Genomics最新文献

STRs are the most commonly used forensic genetic markers for human identification. Nanopore sequencing has shown the advantages of high portability and large data throughput. Previous studies indicate it has great potential for profiling STRs based on the ligation library preparation method. However, this method, which requires more library preparation time and operations, is unsuitable for rapid STR profiling, particularly for field forensic applications. The transposase-based rapid library preparation method offers the possibility to perform human identification using portable instruments. However, the amplicons of conventional STR panels are too small and would be cut into scraps with rapid methods, making them impractical for genotyping. In this study, we developed an 18-STRs multiplex amplification panel with amplicons of ~1.4 Kbp. The PCR conditions were optimized to be finished within 2 h and 12 min, and the PCR products could undergo rapid methods that involved random fragmentation. We found that, on average, 29.16 % of reads from the long-amplicon panel and rapid library kit covered the whole STR region, sufficient for downstream STR profiling analysis. We conducted a small validation experiment on 24 samples using portable instruments powered by a 1.5 kW‧h portable power source. The entire process took 10.5 h and we obtained enough data from 24 samples to perform trustworthy pairwise identification analysis using the STR profiles. The overall accuracy of the analysis was 95.36 %. In sum, the study evaluated and demonstrated the viability and potential of nanopore sequencing for forensic application in the field.

Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder, yet its mechanisms remain elusive. This study employed transcriptome sequencing on granulosa cells from 5 PCOS women and 5 controls, followed by bioinformatic analyses. We identified 684 mRNAs and 167 lncRNAs with significant differential expression. Gene Ontology and KEGG analyses highlighted enrichment in immune and inflammatory responses among these genes. Through CytoHubba plug-in and three machine learning algorithms, CCR7 was identified as the hub gene of PCOS, further validated through analysis of GSE65746, GSE34526 and a cohort of eighty subjects (40 PCOS and 40 controls). Furthermore, a competing endogenous RNA network targeting CCR7 was constructed. Immune infiltration analysis unveiled a significant decrease in monocyte infiltration in PCOS women, with CCR7 expression positively correlated to naïve B cells. Our findings suggest CCR7 and related molecules play a crucial role in the pathogenesis of PCOS, potentially serving as biomarkers for the disorder.

The biotechnological potential of Planctomycetota only recently started to be unveiled. 129 reference genomes and 5194 available genomes (4988 metagenome-assembled genomes (MAGs)) were analysed regarding the presence of Biosynthetic Gene Clusters (BGCs). By antiSMASH, 987 BGCs in the reference genomes and 22,841 BGCs in all the available genomes were detected. The classes Ca Uabimicrobiia, Ca Brocadiia and Planctomycetia had the higher number of BGC per genome, while Phycisphaerae had the lowest number. The most prevalent BGCs found in Planctomycetota reference genomes were terpenes, NRPS, type III PKS, type I PKS. As much as 88 % of the predicted regions had no similarity with known clusters in MIBiG database. This study strengthens the uniqueness of Planctomycetota for the isolation of new compounds and provide an overview of BGCs taxonomic distribution and of the type of predicted product. This outline allows the acceleration and focus of the research on drug discovery in Planctomycetota.

Cuscuta gronovii Willd., a member of the Convolvulaceae family, is noted for its potential medicinal and nutritional benefits. In this study, we utilized a combination of Illumina and Oxford Nanopore sequencing technologies to successfully assemble the complete circular mitochondrial genome (mitogenome) of C. gronovii. The mitogenome, spanning 304,467 base pairs, includes 54 genes: 33 protein-coding genes, three ribosomal RNA (rRNA) genes, and 18 transfer RNA (tRNA) genes. Beyond its primary circular structure, we discovered and validated several alternative genomic conformations, driven by five specific repeat sequences. Three inverted repeats were found to initiate rearrangements, resulting in the creation of seven distinct chromosomal structures, while two direct repeats split a larger molecule into two subgenomic entities. We also mapped 421 RNA editing sites across the protein-coding sequences, influencing 33 protein-coding genes with varying distribution, particularly noting high frequencies in the nad4 and ccmB genes. Sixteen of these RNA editing sites were experimentally validated through PCR amplification and Sanger sequencing, confirming their presence with 100 % accuracy. This research not only introduces the first mitochondrial genome of C. gronovii but also highlights its complex conformational variability induced by repeat-mediated recombination, providing a valuable genomic resource for further molecular breeding efforts and phylogenetic evolution within the genus Cuscuta.