BMC Genomics最新文献

Mahanarva fimbriolata (Distant 1909) (Hemiptera: Cercopidae) is a major pest that reduces forage production in Brazil, yet few viable control alternatives exist. The RNA interference (RNAi) gene silencing method is a specific and efficient approach that may aid the development of a sustainable management strategy for this pest. It is known that some genes involved in the RNAi machinery are lacking in certain Hemiptera species; therefore, verifying their presence in each target species is necessary. Here, transcriptome assembly of Mahanarva fimbriolata at different developmental stages (egg, nymph and adult stages) was performed, differentially expressed genes were identified, RNAi-related genes described in the literature were annotated in the transcriptome, and coexpression network modeling for the identification of potential RNAi targets was performed. The analysis revealed that the most significant differences in gene expression were between samples in the egg stage and samples in the other development stages. Enriched Gene Ontology terms related to insect growth (e.g., cell division, metamorphosis and flight) and corresponding pathways (e.g., DNA replication and glycolysis/gluconeogenesis) were identified. Coexpression networks demonstrated the importance of biosynthetic hormone processes within specific modules and revealed potential silencing targets, including hub genes such as RPB7 and Talin-2. Transcript annotation and analysis revealed more than 20 genes related to five major RNAi-related processes and factors (dsRNA cleavage, endonucleases, dsRNA binding, dsRNA transport and uptake, and auxiliary RISC-associated or regulatory factors). This work provides a comprehensive molecular overview of metamorphosis in M. fimbriolata, confirms the presence of active RNAi machinery, and reveals potential targets for future gene silencing approaches.

Background: Maclura tricuspidata is an important medicinal and horticultural plant. However, the complete mitochondrial genome (mitogenome) of M. tricuspidata has not been reported, hindering molecular phylogenetic studies, species identification, and evolutionary research.

Results: We present the first comprehensive analysis of the M. tricuspidata mitogenome. It features a multi-chromosomal structure comprising three circular-mapping chromosomes, with a total length of 416,801 bp and a GC content of 44.94%. Annotation identified 28 unique protein-coding genes (PCGs), 18 tRNA genes, and 3 rRNA genes. Codon usage analysis revealed GCU and CAA as the predominant codons for alanine and glutamine, respectively, while methionine and tryptophan, as single-codon amino acids, showed no bias. A total of 154 simple sequence repeats (SSRs) were detected: 84 on chromosome 1, 48 on chromosome 2, and 22 on chromosome 3. Analysis identified 19 homologous fragments transferred from the chloroplast genome (cpDNA), accounting for 4.31% of the mitogenome length. Using the Deepred-mt suite, 409 C-to-U RNA editing sites were predicted from the complete set of 28 mitochondrial PCGs, with the highest number in nad4 and the lowest in sdh4. Phylogenetic analysis confirmed the placement of M. tricuspidata within the Moraceae family, showing closest relationships to Ficus carica and Morus notabilis, consistent with the APG IV system. Comparative analysis revealed extensive syntenic blocks between the M. tricuspidata mitogenome and those of related species, alongside regions lacking homology. In addition, dN/dS analysis revealed that most of the protein-coding genes in the mitogenome had undergone negative selection, and only the ccmB and sdh4 gene had undergone potential positive selection in M. tricuspidata.

Conclusions: The unique structural features and complexities of the M. tricuspidata mitogenome, along with its similarities and differences compared to related species, provide valuable insights into plant mitochondrial evolution, energy metabolism, and environmental adaptation. These findings contribute significantly to the understanding of plant mitogenome diversity and biology.

Background: Enterococcus faecium is a commensal of the human gut microbiota that can become an opportunistic pathogen, particularly in immunocompromised individuals. Small RNAs (sRNA) are thought to contribute to this shift by enabling rapid bacterial adaptation to environmental changes. Despite this, knowledge of sRNA in E. faecium remains limited. Ern0160, in particular, has attracted interest for its involvement in antibiotic and biocide responses, as well as its role in intestinal colonization in a murine model.

Results: In this study, we investigated the functions of Ern0160 in E. faecium Aus0004 reference strain and sought to identify its mRNA targets. Transcriptomic and in silico analyses revealed potential regulatory targets, including two homologous genes encoding LysM-containing domain proteins (EFAU004_01059 and EFAU004_01150), both associated with enterococcal pathogenicity. Experimental validation confirmed that increased expression of Ern0160 led to repression of these genes. We further demonstrated direct and specific interactions between Ern0160 and the two homologous target mRNAs. Functional assays in the Galleria mellonella larvae infection model showed that deletion of Ern0160 resulted in increased host mortality, whereas deletion of its targets genes resulted in decreased mortality. These results are consistent with previous findings linking these genes to E. faecium virulence in murine model of systemic and urinary tract infections.

Conclusions: Our findings suggest that Ern0160 contributes to a regulatory network that modulates E. faecium colonization and infection by targeting genes involved in antimicrobial response and virulence. This study highlights the potential of regulatory RNAs such as Ern0160 to shape the pathogenic behavior of a multi-drug resistant and clinically significant bacterium.

