Zhendong Gao

High-altitude environments impose severe physiological challenges on mammals, yet the genetic basis of adaptation in Ethiopian indigenous cattle remains poorly understood. Here, we analyzed whole-genome resequencing data from 70 Ethiopian indigenous cattle representing seven breeds (Abigar, Barka, Boran, Felata, Fogera, Gojjam-Highland, and Horro) distributed across elevations ranging from 523 to 3410 m, obtained from the NCBI Sequence Read Archive. After alignment to the ARS-UCD2.0 reference genome, we identified 49,196,624 high-confidence SNPs and performed population genomic analyses (PCA, phylogenetic reconstruction, and ADMIXTURE), along with genome-wide selection scans using FST and nucleotide diversity (θπ), and in silico virtual knockout of candidate genes in bovine lung single-cell transcriptomics. Population structure analyses revealed marked genetic differentiation between low- and mid-to-high-altitude populations, with substantial genetic connectivity and shared ancestry among high-altitude groups. We identified 398 candidate selective regions showing concordant FST and θπ signals, encompassing 1816 candidate genes, significantly enriched in hypoxia-related and vascular remodeling pathways (phospholipase D, Ras, ErbB, Wnt, Hedgehog). Two hub candidate genes, PIK3CA and RHOA, were prioritized; virtual perturbation of PIK3CA altered extracellular matrix, focal adhesion, and integrin networks, whereas RHOA perturbation activated immune and inflammatory programs (NF-κB, phagocytosis, chemokine pathways) with upregulation of TYROBP, IL1B, TLR4, and NLRP3. Our findings indicate that Ethiopian cattle have evolved distinct genomic signatures associated with adaptation to chronic high-altitude environments, in which PIK3CA and RHOA may represent candidate regulators associated with extracellular matrix organization and immune-related transcriptional regulation, respectively, thereby providing new insights into mammalian adaptation to extreme environments.

Background: The Chungtien schizothoracin (Ptychobarbus chungtienensis) is a threatened freshwater fish endemic to the Qinghai–Tibet Plateau and adjacent high-altitude regions of northwestern Yunnan, China. Although a complete mitochondrial genome of P. chungtienensis has been previously reported, direct comparison with a mitogenome generated using high-accuracy long-read sequencing can provide additional information on mitochondrial genome structure and sequence variation. This study aimed to assemble and annotate a complete mitogenome of P. chungtienensis using PacBio HiFi sequencing and to compare its mitogenomic characteristics with previously published Ptychobarbus mitogenomes. Methods: High-molecular-weight genomic DNA from a single specimen was sequenced using PacBio HiFi long-read technology. The mitochondrial genome was assembled using MitoHiFi, annotated using MitoFinder followed by manual curation, and compared with previously published Ptychobarbus mitogenomes. Phylogenetic relationships were evaluated using maximum-likelihood analysis with expanded taxon sampling, and selection pressure on the 13 mitochondrial protein-coding genes was assessed using dN/dS-based branch and branch-site models. Results: The assembled mitogenome is 16,583 bp in length and contains the typical 37 mitochondrial genes, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes, together with a control region and the origin of light-strand replication (O_L). The overall A + T content was 54.97%. Direct comparison with the previously reported 16,970 bp mitogenome showed that the 387 bp length difference was concentrated in non-coding regions, particularly the control region and the tRNA-Thr–tRNA-Pro intergenic region. Phylogenetic analysis based on 22 complete mitogenomes placed the newly assembled P. chungtienensis sequence in a strongly supported mitochondrial clade with Schizothorax macropogon (bootstrap = 100%), whereas the previously reported P. chungtienensis sequence clustered with P. kaznakovi (bootstrap = 100%), indicating that the two P. chungtienensis records represent distinct mitochondrial lineages. The dN/dS values of all 13 mitochondrial protein-coding genes were below 1, and neither branch nor branch–site analyses detected significant evidence of lineage-specific positive selection. Conclusions: This long-read-based mitogenome provides a high-quality genomic resource for P. chungtienensis and reveals substantial mitochondrial sequence and lineage variation among available records. These results provide a basis for comparative mitogenomic and conservation genetic studies while also indicating that species-level phylogenetic relationships and high-altitude adaptation should not be inferred from mitochondrial data alone.