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. 2019 Feb 5;6:190009.
doi: 10.1038/sdata.2019.9.

The Sequence and De Novo Assembly of Oxygymnocypris Stewartii Genome

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Free PMC article

The Sequence and De Novo Assembly of Oxygymnocypris Stewartii Genome

Hai-Ping Liu et al. Sci Data. .
Free PMC article

Abstract

Animal genomes in the Qinghai-Tibetan Plateau provide valuable resources for scientists to understand the molecular mechanism of environmental adaptation. Tibetan fish species play essential roles in the local ecology; however, the genomic information for native fishes was still insufficient. Oxygymnocypris stewartii, belonging to Oxygymnocypris genus, Schizothoracinae subfamily, is a native fish in the Tibetan plateau living within the elevation from roughly 3,000 m to 4,200 m. In this report, PacBio and Illumina sequencing platform were used to generate ~385.3 Gb genomic sequencing data. A genome of about 1,849.2 Mb was obtained with a contig N50 length of 257.1 kb. More than 44.5% of the genome were identified as repetitive elements, and 46,400 protein-coding genes were annotated in the genome. The assembled genome can be used as a reference for future population genetic studies of O. stewartii and will improve our understanding of high altitude adaptation of fishes in the Qinghai-Tibetan Plateau.

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1. A picture of Oxygymnocypris stewartii.
(a) The appearance of Oxygymnocypris stewartii; (b) Distributed localization (red triangle) of Oxygymnocypris stewartii for the genomic sequencing.
Figure 2
Figure 2. 17-mer frequency distribution in Oxygymnocypris stewartii genomes.
The X-axis is the Kmer depth, and Y-axis represents the frequency of the Kmer for a given depth.
Figure 3
Figure 3. Distribution of the divergence rate of each type of repetitive element in Oxygymnocypris stewartii genome.
The divergence rate was calculated between the identified TE elements in the genome by the homology-based method and the consensus sequence in the Repbase.
Figure 4
Figure 4. Comparisons of the prediction gene models in the Oxygymnocypris stewartii genome to other species.
(a) CDS length distribution and comparison with other species. (b) Exon length distribution and comparison with other species. (c) Exon number distribution and comparison with other species. (d) Gene length distribution and comparison with other species. (e) Intron length distribution and comparison with other species.
Figure 5
Figure 5. Venn diagram of the number of genes with functional annotation using multiple public databases.

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References

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