BMC Genomics最新文献

Background: The Taihe black-boned silky fowl, a distinguished indigenous breed of chicken, is renowned for its dual utility in both traditional medicinal and culinary applications. However, the breed faces significant challenges due to its suboptimal reproductive capabilities and a notably brief egg-laying period, which have impeded its broader development and cultivation. In this research endeavor, we employed an advanced, rapid DIA (Data independent acquisition) quantitative proteomics method on the Astral platform to meticulously analyze the ovarian proteome of these chickens. By analyzing the ovarian proteomic information of Taihe black-boned silky fowl during peak and decline egg-laying periods, we aim to identify potential reproductive candidate proteins and the molecular mechanisms underlying egg-laying decline. This could enable us to implement interventions to improve the reproductive efficiency of this valuable breed.

Result: In this study, a total of 8,281 proteins were identified within the ovarian proteome of the Taihe black-boned silky fowl. Among these, 303 proteins exhibited significant differential expression, with 98 proteins significantly up-regulated and 205 proteins significantly down-regulated. The functional annotation of these proteins illuminated their crucial roles in the steroid hormone synthesis pathways, which are pivotal during the peak of egg production. Furthermore, during the later stages of laying, there was a noticeable upregulation of proteins associated with inflammatory senescence and oxidative stress. This change suggests an increase in reproductive stress within the ovary, highlighting the physiological shifts that affect productivity as the chickens age.

Conclusion: This study identified key candidate protein markers in the Taihe black-boned silky fowl during critical phases of their reproductive cycle, specifically peak and late egg-laying periods. These findings contribute valuable new scientific insights that can be utilized for the breeding optimization and effective management of this unique breed. By elucidating the protein dynamics during different laying phases, the research offers potential strategies aimed at enhancing reproductive performance and extending the reproductive lifespan of the Taihe black-boned silky fowl. This could lead to significant improvements in both the sustainability and profitability of farming this indigenous breed.

Background: The entomopathogenic fungus, Isaria fumosorosea, shows promise as a biological control agent in managing the diamondback moth (DBM) Plutella xylostella, a highly destructive global pest of cruciferous vegetables. To date, the miRNA-mRNA regulatory networks underlying the immune response of DBM to I. fumosorosea infection are still poorly understood. Here, we characterize the expression profiles of miRNA and mRNA, and construct the miRNA-gene regulatory network in DBM infected with I. fumosorosea.

Results: We identified 580 differentially expressed genes (DEGs) and 55 differentially expressed miRNAs (DEMs) in I. fumosorosea-infected DBM. Among these DEGs, we found 28 immunity-related genes, which mainly include pattern recognition receptors, signal modulators, and immune effectors. Integrated analysis discovered 87 negative correlation pairs between miRNA and mRNA, involving 40 DEMs and 62 DEGs in infected DBM. Additionally, 13 miRNAs and 10 corresponding mRNAs were identified as candidate miRNA-mRNA pairs for DBM immunity against fungal infection. Gene functional enrichment analysis indicated that these miRNAs could target genes associated with various pathways, such as the immune system, infectious diseases, digestive system, endocrine system, nervous system, and signal transduction. Finally, the regulatory relationships of six miRNA-mRNA pairs were validated using quantitative reverse transcription PCR.

Conclusions: For the first time, we present integrated miRNA and mRNA data to elucidate the immune response of the DBM to fungal infection. Our findings enhance the understanding of the immune response of the DBM to entomopathogenic fungi infection.

