Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper ( Plectropomus leopardus).

The leopard coral grouper ( Plectropomus leopardus) is a species of significant economic importance. Although artificial cultivation of P. leopardus has thrived in recent decades, the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data. In this study, we identified over 8.73 million single nucleotide polymorphisms (SNPs) through whole-genome resequencing of 326 individuals spanning six distinct groups. Furthermore, we categorized 226 individuals with high-coverage sequencing depth (≥14×) into eight clusters based on their genetic profiles and phylogenetic relationships. Notably, four of these clusters exhibited pronounced genetic differentiation compared with the other populations. To identify potentially advantageous loci for P. leopardus, we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity ( θπ) and fixation index ( F ST) in these four clusters. Using these high-coverage resequencing data, we successfully constructed the first haplotype reference panel specific to P. leopardus. This achievement holds promise for enabling high-quality, cost-effective imputation methods. Additionally, we combined low-coverage sequencing data with imputation techniques for a genome-wide association study, aiming to identify candidate SNP loci and genes associated with growth traits. A significant concentration of these genes was observed on chromosome 17, which is primarily involved in skeletal muscle and embryonic development and cell proliferation. Notably, our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs, showing potential for genetic selective breeding efforts. These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P. leopardus.

Signatures of selection in Mulinia lateralis underpinning its rapid adaptation to laboratory conditions.

The dwarf surf clam, Mulinia lateralis, is considered as a model species for bivalves because of its rapid growth and short generation time. Recently, successful breeding of this species for multiple generations in our laboratory revealed its acquisition of adaptive advantages during artificial breeding. In this study, 310 individuals from five different generations were genotyped with 22,196 single nucleotide polymorphisms (SNPs) with the aim of uncovering the genetic basis of their adaptation to laboratory conditions. Results revealed that M. lateralis consistently maintained high genetic diversity across generations, characterized by high observed heterozygosity (H o: 0.2733-0.2934) and low levels of inbreeding (F is: -0.0244-0.0261). Population analysis indicated low levels of genetic differentiation among generations of M. lateralis during artificial breeding (F st <0.05). In total, 316 genomic regions exhibited divergent selection, with 168 regions under positive selection. Furthermore, 227 candidate genes were identified in the positive selection regions, which have functions including growth, stress resistance, and reproduction. Notably, certain selection signatures with significantly higher F st value were detected in genes associated with male reproduction, such as GAL3ST1, IFT88, and TSSK2, which were significantly upregulated during artificial breeding. This suggests a potential role of sperm-associated genes in the rapid evolutionary response of M. lateralis to selection in laboratory conditions. Overall, our findings highlight the phenotypic and genetic changes, as well as selection signatures, in M. lateralis during artificial breeding. This contributes to understanding their adaptation to laboratory conditions and underscores the potential for using this species to explore the adaptive evolution of bivalves.

Aquaculture Molecular Breeding Platform (AMBP): a comprehensive web server for genotype imputation and genetic analysis in aquaculture.

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.

Post-processing method for the removal of mixed ring artifacts in CT images.

Ring artifacts seriously deteriorate the quality of CT images. Intensity-dependence of detector responses will result in intensity-dependent ring artifacts and time-dependence of CT hardware systems will result in time-dependent ring artifacts. However, only the intensity-dependent ring artifacts are taken into consideration in most post-processing methods. Therefore, the purpose of this study is to propose a general post-processing method, which has a significant removal effect on the intensity-dependent ring artifacts and the time-dependent ring artifacts. First in the proposed method, transform raw CT images into polar coordinate images, and the ring artifacts will manifest as stripe artifacts. Secondly, obtain structure images by smoothing the polar coordinate images and acquire texture images containing some details and stripe artifacts by subtracting the structure images from the polar coordinate images. Third, extract the stripe artifacts from the texture images using mean extraction and texture classification, and obtain the extracted ring artifacts by transforming the extracted stripe artifacts from polar coordinates into Cartesian coordinates. Finally, obtain corrected CT images by subtracting the extracted ring artifacts from the raw CT images, and iterate the corrected CT images in above steps until the ring artifacts extracted in the last iteration are weak enough. Simulation and real data show that the proposed method can remove the intensity-dependent ring artifacts and the time-dependent ring artifacts effectively while preserving image details and spatial resolution. In particular, real data prove that the method is suitable for new CT systems such as the photon counting CT.

The complete mitochondrial genome and phylogenetic analysis of Hiatella sp. J (Mollusca: Hiatellidae).

The genus Hiatella is one of most abundant and widespread marine bivalves. To date, its intra-generic phylogeny remains disputed and mitogenome information is therefore much needed. Here, we first report the complete circular mitogenome of Hiatella sp. J that is distributed in the coast of Asia Pacific. The total length of this mitochondrial genome is 21,233 base pairs. It consists of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a major noncoding region (MNR). Phylogenetic analysis of COI from 25 species (Hiatellidae) revealed that the Hiatella sp. J was closely related to Asian Hiatella in the family Hiatellidae. This Hiatella mitogenome provides new molecular data for the further taxonomic and phylogenetic studies of the genus Hiatella of marine bivalves.

The complete mitochondrial genome and phylogenetic analysis of the dwarf surf clam Mulinia 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.