A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome
文献类型：期刊论文
| 作者 | Liang, Shen-Ao7; Ren, Tianxin6; Zhang, Jiayu7; He, Jiahui5; Wang, Xuankai6; Jiang, Xinrui6; He, Yuan5; Mccoy, Rajiv C.3; Fu, Qiaomei1,4; Akey, Joshua M.8 |
| 刊名 | GENOME BIOLOGY
 |
| 出版日期 | 2025-02-17 |
| 卷号 | 26期号:1页码:20 |
| 关键词 | T2T-CHM13 Archaic admixture Adaptive introgression Database Complete human genome sequence |
| ISSN号 | 1474-760X |
| DOI | 10.1186/s13059-025-03502-z |
| 英文摘要 | BackgroundLeveraging long-read sequencing technologies, the first complete human reference genome, T2T-CHM13, corrects assembly errors in previous references and resolves the remaining 8% of the genome. While studies on archaic admixture in modern humans have so far relied on the GRCh37 reference due to the availability of archaic genome data, the impact of T2T-CHM13 in this field remains unexplored.ResultsWe remap the sequencing reads of the high-quality Altai Neanderthal and Denisovan genomes onto GRCh38 and T2T-CHM13. Compared to GRCh37, we find that T2T-CHM13 significantly improves read mapping quality in archaic samples. We then apply IBDmix to identify Neanderthal-introgressed sequences in 2504 individuals from 26 geographically diverse populations using different reference genomes. We observe that commonly used pre-phasing filtering strategies in public datasets substantially influence archaic ancestry determination, underscoring the need for careful filter selection. Our analysis identifies approximately 51 Mb of Neanderthal sequences unique to T2T-CHM13, predominantly in genomic regions where GRCh38 and T2T-CHM13 assemblies diverge. Additionally, we uncover novel instances of population-specific archaic introgression in diverse populations, spanning genes involved in metabolism, olfaction, and ion-channel function. Finally, to facilitate the exploration of archaic alleles and adaptive signals in human genomics and evolutionary research, we integrate these introgressed sequences and adaptive signals across all reference genomes into a visualization database, ASH (www.arcseqhub.com).ConclusionsOur study enhances the detection of archaic variations in modern humans, highlights the importance of utilizing the T2T-CHM13 reference, and provides novel insights into the functional consequences of archaic hominin admixture. |
| WOS关键词 | ANCESTRY ; ADAPTATION ; DISCOVERY ; FRAMEWORK ; ADMIXTURE ; CAVE ; DNA |
| 资助项目 | National Natural Science Foundation of China[32270668] ; The 111 project[B25056] ; Natural Science Foundation of Chongqing, China[CSTB2024NSCQ- JQX0004] ; Shanghai Jiao Tong University 2030 Initiative[WH510363003/016] |
| WOS研究方向 | Biotechnology & Applied Microbiology ; Genetics & Heredity |
| 语种 | 英语 |
| WOS记录号 | WOS:001423539300001 |
| 出版者 | BMC |
| 源URL | [http://119.78.100.205/handle/311034/24368]  |
| 专题 | 中国科学院古脊椎动物与古人类研究所 |
| 通讯作者 | Mao, Yafei; Chen, Lu |
| 作者单位 | 1.Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing 100044, Peoples R China 2.Zhejiang Univ, Affiliated Hosp 4, Int Inst Med, Ctr Genom Res, Yiwu 322000, Peoples R China 3.Johns Hopkins Univ, Dept Biol, Baltimore, MD 21212 USA 4.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 5.Fudan Univ, Ctr Evolutionary Biol, Sch Life Sci, Minist Educ,Key Lab Contemporary Anthropol, Shanghai 200438, Peoples R China 6.Shanghai Jiao Tong Univ, Bio X Inst, Key Lab Genet Dev & Neuropsychiat Disorders, Minist Educ, Shanghai 200030, Peoples R China 7.Fudan Univ, Ctr Evolutionary Biol, Sch Life Sci, State Key Lab Genet Engn, Shanghai 200438, Peoples R China 8.Princeton Univ, Lewis Sigler Inst Integrat Genom, Princeton, NJ 08540 USA |
| 推荐引用方式 GB/T 7714 | Liang, Shen-Ao,Ren, Tianxin,Zhang, Jiayu,et al. A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome[J]. GENOME BIOLOGY,2025,26(1):20. |
| APA | Liang, Shen-Ao.,Ren, Tianxin.,Zhang, Jiayu.,He, Jiahui.,Wang, Xuankai.,...&Chen, Lu.(2025).A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome.GENOME BIOLOGY,26(1),20. |
| MLA | Liang, Shen-Ao,et al."A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome".GENOME BIOLOGY 26.1(2025):20. |
入库方式： OAI收割
来源：古脊椎动物与古人类研究所
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