RESUMO
Currently, the intraspecific taxonomy of snow sheep (Ovis nivicola) is controversial and needs to be specified using DNA molecular genetic markers. In our previous work using whole-genome single nucleotide polymorphism (SNP) analysis, we found that the population inhabiting Kharaulakh Ridge was genetically different from the other populations of Yakut subspecies to which it was usually referred. Here, our study was aimed at the clarification of taxonomic status of Kharaulakh snow sheep using mitochondrial cytochrome b gene. A total of 87 specimens from five different geographic locations of Yakut snow sheep as well as 20 specimens of other recognized subspecies were included in this study. We identified 19 haplotypes, two of which belonged to the population from Kharaulakh Ridge. Median-joining network and Bayesian tree analyses revealed that Kharaulakh population clustered separately from all the other Yakut snow sheep. The divergence time between Kharaulakh population and Yakut snow sheep was estimated as 0.48 ± 0.19 MYA. Thus, the study of the mtDNA cytb sequences confirmed the results of genome-wide SNP analysis. Taking into account the high degree of divergence of Kharaulakh snow sheep from other groups, identified by both nuclear and mitochondrial DNA markers, we propose to classify the Kharaulakh population as a separate subspecies.
RESUMO
The snow sheep, Ovis nivicola, which is endemic to the mountain ranges of northeastern Siberia, are well adapted to the harsh cold climatic conditions of their habitat. In this study, using long reads of Nanopore sequencing technology, whole-genome sequencing, assembly, and gene annotation of a snow sheep were carried out. Additionally, RNA-seq reads from several tissues were also generated to supplement the gene prediction in snow sheep genome. The assembled genome was â¼2.62 Gb in length and was represented by 7,157 scaffolds with N50 of about 2 Mb. The repetitive sequences comprised of 41% of the total genome. BUSCO analysis revealed that the snow sheep assembly contained full-length or partial fragments of 97% of mammalian universal single-copy orthologs (n = 4,104), illustrating the completeness of the assembly. In addition, a total of 20,045 protein-coding sequences were identified using comprehensive gene prediction pipeline. Of which 19,240 (â¼96%) sequences were annotated using protein databases. Moreover, homology-based searches and de novo identification detected 1,484 tRNAs; 243 rRNAs; 1,931 snRNAs; and 782 miRNAs in the snow sheep genome. To conclude, we generated the first de novo genome of the snow sheep using long reads; these data are expected to contribute significantly to our understanding related to evolution and adaptation within the Ovis genus.
Assuntos
Genoma , Ovinos/genética , Animais , Frio Extremo , MasculinoRESUMO
Insights into the genetic characteristics of a species provide important information for wildlife conservation programs. Here, we used the OvineSNP50 BeadChip developed for domestic sheep to examine population structure and evaluate genetic diversity of snow sheep (Ovis nivicola) inhabiting Verkhoyansk Range and Momsky Ridge. A total of 1,121 polymorphic SNPs were used to test 80 specimens representing five populations, including four populations of the Verkhoyansk Mountain chain: Kharaulakh Ridge-Tiksi Bay (TIK, n = 22), Orulgan Ridge (ORU, n = 22), the central part of Verkhoyansk Range (VER, n = 15), Suntar-Khayata Ridge (SKH, n = 13), and Momsky Ridge (MOM, n = 8). We showed that the studied populations were genetically structured according to a geographic pattern. Pairwise FST values ranged from 0.044 to 0.205. Admixture analysis identified K = 2 as the most likely number of ancestral populations. A Neighbor-Net tree showed that TIK was an isolated group related to the main network through ORU. TreeMix analysis revealed that TIK and MOM originated from two different ancestral populations and detected gene flow from MOM to ORU. This was supported by the f3 statistic, which showed that ORU is an admixed population with TIK and MOM/SKH heritage. Genetic diversity in the studied groups was increasing southward. Minimum values of observed (Ho) and expected (He) heterozygosity and allelic richness (Ar) were observed in the most northern population-TIK, and maximum values were observed in the most southern population-SKH. Thus, our results revealed clear genetic structure in the studied populations of snow sheep and showed that TIK has a different origin from MOM, SKH, and VER even though they are conventionally considered a single subspecies known as Yakut snow sheep (Ovis nivicola lydekkeri). Most likely, TIK was an isolated group during the Late Pleistocene glaciations of Verkhoyansk Range.