| Accession | PRJCA000936 | |||||||||||||||
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| Title | Tibetan genome ZF1 | |||||||||||||||
| Relevance | Evolution | |||||||||||||||
| Umbrella project |
eGPS: evolutionary Genotype-Phenotype Systems biology Plateau Adaptability Analysis of adaptive traits in the Qinghai Tibet Plateau |
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| Data types | Whole genome sequencing | |||||||||||||||
| Organisms | Homo sapiens | |||||||||||||||
| Description | Structure variations (SVs) may play important roles in human adaption to extreme environments such as high altitude. A reference genome of native highlanders can facilitate identification of adaptive SVs. Here, combing long-read sequencing with next-generation mapping, we assembled a high-quality Tibetan genome (ZF1), with a contig N50 length of 24.57 mega-base pair (Mb) and a scaffold N50 length of 58.80Mb. We detected 17,900 SVs, and 6,505 of them are ZF1-specific when compared with two previously published de novo lowlander Asian genomes (AK1 and HX1). Further population comparison uncovered a 163bp deletion (located in the MKL1 gene) showing large divergence between Tibetans and Han Chinese. This deletion is significantly associated with systolic pulmonary arterial pressure, one of the key adaptive physiological traits in Tibetans. Moreover, we observed a much higher rate of archaic hominid (Neanderthal and Denisovan) introgression in ZF1 (1.32%-1.53%) compared to AK1 and HX1 (0.70%-0.98%), reflecting a unique genomic feature of Tibetans. One such archaic-hominid sequence, a 662-bp insertion in the intron of the SCUBE2 gene, showed large divergence between Tibetans and Han Chinese, and is associated with peripheral capillary oxygen saturation in Tibetans. Collectively, we generated the first de novo assembled Tibetan reference genome, and the identified SVs are valuable resources for future evolutionary and medical studies. | |||||||||||||||
| Sample scope | Monoisolate | |||||||||||||||
| Release date | 2019-10-11 | |||||||||||||||
| Publication |
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| Grants |
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| Submitter | Yaoxi He (heyaoxi@mail.kiz.ac.cn) | |||||||||||||||
| Organization | Kunming Institute of Zoology, Chinese Academy of Sciences | |||||||||||||||
| Submission date | 2018-07-17 |
| Resource name | Description |
|---|---|
| BioSample (1) | - |
| SAMC1896243 | ZF1 |