Whole genome sequencing of Crassostrea ariakensis (Mollusca: Ostreidae) and C. hongkongensis expands understandings of stress resistance in sessile oysters.

To understand the environmental adaptations among sessile bivalves lacking adaptive immunity, a series of analyses were conducted, with special emphasis on the widely distributed C. ariakensis. Employing Pacbio sequencing and Hi-C technologies, whole genome for each of a C. ariakensis (southern China) and C. hongkongensis individual was generated, with the contig N50 reaching 6.2 and 13.0 Mb, respectively. Each genome harbored over 30,000 protein-coding genes, with approximately half of each genome consisting of repeats. Genome alignment suggested possible introgression between C. gigas and C. ariakensis (northern China), and re-sequencing data corroborated this result and indicated significant gene flow between C. gigas and C. ariakensis. These introgressed candidates, well-represented by genes related to immunity and osmotic pressure, may be associated with environmental stresses. Gene family dynamics modeling suggested immune-related genes were well represented among the expanded genes in C. ariakensis. These outcomes could be attributed to the spread of C. ariakensis.

iTRAQ and PRM-based quantitative proteomics in T2DM-susceptible and -tolerant models of Bama mini-pig.

Type 2 diabetes mellitus (T2DM) is a complex, multifactorial metabolic disease, and the number of patients with T2DM has continued to increase in recent years. Large-scale proteomic studies on animal models of T2DM are of great importance to understand the pathophysiology of T2DM. Therefore, in our study, Isobaric tags for relative and absolute quantification (iTRAQ) and Parallel reaction monitoring (PRM) were used for proteomic analysis of skeletal muscles from T2DM-susceptible and -tolerant Bama mini-pig models induced by a high-fat, high-sugar diet. In our proteomic analysis, a total of 1646 proteins and 13 differentially expressed proteins (DEPs) were identified by iTRAQ-mass spectrometry, and 6 differentially expressed proteins were validated by PRM. Gene Ontology (GO) analysis revealed that most DEPs were extracellular matrix (ECM) proteins and participated in several biological processes, such as negative regulation of JAK-STAT cascade, negative regulation of STAT cascade, roundabout signaling pathway and peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan, and the molecular functions of roundabout binding, glycosaminoglycan binding, heparin binding, sulfur compound binding, collagen binding, and kinase inhibitor activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis results showed that the differentially expressed proteins were involved in 14 pathways, including human disease pathways, metabolic pathways, signal transduction pathways, signaling molecules and interaction pathways, and the cellular process pathways associated with phagosomes and focal adhesion. In conclusion, the proteomics based on iTRAQ and PRM in T2DM-susceptible and -tolerant Bama mini-pig models showed that changes in amino acid metabolism, inflammation-associated pathways and the impaired function and environment of extracellular matrix are risk factors associated with increased pathogenesis of T2DM in Bama mini-pig.