Building the sequence map of the human pan-genome.
Here we integrate the de novo assembly of an Asian and an African genome with the NCBI reference human genome, as a step toward constructing the human pan-genome. We identified approximately 5 Mb of novel sequences not present in the reference genome in each of these assemblies. Most novel sequences are individual or population specific, as revealed by their comparison to all available human DNA sequence and by PCR validation using the human genome diversity cell line panel. We found novel sequences present in patterns consistent with known human migration paths. Cross-species conservation analysis of predicted genes indicated that the novel sequences contain potentially functional coding regions. We estimate that a complete human pan-genome would contain approximately 19-40 Mb of novel sequence not present in the extant reference genome. The extensive amount of novel sequence contributing to the genetic variation of the pan-genome indicates the importance of using complete genome sequencing and de novo assembly.
Li
Ruiqiang
R
BGI-Shenzhen, Shenzhen 518083, China.
Li
Yingrui
Y
Zheng
Hancheng
H
Luo
Ruibang
R
Zhu
Hongmei
H
Li
Qibin
Q
Qian
Wubin
W
Ren
Yuanyuan
Y
Tian
Geng
G
Li
Jinxiang
J
Zhou
Guangyu
G
Zhu
Xuan
X
Wu
Honglong
H
Qin
Junjie
J
Jin
Xin
X
Li
Dongfang
D
Cao
Hongzhi
H
Hu
Xueda
X
Blanche
Hélène
H
Cann
Howard
H
Zhang
Xiuqing
X
Li
Songgang
S
Bolund
Lars
L
Kristiansen
Karsten
K
Yang
Huanming
H
Wang
Jun
J
Wang
Jian
J
D000818:Animals; D001483:Base Sequence; D005828:Genetics, Population; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity