Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset

Vasanthan Jayakumar, Osamu Nishimura, Mitsutaka Kadota, Naoki Hirose, Hiromi Sano, Yasuhiro Murakawa, Yumiko Yamamoto, Masataka Nakaya, Tomoyuki Tsukiyama, Yasunari Seita, Shinichiro Nakamura, Jun Kawai, Erika Sasaki, Masatsugu Ema, Shigehiro Kuraku, Hideya Kawaji, Yasubumi Sakakibara

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)


Cynomolgus macaque (Macaca fascicularis) and common marmoset (Callithrix jacchus) have been widely used in human biomedical research. Long-standing primate genome assemblies used the human genome as a reference for ordering and orienting the assembled fragments into chromosomes. Here we performed de novo genome assembly of these two species without any human genome-based bias observed in the genome assemblies released earlier. We assembled PacBio long reads, and the resultant contigs were scaffolded with Hi-C data, which were further refined based on Hi-C contact maps and alternate de novo assemblies. The assemblies achieved scaffold N50 lengths of 149 Mb and 137 Mb for cynomolgus macaque and common marmoset, respectively. The high fidelity of our assembly is also ascertained by BAC-end concordance in common marmoset. Our assembly of cynomolgus macaque outperformed all the available assemblies of this species in terms of contiguity. The chromosome-scale genome assemblies produced in this study are valuable resources for non-human primate models and provide an important baseline in human biomedical research.

Original languageEnglish
Article number159
JournalScientific Data
Issue number1
Publication statusPublished - 2021 Dec

ASJC Scopus subject areas

  • Statistics and Probability
  • Information Systems
  • Education
  • Computer Science Applications
  • Statistics, Probability and Uncertainty
  • Library and Information Sciences


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