BMC Genomics最新文献

Background: Wheat rust fungi can cause significant damage to wheat crops, leading to reduced yields and economic losses. To combat disease, certain plant varieties can trigger defense responses upon recognition of specific pathogen effector proteins, thereby conferring avirulence. Identifying such avirulence (Avr) genes is crucial for developing strategies to protect crops from devastating losses, ranging from identifying matching resistance genes to designing diagnostic assays for monitoring pathogen populations. Puccinia triticina (Pt) causes wheat leaf rust and is an obligate biotrophic fungus, and because of its life cycle and mode of reproduction, it is difficult to study genetically.

Results: To identify Avr genes in Pt, a F₂ population of fifty-seven progeny was generated from a sexual cross of race 9 (SBDG) and race 161 (FBDJ) on the alternate host Thalictrum speciosissimum under controlled conditions. The population segregated for avirulent/virulent traits screened at the seedling stage on thirteen single gene resistance lines in the wheat host cultivar Thatcher background. The genomes of the parents, F₁, and progeny were sequenced and mapped onto an assembled parental race 9 phased haplotype B genome, resulting in the generation of 21,154 high-quality SNP markers suitable for genetic mapping of the F₂ population. A genetic map composed of 61 linkage groups was obtained, containing a total of 10,923 markers, and spanning 10,730.5 centimorgans. Effector loci correlating with avirulence to specific leaf rust resistance (Lr) genes, PtAvrLr14a, PtAvrLr11 and PtAvrLr2a, were mapped to chromosome 1, chromosome 3 and chromosome 4, respectively. To strengthen the identification of candidate Avr genes, a region-specific association study was done on a natural population of fifty-nine Pt isolates that were collected in Canada and whose genomes were sequenced using Illumina.

Conclusion: Significant markers and corresponding candidate effector genes were identified for these mapped Avr loci. The identification of these candidate genes is an essential step towards cloning Avr and subsequentially their matching host resistance genes, and for studying the molecular mechanisms underlying pathogen-host interactions and host defense.

Background: The exploration of toxin diversity is crucial for understanding the evolutionary adaptation of venomous taxa. Despite being active venomous predators, neogastropods are largely understudied beyond Conidae. This study targets two predatory gastropods, Monoplex corrugatus and Stramonita haemastoma, aiming to characterize their toxin-producing tissues, evaluate the diversity and function of their toxins, and compare gene expression profiles across tissues. Specimens of both species were dissected to isolate multiple replicates of secretory glands and other tissues. Transcriptomic data were complemented by shotgun proteomics for S. haemastoma and used to identify putative toxin genes using the DeTox pipeline. Differentially expressed genes were identified and putative toxins were manually annotated.

Results: The study identified 2,565 and 1,777 putative toxins in S. haemastoma and M. corrugatus, respectively. Salivary glands were the major toxin-producing organ in both species, with additional toxin expression in mid-esophageal and accessory salivary glands. Manual annotation confidently identified 115 -S. haemastoma- and 143 -M. corrugatus- venom proteins, highlighting significant interspecies and inter-tissue differences. Functional categorization revealed the presence of enzymatic and peptide toxins, as well as venom-processing proteins, with M. corrugatus showing expression in non-secretory tissues. Despite their phylogenetic distance, shared orthologs were identified between the two species, namely for venom-processing proteins like calglandulin and disulfide isomerases, suggesting conserved functions. Toxins unique to each species analyzed, including echotoxins and plancitoxins in M. corrugatus, indicate lineage-specific venom adaptations. Proteomic validation supported transcriptomic predictions in S. haemastoma.

Conclusions: These findings underscore the value of multi-omics approaches for toxin discovery and for investigating the complexity of gastropod venom evolution and expand our understanding of how venom systems evolve and diversify in marine snails, highlighting both shared and unique toxin strategies that may reflect different ecological adaptations.

Background: Argentina anserina and Argentina lineata are alpine plant species endemic to the Qinghai-Tibet Plateau (QTP). However, the dynamic features of their mitochondrial genome characteristics remain poorly characterized.

Methods: We conducted de novo assembly and annotation of the mitochondrial genomes of two Argentina species using PacBio HiFi and Illumina sequencing technologies.

Results: The mitochondrial genomes of A. anserina and A. lineata both exhibit a single circular structure, with sizes of 294,533 bp and 338,624 bp, respectively. Both genomes encode 30 protein-coding genes (PCGs) and 3 ribosomal RNA (rRNA) genes, but differ in the number of transfer RNA (tRNA) genes (18 vs. 19), with A. lineata harboring the unique trnS-UGA. Codons exhibit a preference for A/U endings, consistent with their respective genomic GC contents (44.48% and 43.98%). A total of 217 high-confidence RNA editing sites were detected in A. anserina and 209 in A. lineata, with the majority of these edits leading to hydrophobic amino acid substitutions. Experimental validation confirmed RNA editing at four target sites (i.e., nad1-2, nad4L-2, atp6-718, and ccmFC-1312) in A. anserina. Horizontal gene transfer (HGT) analysis identified 20 and 29 chloroplast derived sequences in mitochondrial genomes of A. anserina and A. lineata, respectively, including the complete trnD-GUC gene and fragments of atpB, rpoC1, and rpoC2 genes, which contributes to the remodeling of energy metabolic pathways. Phylogenetic analysis indicated that the genus Argentina is more closely related to Potentilla than to Fragaria, and synteny analysis further revealed genomic structural divergence among these genera.

Conclusions: This study elucidates the potential roles of RNA editing and HGT events in the mitochondrial genome evolution of the two Argentina species, and furnishes valuable mitochondrial genomic resources for alpine plant research.