scholarly journals Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

Science ◽  
2020 ◽  
Vol 370 (6523) ◽  
pp. eabc6617
Author(s):  
Wesley C. Warren ◽  
R. Alan Harris ◽  
Marina Haukness ◽  
Ian T. Fiddes ◽  
Shwetha C. Murali ◽  
...  
Keyword(s):  
Rhesus Macaque ◽  
Rhesus Macaques ◽  
Gene Families ◽  
Segmental Duplications ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Isoform Diversity ◽  
Macaque Genome ◽  
Lineage Specific Genes ◽  
Rhesus Macaque Genome

The rhesus macaque (Macaca mulatta) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Whole-genome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.

scholarly journals Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

Science ◽  
2007 ◽  
Vol 316 (5822) ◽  
pp. 222-234 ◽  
Author(s):  
◽  
R. A. Gibbs ◽  
J. Rogers ◽  
M. G. Katze ◽  
R. Bumgarner ◽  
...  
Keyword(s):  
Rhesus Macaque ◽  
Macaque Genome ◽  
Rhesus Macaque Genome

scholarly journals Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies

2008 ◽  
Vol 17 (8) ◽  
pp. 1127-1136 ◽  
Author(s):  
Arthur S. Lee ◽  
María Gutiérrez-Arcelus ◽  
George H. Perry ◽  
Eric J. Vallender ◽  
Welkin E. Johnson ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Rhesus Macaque ◽  
Human Disease ◽  
Copy Number ◽  
Macaque Genome ◽  
Number Variation ◽  
Candidate Loci ◽  
Rhesus Macaque Genome

scholarly journals Mobile DNA in Old World Monkeys: A Glimpse Through the Rhesus Macaque Genome

Science ◽  
2007 ◽  
Vol 316 (5822) ◽  
pp. 238-240 ◽  
Author(s):  
K. Han ◽  
M. K. Konkel ◽  
J. Xing ◽  
H. Wang ◽  
J. Lee ◽  
...  
Keyword(s):  
Rhesus Macaque ◽  
Old World Monkeys ◽  
Mobile Dna ◽  
Old World ◽  
Macaque Genome ◽  
Rhesus Macaque Genome

scholarly journals Host- and Species-Dependent Quasispecies Divergence of Severe Acute Respiratory Syndrome Coronavirus-2 in Non-human Primate Models

2021 ◽  
Vol 12 ◽  
Author(s):  
Eun-Ha Hwang ◽  
Hoyin Chung ◽  
Green Kim ◽  
Hanseul Oh ◽  
You Jung An ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Rhesus Macaques ◽  
Vero Cells ◽  
Frequency Variation ◽  
Nucleotide Polymorphisms ◽  
Human Beings ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Coding Regions ◽  
Variant Analysis

Recently, newly emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been continuously reported worldwide. However, the precise evaluation of SARS-CoV-2 microevolution in host is very limited because the exact genetic information of infected virus could not be acquired in human researches. In this report, we performed deep sequencing for seed virus and SARS-CoV-2 isolated in eight cynomolgus and rhesus macaques at 3 days postinoculation and evaluated single-nucleotide polymorphisms (SNPs) in SARS-CoV-2 by variant analysis. A total of 69 single-nucleotide variants (SNVs) were present in the 5′-untranslated region (UTR), 3′-UTR, ORF1ab, S, ORF3a, ORF8, and N genes of the seed virus passaged in VERO cells. Between those present on the seed virus and those on each SARS-CoV-2 isolated from the lungs of the macaques, a total of 29 variants was identified in 4 coding proteins (ORF1ab, S, ORF3a, and N) and non-coding regions (5′- and 3′-UTR). Variant number was significantly different according to individuals and ranged from 2 to 11. Moreover, the average major frequency variation was identified in six sites between the cynomolgus monkeys and rhesus macaques. As with diverse SNPs in SARS-CoV-2, the values of viral titers in lungs were significantly different according to individuals and species. Our study first revealed that the genomes of SARS-CoV-2 differ according to individuals and species despite infection of the identical virus in non-human primates (NHPs). These results are important for the interpretation of longitudinal studies evaluating the evolution of the SARS-CoV-2 in human beings and development of new diagnostics, vaccine, and therapeutics targeting SARS-CoV-2.

scholarly journals Advantages of an Improved Rhesus Macaque Genome for Evolutionary Analyses

PLoS ONE ◽  
2016 ◽  
Vol 11 (12) ◽  
pp. e0167376 ◽  
Author(s):  
Julien S. Gradnigo ◽  
Abhishek Majumdar ◽  
Robert B. Norgren ◽  
Etsuko N. Moriyama
Keyword(s):  
Rhesus Macaque ◽  
Macaque Genome ◽  
Rhesus Macaque Genome

scholarly journals Cynomolgus and Chinese rhesus macaque genome assembly and analysis

2011 ◽  
Author(s):  
Zhiyong Huang ◽  
Zhiyong Huang ◽  
Guangmei Yan ◽  
Jun Wang ◽  
Xiaoning Wang ◽  
...  
Keyword(s):  
Rhesus Macaque ◽  
Genome Assembly ◽  
Chinese Rhesus Macaque ◽  
Macaque Genome ◽  
Rhesus Macaque Genome

scholarly journals Identification of novel homologous microRNA genes in the rhesus macaque genome

BMC Genomics ◽  
2008 ◽  
Vol 9 (1) ◽  
pp. 8 ◽  
Author(s):  
Junming Yue ◽  
Yi Sheng ◽  
Kyle E Orwig
Keyword(s):  
Rhesus Macaque ◽  
Macaque Genome ◽  
Microrna Genes ◽  
Rhesus Macaque Genome
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