BMC Genomics最新文献

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.

Background: Sheep have diversified into distinct breeds worldwide through both natural adaptation and human-driven selection, with hybridization serving as an effective strategy for rapid trait improvement. The Tianhua mutton sheep (TMS) is a novel breed derived from crossing South African Mutton Merino (SAMM) with Gansu alpine fine-wool sheep (GAFS). After nearly two decades of selective breeding, TMS has developed great meat quality traits and impressive cold tolerance at high altitudes. To study the genetic mechanism and provide new insights into phenotypic variation, we analyzed the genetic diversity, population structure, and selective signatures of TMS based on whole-genome sequencing of 55 TMS, 11 SAMM, and 197 public sheep genomes worldwide.

Results: Population genetic analysis revealed that TMS forms a distinct branch, with a pedigree composition showing an approximate 5:3 ratio of SAMM to GAFS lineages, consistent with the breeding design. Genetic diversity assessment showed that TMS exhibits higher genetic diversity and a lower inbreeding coefficient than commercial sheep from Africa, the Americas, and Europe, suggesting that TMS has considerable breeding potential to be tapped. Genome-wide scanning using the F_ST and XP-EHH methods was also performed to detect the signatures of selection in TMS, with significance thresholds set at Z(F_ST) >2.57 and XP-EHH >2.31. Functional annotation analysis revealed that the selected genes were related to meat quality traits, high-altitude adaptation, and disease resistance. Specifically, genes such as PLA2G10, SAMD12, CKMT2, ACOT12, and TNS3 are implicated in the processes related to fat metabolism. ZNF280D, RANBP3L, CSRP1, TNNI1, and AGBL4 are related to muscle growth and development. ABCB1 regulates energy metabolism via ATP transport to enhances low-oxygen adaptation, while NOTCH3, FBXO32, and LAMA1 regulate cardiopulmonary function and reduce pulmonary hypertension. Additionally, ATM, GALNTL6, and B4GALT5 may improve disease resistance and enhance environmental adaptability.

Conclusion: The results provide valuable insights for investigating the genetic mechanisms underlying TMS fine traits, enhancing TMS breeding, and developing mutton sheep suited to high-altitude and cold environments. Furthermore, it also indicates that hybrid breeding represents an effective strategy to provide a source of phenotypic variation for local adaptation and rapid acquisition of agronomically important traits.