. 2020 Jul 1;9(7):giaa069.

doi: 10.1093/gigascience/giaa069.

Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding

Morteza Roodgar^{1

2}, Afshin Babveyh¹, Lan H Nguyen³, Wenyu Zhou^{1

4}, Rahul Sinha², Hayan Lee¹, John B Hanks⁵, Mohan Avula¹, Lihua Jiang¹, Ruiqi Jian¹, Hoyong Lee⁶, Giltae Song⁶, Hassan Chaib⁴, Irv L Weissman², Serafim Batzoglou⁷, Susan Holmes⁸, David G Smith⁹, Joseph L Mankowski¹⁰, Stefan Prost^{11

12}, Michael P Snyder^{1

4}

Affiliations

¹ Department of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA.
² Institute for Stem Cell Biology and Regenerative Medicine, 265 Campus Dr., Stanford University, Stanford, CA 94305, USA.
³ Institute for computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.
⁴ Stanford Center for Genomics and Personalized Medicine, Stanford University, 3165 Porter Dr. Palo Alto, CA 94305, USA.
⁵ Stanford Research Computing Center, Stanford University, Stanford, CA 94305, USA.
⁶ School of Computer Science and Engineering, Pusan National University, Busan 46241, South Korea.
⁷ Department of Computer Science, Stanford University, Stanford, CA 94305, USA.
⁸ Department of Statistics, Stanford University, Stanford, CA 94305, USA.
⁹ California National Primate Research Center, University of California, Davis, CA 95616, USA.
¹⁰ Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
¹¹ LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg 25, 60325 Frankfurt am Main, Germany.
¹² South African National Biodiversity Institute, National Zoological Garden, Pretoria, 0184, South Africa.

PMID: 32649757
PMCID: PMC7350979
DOI: 10.1093/gigascience/giaa069

Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding

Morteza Roodgar et al. Gigascience. 2020.

. 2020 Jul 1;9(7):giaa069.

doi: 10.1093/gigascience/giaa069.

Authors

Affiliations

¹ Department of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA.
² Institute for Stem Cell Biology and Regenerative Medicine, 265 Campus Dr., Stanford University, Stanford, CA 94305, USA.
³ Institute for computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.
⁴ Stanford Center for Genomics and Personalized Medicine, Stanford University, 3165 Porter Dr. Palo Alto, CA 94305, USA.
⁵ Stanford Research Computing Center, Stanford University, Stanford, CA 94305, USA.
⁶ School of Computer Science and Engineering, Pusan National University, Busan 46241, South Korea.
⁷ Department of Computer Science, Stanford University, Stanford, CA 94305, USA.
⁸ Department of Statistics, Stanford University, Stanford, CA 94305, USA.
⁹ California National Primate Research Center, University of California, Davis, CA 95616, USA.
¹⁰ Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
¹¹ LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg 25, 60325 Frankfurt am Main, Germany.
¹² South African National Biodiversity Institute, National Zoological Garden, Pretoria, 0184, South Africa.

PMID: 32649757
PMCID: PMC7350979
DOI: 10.1093/gigascience/giaa069

Abstract

Background: Macaque species share >93% genome homology with humans and develop many disease phenotypes similar to those of humans, making them valuable animal models for the study of human diseases (e.g., HIV and neurodegenerative diseases). However, the quality of genome assembly and annotation for several macaque species lags behind the human genome effort.

Results: To close this gap and enhance functional genomics approaches, we used a combination of de novo linked-read assembly and scaffolding using proximity ligation assay (HiC) to assemble the pig-tailed macaque (Macaca nemestrina) genome. This combinatorial method yielded large scaffolds at chromosome level with a scaffold N50 of 127.5 Mb; the 23 largest scaffolds covered 90% of the entire genome. This assembly revealed large-scale rearrangements between pig-tailed macaque chromosomes 7, 12, and 13 and human chromosomes 2, 14, and 15. We subsequently annotated the genome using transcriptome and proteomics data from personalized induced pluripotent stem cells derived from the same animal. Reconstruction of the evolutionary tree using whole-genome annotation and orthologous comparisons among 3 macaque species, human, and mouse genomes revealed extensive homology between human and pig-tailed macaques with regards to both pluripotent stem cell genes and innate immune gene pathways. Our results confirm that rhesus and cynomolgus macaques exhibit a closer evolutionary distance to each other than either species exhibits to humans or pig-tailed macaques.