Plant HKTs (High-affinity K⁺ transporters) are essential transporters for ion transport and homeostasis and play crucial roles in plant growth and stress responses. However, the evolution of HKTs in Populus species and their functions require further investigation. In this study, we identified 16 HKTs from six Populus species. All poplar HKTs were classified as Class I HKTs because of their physiological relationships and the conservation of amino acids in key structures, which aligns with their conserved evolutionary coding sequences. The analysis of the protein domains, motifs and gene structures of 16 poplar HKTs revealed consistent conservation, with the exception of two members. The number of homologs and their chromosome locations indicated the differentiation of HKTs during poplar evolution and adaptation. Poplar HKTs can be classified into two subgroups on the basis of their physiological relationships and distinct protein structures. Gene expression pattern analysis revealed that poplar HKTs presented relatively high expression levels in roots and stems under salt stress. Furthermore, cis-element analysis and protein interaction predictions provide insights into the functions of HKTs under salt stress through the activation of ion transporters, proline content, and ATPases regulated by hormonal signals and MYB transcription factors. In conclusion, our research established a theoretical framework for investigating the evolutionary relationships and functional roles of HKTs in Populus species and offered valuable insights into the functions and underlying mechanisms of poplar HKTs in specific tissues under various stress conditions.

Background: Improving the germination performance of bread wheat is an important breeding target in many wheat-growing countries where seedlings are often established in soils with high salinity levels. This study sought to characterize the molecular mechanisms underlying germination performance in salt-stressed wheat. To achieve this goal, a genome-wide association study (GWAS) was performed on 292 Iranian bread wheat accessions, including 202 landraces and 90 cultivars.

Results: A total of 10 and 15 functional marker-trait associations (MTAs) were detected under moderate (60 mM NaCl) and severe (120 mM NaCl) salinity, respectively. From genomic annotation, 17 candidate genes were identified that were functionally annotated to be involved in the germination performance of salt-stressed wheat, such as CHX2, PK2, PUBs, and NTP10. Most of these genes play key roles in DNA/RNA/ATP/protein binding, transferase activity, transportation, phosphorylation, or ubiquitination and some harbored unknown functions that collectively may respond to salinity as a complex network.

Conclusion: These findings, including the candidate genes, respective pathways, marker-trait associations (MTAs), and in-depth phenotyping of wheat accessions, improve knowledge of the mechanisms responsible for better germination performance of wheat seedlings under salinity conditions.

Background: Since their domestication, recent inbreeding together with intensive artificial selection and population bottlenecks have allowed the prevalence of deleterious mutations and the increase of runs-of-homozygosity (ROH) in domestic pigs. This makes pigs a good model to understand the genetic underpinnings of inbreeding depression.

Results: Here we integrated a comprehensive dataset comprising 7239 domesticated pigs and wild boars genotyped by single nucleotide polymorphism (SNP) chips, along with phenotypic data encompassing growth, reproduction and disease-associated traits. Our study revealed differential ROH landscapes during domestication and artificial selection of Eurasian pigs. We observed associations between ROH burden and phenotypic traits such as body conformation and susceptibility to diseases like scrotal hernia. By examining associations of whole-genome and regional ROH burden with gene expression, we identified specific genes and pathways affected by inbreeding depression. Associations of regional ROH burden with gene expression also enabled the discovery of novel regulatory elements. Lastly, we inferred recessive lethal mutations by examining depletion of ROH in an inbred population with relatively small sample size, following by fine mapping with sequencing data.

Conclusions: These findings suggested that both phenotypic and genetic variations have been reshaped by inbreeding, and provided insights to the genetic mechanisms underlying inbreeding depression.

The current study aimed to detect the mutagenic impacts of aflatoxin B1 (AFB1), which is produced by Aspergillus group fungi, via a high-plant genotoxicity test. Different durations of treatment (3 h, 6 h, and 12 h) were used to treat the Vicia faba root tips with varying concentrations of Aflatoxin B1 (AFB1) following the approved protocol for plant assays published by the International Program on Chemical Safety (IPCS) and the World Health Organization (WHO). The data obtained indicated that AFB1 not only has the ability to induce various alterations in the process of mitosis, ranging from increasing to decreasing mitotic and phase indices but also leads to many mitotic aberrations. The abnormalities observed varied on the basis of the ratio of AFB1 to treatment time. The aberrations included micronuclei in interphase, stickiness; two groups ring star disturbed and oblique metaphase late separation diagonal bridge and laggard and disturbed. anaphase and telophase. This study showed that biomonitoring Vicia faba is a sustainable method for estimating the cytotoxicity and genotoxicity of applied AFB1. Additionally, AFB1 caused changes in the protein profile detected by SDS‒PAGE, with each treated sample displaying a unique electrophoretic pattern due to the formation and disappearance of certain bands. The ISSR and RAPD assays changes in band numbers in all samples compared with the untreated control, and a decrease in genetic template stability (GTS) ratios was observed with higher levels of AFB1. The image cytometric data revealed a correlation between the dosage of AFB1 and its impact on cell cycle components in the meristematic cells of Vicia faba roots. Furthermore, an increase in AFB1 concentrationled to a decrease in B-cell lymphoma 2 (Bcl2) levels, an increase in chromatin condensation levels, and an increase in poly ADP‒ribose polymorphism (PARP) levels.

