Journal
GIGASCIENCE
Volume 8, Issue 8, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gigascience/giz098
Keywords
high-quality; Rhinopithecus roxellana; genome assembly; annotation; BioNano optical maps
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Funding
- Strategic Priority Research Program of the Chinese Academy of Sciences [XDB31020302]
- National Natural Science Foundation of China [31 622 053]
- Promotional project for Innovation team
- Department of Science and Technology of Shaanxi Prov. China [2018TD-017]
- National Key Programme of Research and Development, the Ministry of Science and Technology of China [2016YFC0503200]
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Background: The golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered colobine species endemic to China, which has several distinct traits including a unique social structure. Although a genome assembly for R. roxellana is available, it is incomplete and fragmented because it was constructed using short-read sequencing technology. Thus, important information such as genome structural variation and repeat sequences may be absent. Findings: To obtain a high-quality chromosomal assembly for R. roxellana qinlingensis, we used 5 methods: Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, BioNano optical maps, 10X Genomics link-reads, and high-throughput chromosome conformation capture. The assembled genome was similar to 3.04 Gb, with a contig N50 of 5.72 Mb and a scaffold N50 of 144.56 Mb. This represented a 100-fold improvement over the previously published genome. In the new genome, 22,497 protein-coding genes were predicted, of which 22,053 were functionally annotated. Gene family analysis showed that 993 and 2,745 gene families were expanded and contracted, respectively. The reconstructed phylogeny recovered a close relationship between R. rollexana and Macaca mulatta, and these 2 species diverged similar to 13.4 million years ago. Conclusion: We constructed a high-quality genome assembly of the Qinling golden snub-nosed monkey; it had superior continuity and accuracy, which might be useful for future genetic studies in this species and as a new standard reference genome for colobine primates. In addition, the updated genome assembly might improve our understanding of this species and could assist conservation efforts.
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