Conclusions: These findings demonstrate that pig-tailed macaques can serve as an excellent animal model for the study of many human diseases particularly with regards to pluripotency and innate immune pathways.

Keywords: HiC; chromosome-level assembly; linked-read; nonhuman primate; pig-tailed macaque.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

**Figure 1:**
(A) Schematic figure of the methods used for the assembly of the pig-tailed macaque genome (Ma2). (1) The linked-read method resulted in a scaffold N50 of 8.6 Mb. (2) Proximity ligation assay followed by scaffolding using HiC method resulted in a scaffold N50 of 127.5 Mb (almost chromosome level). (B) Comparison of the number of scaffolds (X axis) and the proportion of the genome covered by the assembled scaffolds (Y axis). The 23 largest pig-tailed macaque scaffolds (blue line) cover ~90% of the genome. The red line presents the scaffold sizes of human genome (GRCh38) assembly, and the green line is the current assembly of pig-tailed macaque on NCBI (Mnem_1.0). (C) Karyotype of the pig-tailed macaque chromosomes.

**Figure 2:**
Synteny analysis and structural differences between pig-tailed macaque (PM) chromosomes 1 (PM1), PM chromosome 2 (PM2), through PM chromosomes X (PMX) and Y (PMY) with (A) human chromosomes 1 through Y (HS1–HSY), (B) rhesus macaque (RM) chromosomes. (C) Alignment identity scores between human genome and PM chromosome 3 (PM3), (D) Alignment identity score between RM genome and PM chromosome 3 (PM3), (E) Alignment identity score between human genome and PM chromosome 7 (PM7), (F) Alignment identity score between RM genome and PM chromosome 7 (PM7).

**Figure 3:**
(A) Linked density histogram of the assembled scaffolds of the pig-tailed macaque genome. The numbers mark the largest assembled scaffolds corresponding to the 22 chromosomes. (B, C) Mapping of HiC read pairs on the pig-tailed macaque chromosome 7 (B) and the pig-tailed macaque chromosome 12 (C). Dark purple dots indicate read pairs. As can be seen read pair coverage is even over the chromosomes, indicating that the observed chromosomal changes compared to the human genome are likely genuine and not caused my misassemblies.

**Figure 4:**
Reconstruction of the phylogenetic relationships among the 3 macaque species and human. (A) The tree topology that is represented by most of the conserved genes among human, pig-tailed macaque (PM), rhesus macaque (RM), cynomolgus macaque (CM), and mouse as an outgroup. Of the 4,434 most conserved orthologs, 52.8% follow the topology of tree 1. Also, 452 (49.9%) orthologs out of 906 most conserved innate immune (IM) genes and 30 (44.8%) of 67 most conserved pluripotent stem cell (PSC) genes follow the topology of tree 1. (B) Trees 2, 3, and 4, each representing different proportions of all of conserved orthologs, IM genes, and PSC genes among the 3 macaque species, human, and mouse.

See this image and copyright information in PMC

References

1. Gibbs RA, Rogers J, Katze MG, et al. . Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007;316(5822):222–34. - PubMed
1. Boffelli D, McAuliffe J, Ovcharenko D, et al. . Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science. 2003;299(5611):1391–4. - PubMed
1. Shibata R, Igarashi T, Haigwood N, et al. . Neutralizing antibody directed against the HIV–1 envelope glycoprotein can completely block HIV–1/SIV chimeric virus infections of macaque monkeys. Nat Med. 1999;5(2):204. - PubMed
1. Hatziioannou T, Evans DT. Animal models for HIV/AIDS research. Nat Rev Microbiol. 2012;10(12):852. - PMC - PubMed
1. Joag SV, Li Z, Foresman L, et al. . Chimeric simian/human immunodeficiency virus that causes progressive loss of CD4+ T cells and AIDS in pig-tailed macaques. J Virol. 1996;70(5):3189–97. - PMC - PubMed

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Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding

Affiliations

Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Miscellaneous