BMC Genomics最新文献

Whole genome sequencing (WGS) via next-generation sequencing (NGS) platforms offers a powerful approach for investigating viral genetic diversity. Orbiviruses are an economically important group of arboviruses with a double-stranded RNA (dsRNA) genome consisting of 10 segments. Traditional approaches to virus sequencing relied primarily on processing with various treatments such as lithium chloride to enrich dsRNAs and then sequencing on Illumina platforms due to its lower error rate. To reduce the time and cost associated with orbivirus sequencing, we simplified the sample preparation, sequencing, and analysis protocols. Our optimized sample and library preparation protocols achieved comparable results to established methods while benefiting from simpler sample preparation. The optimized protocols for Illumina and Nanopore platforms (which produces longer reads) resulted in both platforms producing high quality whole genome sequences. To streamline the data analysis, we developed OrbiSeq, a reproducible Nextflow workflow for analysis and consensus sequence generation of orbivirus genomes from Illumina and Nanopore sequence data. While the OrbiSeq pipeline was optimized with orbivirus sequences, it can be used to recover consensus sequences for any segmented or non-segmented viral genome, provided that the sequence is sufficiently similar to existing reference sequences. The optimized protocols for producing viral sequences enhance opportunities for extensive genomic surveillance and in turn deeper evolutionary insights.

Xiang pig is a native inbred line originating from a warm and humid mountainous region and is prone to infections by pathogens causing lung lesions. However, the underlying genetic factors still remain unclear. Our previous genomic resequencing comparisons found a deletion type of structural variation (SV) within the intron of gene cerebellar degeneration related protein 2 (CDR2) with a higher frequency in Xiang pigs compared with European pig breeds. This study is aimed to explore the relationship between the SV and the lung injury in Xiang pig populations. It demonstrated that the deletion genotype (MM) was dominant in Xiang pig herds and with a higher percentage of allele M than that in Xiang pig with pulmonary lesions and Large White breeds. By Sanger sequencing and RepeatMasker analysis, a SINE in 277 bp (namely SINE-277) was detected and located in the opposite orientation of CDR2 gene. The inhibit effects of SINE-277 on transcription was confirmed by EGFP reporter gene after transfected into HEK-293T cells. And the expression levels of CDR2 was increased in the lungs with MM types (P < 0.05) via both RT-qPCR and Western blotting assays. Moreover, significant differences were estimated between the SV genotypes and the lung lesion severity scores, the antibody concentrations against pathogens, and expressions of nine inflammation factor genes including NFκB. It reinforced the effects of SINE on gene CDR2 expression and might be taken as a DNA marker for the resistance/susceptibility to lung diseases in pigs.

Background: The pleiotropic drug resistance (PDR) transporter stands out as one of the largest subfamilies within ABC transporters. These transporters play crucial roles in a multitude of biological processes, including detoxification, phytohormone transportation, stomatal movement, the translocation of various secondary metabolites, tolerance to heavy metal and adaptation to the diverse stress conditions. However, the structural and functional characterization of PDR gene family members in wheat has yet to be fully elucidated.

Results: In this investigation, we identified 66 TaPDR genes in the genome of wheat. The subsequent phylogenetic tree revealed that the genes clustered into four subfamilies. Chromosomal mapping unveiled the dispersal of 66 TaPDR genes across 17 wheat chromosomes. The twenty-two pairs of duplicated gene were identified in the PDR family. Ka/Ks ratio revealed that 22 duplicated TaPDR genes went through purifying selection. It was noted that the TaPDR genes displayed significant diversity in their gene structures. In addition, the presence of numerous cis-regulatory elements in the promoter regions of the TaPDR genes were identified. Differential expression patterns were observed among TaPDR family members across various tissues and in response to multiple stress conditions. Moreover, this investigation explored the miRNAs targeting TaPDR genes and their expression profiles in various tissues.

Conclusion: Thus, the results of this study establish a strong basis for further investigation of the functions of TaPDR genes across different tissues, developmental stages, phytohormone responses, and diverse stress in wheat.

Background: The endangered fish Percocypris pingi is a national second-class protected animal in China. Comprehensive evaluation of the genetic structure according to more reliable data and exploration of effective conservation measures are urgently needed for P. pingi. In this study, the genetic diversity, population structure, and adaptive evolutionary mechanism of circadian entrainment for P. pingi were performed.

Results: Our results revealed that eight wild populations (69 samples) and nine hatchery populations (90 samples) presented relatively low genetic diversity and simple population structure on the basis of whole-genome resequencing data. Compared to other 13 populations, the Datuo (DT) and Woluo (WL) wild populations and the Jinping (JP) and Yaan (YA) hatchery populations presented relatively high genetic diversity. The Fst‒Pi and XP‒EHH sites from the population group differentiation from DT, WL, JP, and YA were screened. Several GO terms (e.g. MAP kinase activity and monoatomic ion channel activity] and KEGG pathways (e.g. aldosterone synthesis and secretion and MAPK signaling) were enriched in circadian entrainment-related signaling. Then, the multiple candidate genes, such as pkc, pkd, Ac, mapk6, ampar, rorcb, rorab1, rorab2, lamb4, and ck1[Formula: see text]/∂ were shown to be enriched in the circadian entrainment pathway. Furthermore, the expression patterns of cry1a, cry2, per2a, per1b, clock1a, clock1b, baml2a, lamb4, and rorab1 and the melatonin levels in the livers demonstrated circadian oscillation within 24 h.

Conclusions: Low genetic diversity and a simple population structure of P. pingi were determined. The Wuoluo River and Litang River can be recognized as new refuges for wild P. pingi and that the JP and YA hatchery populations are needed for the sustainable conservation and utilization of resources in the Yalong River and Jinsha River. The circadian entrainment may be an important adaptive evolutionary mechanism of P. pingi. The above results can help formulate science-based breeding protocols and provide necessary genetic data for managing both captive propagation and wild population reinforcement.