A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). Issue 8 (22nd August 2019)

• Record Type: Journal Article
• Authors: Wang, Lu; Wu, Jinwei; Liu, Xiaomei; Di, Dandan; Liang, Yuhong; Feng, Yifei; Zhang, Suyun; Li, Baoguo; Qi, Xiao-Guang
• Is Part Of: GigaScience. Volume 8:Issue 8(2019)
• Publication Date: 2019-08-22
• Subjects: high-quality -- Rhinopithecus roxellana -- genome assembly -- annotation -- BioNano optical maps; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giz098
• Languages: English
• ISSNs: 2047-217X

Abstract

Abstract: 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 ∼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 ∼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.