BMC Genomics最新文献

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.

Background: GATA transcription factors are ubiquitous in plants, where they regulate target gene expression to modulate plant growth, development, and responses to environmental stresses. The GATA gene family has been identified in numerous plant species, with characterization reported in cucumber and melon among Cucurbitaceae crops. However, the GATA gene family remains unstudied in most other Cucurbitaceae species. Here, we systematically identified GATA genes in 10 Cucurbitaceae species (watermelon, cucumber, melon, pumpkin, wax gourd, sponge gourd, bottle gourd, bitter gourd, chayote, snake gourd) using the latest high-quality genomic datasets.

Results: A total of 281 GATA genes were identified across these 10 species, and phylogenetic analysis clustered them into four subgroups (Groups A, B, C, D). For watermelon GATA (ClGATA) genes, cis-acting element analysis revealed abundant stress-responsive elements in their promoter regions. Predictions of ClGATA protein secondary and tertiary structures showed random coils as the dominant secondary structural component, with subgroup-specific tertiary characteristics supporting functional synergy within each subgroup. Intraspecific synteny analysis identified 7 segmentally duplicated ClGATA gene pairs, with no tandem duplications detected, indicating segmental duplication drove the expansion of the ClGATA family. Transcriptome reanalysis under 17 types of abiotic and biotic stresses showed ClGATA7 exhibited significant differential expression under 5 abiotic and 3 biotic stress types, and ClGATA11 showed significant differential expression under 3 abiotic and 5 biotic stress types. Quantitative real-time PCR (qRT-PCR) validation of 6 key ClGATA genes further confirmed the role of ClGATA7 in mediating abiotic stress responses, with consistent down-regulation under low temperature in both leaf and root tissues. Protein-protein interaction prediction identified potential interactions among 21 of the 24 ClGATA proteins, including a direct interaction between ClGATA7 and ClGATA17.

Conclusions: These findings advance our understanding of GATA gene family evolution and function in Cucurbitaceae. Given the broad stress responsiveness of ClGATA7 and ClGATA11, they are highlighted as priority candidate genes for functional studies and genetic improvement of stress tolerance in watermelon.