A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana)

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.

Fifty Years of Research on European Mink Mustela lutreola L., 1761 Genetics: Where Are We Now in Studies on One of the Most Endangered Mammals?

“…The whole-genome approach was previously applied to the conservation of African wild dog Lycaon pictus to detect inbreeding and population-specific selection [ 170 ]. Genomics provides tools for population evaluation monitoring and management of small populations in the wild and in captivity, species delineation, and to enhance wildlife health management and identify risk factors for genetic disorders of endangered primates [ 171 , 172 , 173 ]. Conservation genomics helped to identify the conservation implications of admixture in the Eastern wolf Canis lupus lycaon [ 165 ].…”

Advances in optical mapping for genomic research

“…In current genome-assembly pipelines, optical maps are commonly used with a combination of PacBio or Oxford Nanopore reads with Hi-C data to build reference-quality genome assemblies. This technology combination has been applied to genome analysis in various species, such as humans [91] , [92] , other animals [93] , [94] , [95] , [96] , and plants [97] , [98] , [99] , [100] , [101] , [102] , [103] , [104] , [105] , [106] , [107] , [108] , [109] , [110] . In particular, the Genome Reference Consortium (GRC), in an effort to improve the quality of reference genomes by error correction, gap closure, and variation representation, has been producing optical mapping data for humans and other model organisms [36] .…”

A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia IllucensL.)

“…Nonetheless, integrating long read and linked-read sequencing has greatly facilitated de novo assemblies [24]. Combined with high-throughput chromosome conformation capture (Hi-C) sequencing, the assembly of chromosome-level reference genomes in vertebrates, invertebrates and plants is far more approachable [25][26][27].…”