No abstract

The Pacific white shrimp Litopenaeus vannamei is among the top aquatic species of commercial importance around the world. Over the last four decades, the breeding works of L. vannamei have been carried out intensively and have generated multiple strains with improved production and performance traits. However, signatures of domestication and artificial selection across the L. vannamei genome remain largely unexplored. In the present study, we conducted whole genomic resequencing of 180 Pacific white shrimps from two artificially selective breeds and four market-leading companies. A total of 37 million single nucleotide polymorphisms (SNPs) were identified with an average density of 22.5 SNPs/Kb across the genome. Ancestry estimation, principal component analysis, and phylogenetic inference have all revealed the obvious stratifications among the six breeds. We evaluated the linkage disequilibrium (LD) decay in each breed and identified the genetic variations driven by selection. Pairwise comparison of the fixation index (Fst) and nucleotide diversity (θπ) has allowed for mining the genomic regions under selective sweep in each breed. The functional enrichment analysis revealed that genes within these regions are mainly involved in the cellular macromolecule metabolic process, proteolysis, structural molecule activity, structure of the constituent ribosome, and responses to stimulus. The genome-wide SNP datasets provide valuable information for germplasm resources assessment and genome-assisted breeding of Pacific white shrimps, and also shed light on the genetic effects and genomic signatures of selective breeding.

It is of vital importance to understand the population structure, dissect the genetic bases of performance traits, and make proper strategies for selection in breeding programs. However, there is no single webserver covering the specific needs in aquaculture. We present Aquaculture Molecular Breeding Platform (AMBP), the first web server for genetic data analysis in aquatic species of farming interest. AMBP integrates the haplotype reference panels of 18 aquaculture species, which greatly improves the accuracy of genotype imputation. It also supports multiple tools to infer genetic structures, dissect the genetic architecture of performance traits, estimate breeding values, and predict optimum contribution. All the tools are coherently linked in a web-interface for users to generate interpretable results and evaluate statistical appropriateness. The webserver supports standard VCF and PLINK (PED, MAP) files, and implements automated pipelines for format transformation and visualization to simplify the process of analysis. As a demonstration, we applied the webserver to Pacific white shrimp and Atlantic salmon datasets. In summary, AMBP constitutes comprehensive resources and analytical tools for exploring genetic data and guiding practical breeding programs. AMBP is available at http://mgb.qnlm.ac.

Dwarf surf clam, Mulinia lateralis, is widely considered as a model species for bivalves. The development of a standard culture system could greatly promote the production of high-quality individuals, yet information on the culture conditions for M. lateralis spat is still limited. This study aims to determine the suitable microalgae diet, temperature, and salinity for M. lateralis spat culture. The typically fed microalgae species, including Chlorella pyrenoidesa (Cp), Platymonas helgolandica (Ph), Dunaliella salina (Ds), Nitzschia closterium (Nc), and Chaetoceros muelleri (Cm), could be taken up by M. lateralis spat, and their filtration rates on Cp, Nc, and Cm were higher than those on Ds and Ph. For the entire spat culture, all diet trials showed similar survival percentages, while the mono-specific diet Cp exhibited the highest growth rate, suggesting that Cp was the optimal microalgae species for M. lateralis spat. Through simultaneously maximizing the growth and survival of spat, the optimal microalgae concentration and stocking density were 5 × 104 cells ml–1 and 400–600 individuals m–2 for 30–40-day-old spat as well as 1 × 105 cells ml–1 and 400–600 individuals m–2 for 40–50-day-old spat, respectively. In addition, the spat had higher growth rates and survival percentages at the temperature of 20–22°C and salinity of 22–25 ppt. The results of this study provide a basis for further culture of M. lateralis spat, and the optimized conditions will be of great significance for the construction of the standard culture system of M. lateralis.

Mulinia lateralis (Say, 1822) is a species of the bivalve family Mactridae and represents a promising model species for molluscan research. In this study, the complete mitochondrial genome (mitogenome) of M. lateralis was sequenced and assembled for the first time. The 21,668 bp mitogenome contained 13 protein-coding genes, 2 rRNAs, 22 tRNA genes, and an AT-rich region. The overall AT content (69.56%) was higher than GC content (30.44%). Phylogenetic analysis supported that M. lateralis belongs to the family Mactridae. The mitochondrial genome of M. lateralis provides a valuable resource for further understanding the phylogeny of the family Mactridae and for functional studies of molluscan mitochondrial genes.