BMC Genomics最新文献

Background: Class Ⅲ peroxidases (PODs) are widely involved in multiple physiological processes, including lignin biosynthesis and stress responses. However, there are no reports on the identification and function of POD family in Hippophae rhamnoides subsp. sinensis Rousi.

Results: In this study, we identified 71 non-redundant HrPODs. Based on phylogenetic analysis, these genes were classified into 7 subgroups. Then, we analyzed the conserved domains of HrPODs proteins and found that they contain highly conserved domain. We also investigated their expression patterns in three developmental stages of sea buckthorn fruit, and the results showed that most of them were highly expressed in early stage. The GO and KEGG functional enrichment analysis showed that they widely involved in oxidative stress response and phenylpropanoid biosynthesis, respectively. According to the Pearson correlation analysis of HrPODs expression with lignin content and peroxidase activity, we further screened five HrPODs that may be involved in fruit texture quality by regulating lignin biosynthesis during fruit development. Sea buckthorn is usually distributed in arid areas with higher salt and alkaline content, and our findings showed that the different degrees of drought, salt, or alkali treatment can also affect the expression of these genes and lignin content during the germination stage. These results will help us better investigate the role of HrPODs in lignin biosynthesis to provide certain theoretical foundation in ideal berry breeding and broad spectrum stress resistance in cultivated sea buckthorn.

Conclusion: In this study, the findings not only provide us with a comprehensive identification and analysis of HrPODs from a bioinformatics perspective, but also preliminary intimation that the POD family may be tightly associated with fruit texture quality and abiotic stress response. These results will help us better investigate the role of HrPODs in lingin biosynthesis, enrich the theoretical research on the formation of sea buckthorn texture quality and understand the roles of HrPODs in abiotic stress resistance in cultivated sea buckthorn.

Background: Sexual maturation in boars impacts reproductive efficiency in swine production, yet the molecular mechanisms underlying this developmental transition remain poorly understood. This study aimed to investigate the transcriptomic changes in sperm from Duroc boars during sexual maturation, conducting a longitudinal analysis. The total RNA and miRNA profiles from the same individuals (n = 6) at puberty (7.24 ± 0.39 months) and sexual maturity (10 ± 0.40 months) were compared, identifying molecular signatures associated with reproductive development. Total RNA sequencing (Illumina NovaSeq-6000) and miRNA sequencing (Illumina NextSeq-500) were performed on all 12 paired samples (6 boars at 2 time points), followed by differential expression analysis using a paired statistical model in DESeq2 to account for repeated measures.

Results: Differential expression analysis identified 60 differentially expressed genes using stringent criteria (adj P < 0.05, |log₂FC| ≥ 0.5), with 65% upregulated in sperm of boars 10-months versus 7-months of age. Key upregulated genes included NCLN, RGS12, CIB2, FOXP4, PHC1, CDC25B and AKAP1, while HSP90AA1, EVI5, FSIP2, VDAC3, and ALMS1 were key downregulated genes. Furthermore, Gene ontology analysis revealed significant enrichment of 11 biological processes, mostly related to reproductive development, and four molecular functions (transferase activity, transferring phosphorus-containing groups, protein serine/threonine kinase activity, protein kinase activity and signal sequence binding). Additionally, our miRNA analysis identified six differentially abundant miRNAs (adj P < 0.05 & |log₂FC| ≥ 0.5); ssc-miR-193a-5p, ssc-miR-574-3p, ssc-miR-126-3p, ssc-miR-196a, ssc-miR-210 were upregulated, and ssc-miR-338 showed downregulation in 10-months age. Integrated analysis of differentially expressed mRNA and predicted miRNA targets identified 18 miRNA-mRNA regulatory pairs, enriched in pathways related to cell cycle processes and chromatin binding, suggesting coordinated regulation across RNA biotypes in sperm during sexual maturation.

Conclusions: Our study reveals coordinated transcriptomic shifts in boar sperm during sexual maturation. Most genes show increased RNA abundance at 10 months of age, with enrichment in terms of reproductive development. Several miRNAs appear to regulate these changes through targeted mRNA interactions. These findings expand our understanding of the biological processes underlying sexual maturation in pigs.