TY - JOUR
T1 - Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset
AU - Jayakumar, Vasanthan
AU - Nishimura, Osamu
AU - Kadota, Mitsutaka
AU - Hirose, Naoki
AU - Sano, Hiromi
AU - Murakawa, Yasuhiro
AU - Yamamoto, Yumiko
AU - Nakaya, Masataka
AU - Tsukiyama, Tomoyuki
AU - Seita, Yasunari
AU - Nakamura, Shinichiro
AU - Kawai, Jun
AU - Sasaki, Erika
AU - Ema, Masatsugu
AU - Kuraku, Shigehiro
AU - Kawaji, Hideya
AU - Sakakibara, Yasubumi
N1 - Funding Information:
This study was supported Drug Discovery & Development program in the Japan Agency for Medical Research and Development (AMED) under grant number JP17kk0305008, and research grants to RIKEN Preventive Medicine and Diagnosis Innovation Program and RIKEN Center for Integrative Medical Sciences from The Ministry of Education, Culture, Sports, Science and Technology (MEXT). In addition, Y.S. was supported by JSPS KAKENHI Grant Numbers 18H04127, and a Grant-in-Aid for Scientific Research on Innovative Areas “Frontier Research on Chemical Communications” [no. 17H06410] from the Ministry of Education, Culture, Sports, Science and Technology of Japan. Non-Clinical Evaluation Expert Committee in Drug Evaluation Committee in Japan Pharmaceutical Manufacturers Association (JPMA) gave us constructive comments and warm encouragements. The authors have had a lot of supports and encouragements of discussion with Dr. Takao Inoue in the National Institute of Health Sciences. Special thanks to Dr. Yoshihide Hayashizaki in RIKEN Preventive Medicine and Diagnosis Innovation Program and Dr. Yasushi Okazaki in RIKEN Center for Integrative Medical Sciences.
Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12
Y1 - 2021/12
N2 - 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.
AB - 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.
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U2 - 10.1038/s41597-021-00935-6
DO - 10.1038/s41597-021-00935-6
M3 - Article
C2 - 34183680
AN - SCOPUS:85109750607
SN - 2052-4463
VL - 8
JO - Scientific Data
JF - Scientific Data
IS - 1
M1 - 159
ER -