Wool growth and fineness regulation is influenced by some factors such as genetics and environment. At the same time, lncRNA participates in numerous biological processes in animal production. In this research, we conducted a thorough analysis and characterization of the microstructure of wool, along with long non-coding RNAs (lncRNAs), their target genes, associated pathways, and Gene Ontology terms pertinent to the wool fineness development. The investigation utilized scanning electron microscopy and transcriptomic technology, focusing on two distinct types in Gansu alpine fine-wool sheep: coarse type (group C, MFD = 22.26 ± 0.69 μm, n = 6) and fine type (group F, MFD = 16.91 ± 0.29 μm, n = 6), which exhibit differing wool fiber diameters. The results showed that fine type wool fiber scales were more regularly distributed in rings with large scale spacing and smooth edges, while coarse type wool fiber scales were more irregularly arranged in tiles with relatively rougher edges, and the density of wool scales was greater than that of fine type wool. Furthermore, a comprehensive analysis revealed 164 differentially expressed lncRNAs along with 146 potential target genes linked to these lncRNAs in the skin tissues from groups C and F. Utilizing functional enrichment analysis on the target genes, we successfully identified a number of target genes might be associated with the improvement of wool fineness, such as FOXN1, LIPK, LOC101116068, LOC101106296, KRTAP5.4, KRT71, KRT82, DNASE1L2, which are related to hair follicle development, histidine metabolism, epidermal cell differentiation, oxidative phosphorylation and hair cycle process. Additionally, the interoperability network involving lncRNAs-mRNAs indicated lncRNAs (MSTRG.17445.2, XR_006060725.1, MSTRG.871.1, MSTRG.10907.4) might play a significant role in the wool growth development and fineness improvement process. In conclusion, the research enlarges the current lncRNAs database, providing a new insight for the investigation of wool fineness development in fine-wool sheep.

Background: Glycyrrhiza glabra, which is widely used in medicine and therapy, is known as the 'king of traditional Chinese medicine'. In this study, we successfully assembled and annotated the mitochondrial and chloroplast genomes of G. glabra via high-throughput sequencing technology, combining the advantages of short-read (Illumina) and long-read (Oxford Nanopore) sequencing.

Results: We revealed the ring structure of the mitochondrial genome, which spans 421,293 bp with 45.1% GC content and 56 annotated genes. Notably, we identified 514 repetitive sequences, including 123 Simple sequence repeats (SRs), 3 Tndem sequence repeats (TSRs), and 388 Dispersed sequence repeats (DSRs). We identified 79 out of the 388 DSRs as potentially involved in homologous recombination. We identified five forward repeats and four palindromic repeats that facilitate homologous recombination and induce alterations in the mitochondrial genome structure. We corroborated this finding via polymerase chain reaction (PCR). Furthermore, we identified chloroplast-derived sequence fragments within the mitochondrial genome, offering novel insights into the evolutionary history of plant mitochondrial genomes. We predicted 460 potential RNA editing sites, primarily involving cytosine-to-uracil transitions. This study reveals the complexity of repetitive sequence-mediated homologous recombination in the mitochondrial genome of G. glabra and provides new insights into its structure, function, and evolution.

Conclusions: These findings have important implications for conservation biology, population genetics, and evolutionary studies, underscoring the role of repetitive sequences in genome dynamics and highlighting the need for further research on mitochondrial genome evolution and function in plants.