Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs

Integrated transcriptomic and metabolomic analyses reveal heterosis for meat quality of Neijiang pigs

Obese pig breeds have excellent meat quality, while lean pig breeds have high lean meat percentage and feed conversion rate. However, due to their respective shortcomings, obese pig and lean pig breeds are unable to balance production and consumption needs. Therefore, this study crossbred the obese Chinese pig breed Neijiang (NJ) with lean type Large White pigs (LW) to produce Neijiang × Large White(NL) pigs. This study compared the differences in carcass and meat quality traits between NJ pigs and NL pigs, and for the first time comprehensively analyzed the longissimus dorsi muscle of NJ pigs and NL pigs using transcriptomics and metabolomics. The results of slaughter and meat quality testing indicate that the carcass performance of NL pigs was significantly higher than that of NJ pigs, and the excellent meat quality characteristics of NJ pigs were also retained on NL pigs. The results of transcriptomics and metabolomics showed that there were 635 differentially expressed genes (DEGs) and 11 significantly different metabolites (SDM) in the longissimus dorsi muscle of NJ and NL pigs. The results of multi omics joint analysis showed that betaine, uridine triphosphate, glycerol 3-phosphate, and glutathione in SDMs were enriched in the shared KEGG pathway and significantly correlated with C1QTNF12, GGA3, SLC16A6, and RXRG in DEGs. In general, it is feasible to enhance the production performance of NJ pigs through crossbreeding with LW pigs. The hybrid offspring inherit the advantages of these two varieties, maintaining excellent meat quality while also having better carcass performance.

Small Insertions and Deletions Drive Genomic Plasticity during Adaptive Evolution of Yersinia pestis

The life cycle of Yersinia pestis has changed a lot to adapt to flea-borne transmission since it evolved from an enteric pathogen, Yersinia pseudotuberculosis. Small insertions and deletions (indels), especially frameshift mutations, can have major effects on phenotypes and contribute to virulence and host adaptation through gene disruption and inactivation. Here, we analyzed 365 Y. pestis genomes and identified 2,092 genome-wide indels on the core genome. As recently reported in Mycobacterium tuberculosis, we also detected "indel pockets" in Y. pestis, with average complexity scores declining around indel positions, which we speculate might also exist in other prokaryotes. Phylogenic analysis showed that indel-based phylogenic tree could basically reflect the phylogenetic relationships of major phylogroups in Y. pestis, except some inconsistency around the Big Bang polytomy. We observed 83 indels arising in the trunk of the phylogeny, which played a role in accumulation of pseudogenes related to key metabolism and putatively pathogenicity. We also discovered 32 homoplasies at the level of phylogroups and 7 frameshift scars (i.e., disrupted reading frame being rescued by a second frameshift). Additionally, our analysis showed evidence of parallel evolution at the level of genes, with sspA, rpoS, rnd, and YPO0624, having enriched mutations in Brazilian isolates, which might be advantageous for Y. pestis to cope with fluctuating environments. The diversified selection signals observed here demonstrates that indels are important contributors to the adaptive evolution of Y. pestis. Meanwhile, we provide potential targets for further exploration, as some genes/pseudogenes with indels we focus on remain uncharacterized. IMPORTANCE Yersinia pestis, the causative agent of plague, is a highly pathogenic clone of Yersinia pseudotuberculosis. Previous genome-wide SNP analysis provided few adaptive signatures during its evolution. Here by investigating 365 public genomes of Y. pestis, we give a comprehensive overview of general features of genome-wide indels on the core genome and their roles in Y. pestis evolution. Detection of "indel pockets," with average complexity scores declining around indel positions, in both Mycobacterium tuberculosis and Y. pestis, gives us a clue that this phenomenon might appear in other bacterial genomes. Importantly, the identification of four different forms of selection signals in indels would improve our understanding on adaptive evolution of Y. pestis, and provide targets for further physiological mechanism researches of this pathogen. As evolutionary research based on genome-wide indels is still rare in bacteria, our study would be a helpful reference in deciphering the role of indels in other species.

Development of Wild Boar Species-Specific DNA Markers for a Potential Quality Control and Traceability Method in Meat Products

In the food supply chain, quality control has a very important role in maintaining customer confidence. In the EU, food safety aspects are strictly regulated; however, composition requirements and standard control methods are generally undefined. The rapidly increasing wild boar population has a growing market share in venison or game meat production. Several methods have been described for species identification and control of composition in food products, but only some of these are suitable for routine measurements. The aim of our research was to design a rapid, reliable and simple PCR insertion/deletion (InDel)-based genetic tool suitable for species identification in food quality control laboratories. In total, 59 different swine (Sus scrofa) whole genomes were tested with bioinformatic tools to identify wild boar-specific insertions or deletions. Three independent InDels were suitable for marker development, multiplex PCR amplification and separation in agarose gel. Altogether, 209 samples of wild boar and ten other domestic pig breeds were taken for DNA extraction and validation of the three multiplexed InDel markers. Statistical analysis showed a very high combined predictive value (0.996), indicating the capability of the newly developed markers to detect wild boars with a probability over 99%. Breed assignment tests confirm that the InDel markers developed are suitable for rapid, sensitive and reliable identification of the wild boar meat content of food products. The use of the reported method in food quality control can mean a simple and cost-effective way to maintain consumer confidence and to support the competitiveness of fair producers.