This study systematically analyzed the BBX gene family in kiwifruit (Actinidia chinensis) to investigate its roles in abiotic stress responses. Bioinformatics analyses were performed, including gene localization, collinearity assessment, gene structure characterization, phylogenetic reconstruction, three-dimensional protein modeling, protein-protein interaction networks, and cis-acting element screening. These approaches elucidated the evolutionary relationships and structural features of the kiwifruit BBX genes. Transcriptome data revealed differential expression patterns under boron deficiency, salt stress, and cadmium stress, visualized through heatmaps. Quantitative real-time PCR validation confirmed that AcBBX4, AcBBX5, AcBBX15, AcBBX17, and AcBBX36 were significantly differentially expressed under all three stress conditions, suggesting their coordinated function in stress adaptation. Protein-protein interaction analysis identified AcBBX17 as a central hub in the regulatory network. Promoter analysis indicated that AcBBX17 contains a high proportion of methyl jasmonate responsive elements, and functional enrichment supported its involvement in the jasmonic acid signaling pathway. Based on these findings, a jasmonic acid-mediated regulatory model centered on AcBBX17 was proposed. In summary, the BBX gene family functions as key transcriptional regulators in plant development and stress response pathways, with this study providing specific insights into its role in kiwifruit abiotic stress tolerance.

Background: Glyceraldehyde-3-phosphate dehydrogenases (GAPDHs) are glycolytic enzymes involved in plant metabolism, growth, signal transduction and stress responses. Beet western yellows virus (BWYV), which belongs to the Polerovirus, causes substantial yield and quality losses in pepper. However, the roles of GAPDHs in pepper responses to BWYV infection remain largely unexplored.

Results: Transcriptome analyses revealed altered expression of GAPDH genes in Capsicum annuum following BWYV infection. Genome-wide analysis identified seven CaGAPDH genes in pepper, and qRT-PCR showed that CaGAPC2 transcripts were most strongly down-regulated after infection. Previous studies have shown that GAPCs contribute to autophagy regulation. Here, silencing CaGAPC2 enhances autophagy and reduces BWYV accumulation, and BWYV CP-RT was targeted for autophagic degradation through its interaction with the key autophagy protein ATG8f. Furthermore, autophagy activator BTH treatment inhibits BWYV infection.

Conclusion: This study establishes that CaGAPC2 functions as a negative regulator of autophagy; its silencing enhances autophagy and limits BWYV. CP-RT interacts with ATG8f and is degraded by the autophagy pathway. Critically, activating autophagy using BTH effectively inhibits BWYV infection. These findings elucidate a CaGAPC2-mediated molecular defense mechanism against BWYV and provide a foundation for developing novel control strategies.

Background: Long non-coding RNAs (lncRNAs) constitute a substantial portion of the plant transcriptomes and performs important functions in numerous molecular, regulatory, growth and developmental processes and stress responses. However, functional characteristics supported by experimental evaluation are known only for a small part of lncRNAs. In this regard, evolutionary and comparative analysis of lncRNA sequences can provide additional information about the functional role of these molecules.

Results: Analysis of RNA-seq libraries from 503 maize inbred lines obtained by Hirsch et al. (2014) enabled the assessment of sequence diversity and evolutionary patterns of maize lncRNAs within the pan-transcriptome framework and their comparison with analogous mRNA characteristics. The lncRNA pan-transcriptome comprises a greater number of representative sequences (595,198), compared to mRNA pan-transcriptome (245,436), smaller fraction of core and shell parts and larger cloud component (52.5% vs 11%). However, both pan-transcriptomes are closed according to estimates of the power-law parameters. Nucleotide diversity of the lncRNAs significantly higher compared to mRNAs. Moreover, nucleotide substitution rates estimates for coding and non-coding sequences demonstrated systematic increase of the gamma distribution shape parameter α in the order α(K_a) < α(K_s) < α(K_n) across all pan-transcriptome components (core, shell, cloud). Comparison of evolutionary characteristics also demonstrated that antisense lncRNAs are the most conserved in terms of both nucleotide substitution rates and their representation in the core; intronic lncRNAs display the highest mutation rate, while intergenic lncRNAs exhibit the greatest sequence repertoire diversity and highest line specificity.

Conclusions: These results allowed to evaluate the diversity of lncRNAS from the pan-transcriptomic point of view and supported their high lineage-specificity and sequence variation across maize inbred lines in comparison to mRNA sequences.

Background: Understanding the genetic basis of hybridization trait between Chinese indigenous pig and their commercial relatives may contribute to germplasm innovation. The Qinchuan black (QCB) pig is a new composite breed under development generated from Chinese indigenous pig breeds (i.e., Guanzhong black pig, GZB) and intensive pig breeds (i.e., Yorkshire, also called Large white pig, LW). Investigated gene functions inherited from parent help us to understand the genetic basis of excellent phenotype similar with their parents, in which parents correspond to grandparents for hybrid population in our study.

Result: Here, we performed population structure and admixture analyses to elucidate the genetic position of QCB among Asian and European pig breeds. Ancestral track analysis revealed the LW contributed more genomic components in QCB genome, particularly on chromosome 7. This asymmetric inheritance may be influenced by linkage disequilibrium blocks. The offspring genome exhibited high genetic diversity, as did its maternal genome (GZB). Both genomes were characterized by a reduced number and shorter length of Run of Homozygosity (ROH). Finally, we used HKA test to investigated key gene in QCB that were inherited from its parents and that regulate important economic traits. Our results identified a significant association between an NPC1L1 haplotype inherited from the LW genome and body weight in four-month-old QCB.

Conclusion: Our research provides a novel strategy for utilizing previously identified functional loci or genes to guide the breeding of domestic pig for improvement economic traits in crossbreeding systems.