significance in selective breeding programs. Additionally, the evident gender-specific methylation differences observed in somatic tissues must be considered in oyster epigenetic research.
Pacific oyster is one of the leading species in world aquaculture, but heritability estimation applying mixed-family approach has not been actively pursued. In this study, heritability for growth-related traits in the Pacific oyster was first estimated by creating a single cohort of 45 families in a full-factorial mating design consisting of nine sires and five dams. A total of 270 offspring were analysed and parentage assignment inferred by six microsatellite markers achieved 100% success. All parents contributed to the spawn and a total of 42 full-sib families were represented. Using an animal model, heritability estimates at 12 months of age were 0.49 ± 0.25 for shell height, 0.36 ± 0.19 for shell length, 0.45 ± 0.23 for shell width and 0.35 ± 0.17 for wet weight. Genetic correlation between shell height and wet weight was quite high (0.79 ± 0.25), suggesting that direct selection of shell height, which is an easily measurable trait, also improves wet weight. The results obtained in this study indicate that growth-related traits could be improved by exploiting additive genetic effects through selective breeding.
Summary We present the first genetic maps of the sea cucumber ( Apostichopus japonicus ), constructed with an F 1 pseudo‐testcross strategy. The 37 amplified fragment length polymorphism (AFLP) primer combinations chosen identified 484 polymorphic markers. Of the 21 microsatellite primer pairs tested, 16 identified heterozygous loci in one or other parent, and six were fully informative, as they segregated in both parents. The female map comprised 163 loci, spread over 20 linkage groups (which equals the haploid chromosome number), and spanned 1522.0 cM, with a mean marker density of 9.3 cM. The equivalent figures for the male map were 162 loci, 21 linkage groups, 1276.9 and 7.9 cM. About 2.5% of the AFLP markers displayed segregation distortion and were not used for map construction. The estimated coverage of the genome was 84.8% for the female map and 83.4% for the male map. The maps generated will serve as a basis for the construction of a high‐resolution genetic map and mapping of the functional genes and quantitative trait loci, which will then open the way for the application of a marker‐assisted selection breeding strategy in this species.
Nassarius graniferus is a marine gastropod species in family Nassariidae. In the present study, we firstly determined the complete mitochondrial genome of N. graniferus by next-generation sequencing. The mitochondrial sequence is a circular molecule of 16,417bp in length, with the typical structure of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA genes. The GC% across the genome is 30.7%.
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