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Auditorium 2 Auditorium 2 - Symposium 18 - Asia/Australia/Oceana Hub - Genome assembly, spatiotemporal variation, and genetic admixture in Asia 7:00 - 10:00pm Sunday, 4th July, 2021 Presentation type Oral Symposia organisers: Shuhua Xu, Qiaomei Fu Please note, some speakers in this symposium also have a poster available to view. Oral presentations occur in the Auditorium listed and the Posters are available in one of two Poster Halls. Please do a search for "Presenters" via the search function of the online program for more information. SYMP18-1 Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references Haiyi Lou1, Yang Gao1,2, Bo Xie1, Yimin Wang1, Haikuan Zhang3, Miao Shi3, Sen Ma1, Xiaoxi Zhang1,2, Chang Liu1, Shuhua Xu1,2,4,5,6 1Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. 2School of Life Science and Technology, ShanghaiTech University, Shanghai, China. 3Berry Genomics, Beijing, China. 4Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China. 5Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China. 6Collaborative Innovation Center of Genetics and Development, Shanghai, China Abstract While the human reference assembly is continually being improved, it remains debatable whether a population-specific reference is necessary for each ethnic group. We applied multiple sequencing technologies to de novo assemble an individual genome (TJ1) from the Tujia population, an ethnic minority group most closely related to the Han Chinese. TJ1 provides a haplotype-resolved assembly of chromosome-scale high quality with N50 scaffold size >78 Mb. Notably, compared with GRCh38 and other de novo assemblies, TJ1 remarkably improved short-read mapping by ~2%, comparable to inter-individual genome-length difference, and enhanced calling precision by ~6-16% for structural variants. Furthermore, TJ1 facilitates detecting rare or low-frequency variants and identifying the fine-scale difference between closely-related populations, outstanding examples including population-stratified variants between Tujia and Han Chinese on genes like LCT and UBXN8. Our results support the necessity of a population-specific assembly and exemplify its particular value in the genetic analysis, especially for studying close-related populations. Keywords de novo assembly; Tujia; Population-specific reference genome; Haploid genome; Structural variation. All authors contributed equally to this work. SYMP18-2 Genetic admixture in the culturally unique Peranakan Chinese population in Southeast Asia Degang Wu1, Roger Foo2, Chaolong Wang1 1Huazhong University of Science and Technology, Wuhan, Hubei, China. 2National University of Singapore, Singapore, Singapore Abstract The Peranakan Chinese are culturally unique descendants of immigrants from China who settled in the Malay Archipelago ~300-500 years ago. Today, among large communities in Southeast Asia, the Peranakans have preserved Chinese traditions with strong influence from the local indigenous Malays. Yet, whether or to what extent genetic admixture co-occurred with the cultural mixture has been a topic of ongoing debate. We performed whole-genome sequencing (WGS) on 177 Singapore (SG) Peranakans and analyzed the data jointly with WGS data of Asian and European populations. We estimated that Peranakan Chinese inherited ~5.62% (95% confidence interval [CI]: 4.75-6.46%) Malay ancestry, much higher than that in SG Chinese (1.08%, 0.69- 1.53%), southern Chinese (0.86%, 0.57-1.31%), and northern Chinese (0.25%, 0.18-0.33%). A sex-biased admixture history, in which the Malay ancestry was contributed primarily by females, was supported by X chromosomal variants, and mitochondrial (MT) and Y haplogroups. Finally, we identified an ancient admixture event shared by Peranakan Chinese and SG Chinese ~1,612 (95% CI: 1,345-1,923) years ago, coinciding with the settlement history of Han Chinese in southern China, apart from the recent admixture event with Malays unique to Peranakan Chinese ~190 (159-213) years ago. These findings greatly advance our understanding of the dispersal history of Chinese and their interaction with indigenous populations in Southeast Asia. SYMP18-3 A dynamic 6,000-year genetic history of Eurasia’s eastern steppe Choongwon Jeong1, Ke Wang2, Shevan Wilkin2, William Timothy Treal Taylor2, Bryan K. Miller2, Jan H. Bemmann3, Raphaela Stahl2, Chelsea Chiovelli2, Florian Knolle2, Sodnom Ulziibayar4, Dorjpurev Khatanbaatar5, Diimaajav Erdenebaatar6, Ulambayar Erdenebat7, Ayudai Ochir8, Ganbold Ankhsanaa9, Chuluunkhuu Vanchigdash5, Battuga Ochir10, Chuluunbat Munkhbayar11, Dashzeveg Tumen7, Alexey Kovalev12, Nikolay Kradin13, Bilikto A. Bazarov14, Denis A. Miyagashev14, Prokopiy B. Konovalov14, Elena Zhambaltarova15, Alicia Ventresca Miller2, Wolfgang Haak2, Stephan Schiffels2, Johannes Krause2, Nicole Boivin2, Myagmar Erdene7, Jessica Hendy2, Christina Warinner2 1Seoul National University, Seoul, Korea, Republic of. 2Max Planck Institute for the Science of Human History, Jena, Germany. 3Rheinische Friedrich-Wilhelms-Universitat, Bonn, Germany. 4Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia. 5Mongolian University of Science and Technology, Ulaanbaatar, Mongolia. 6Ulaanbaatar State University, Ulaanbaatar, Mongolia. 7National University of Mongolia, Ulaanbaatar, Mongolia. 8International Institute for the Study of Nomadic Civilizations, Ulaanbaatar, Mongolia. 9National Centre for Cultural Heritage of Mongolia, Ulaanbaatar, Mongolia. 10Institute of History and Ethnology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia. 11University of Khovd, Khovd, Mongolia. 12Institute of Archaeology, Russian Academy of Sciences, Moscow, Russian Federation. 13Far East Branch of the Russian Academy of Sciences, Vladivostok, Russian Federation. 14Siberian Branch of the Russian Academy of Sciences, Ulan-Ude, Russian Federation. 15East Siberian State Institute of Culture, Ulan-Ude, Russian Federation Abstract The Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region’s population history. Here, we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe. SYMP18-4 Genetic connections and shared evolution of dark-skinned indigenous peoples in Asia Lian Deng1, Yuwen Pan1, Yinan Wang1, Hao Chen1, Kai Yuan1, Sihan Chen2, Dongsheng Lu1, Siti Shuhada Mokhtar3, Thuhairah Abdul Rahman4, Boon-Peng Hoh5, Shuhua Xu1,6 1Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Shanghai, China. 2Human Phenome Institute, Fudan University, Shanghai, China. 3Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Selangor, Malaysia. 4Clinical Pathology Diagnostic Centre Research Laboratory, Faculty of Medicine, Universiti Teknologi MARA, Selangor, Malaysia. 5Faculty of Medicine and Health Sciences, UCSI University, Kuala Lumpur, Malaysia. 6State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China Abstract Dark-skinned indigenous (DSI) people attract much attention for their unique and outstanding appearance, nevertheless, their genetic history and adaptive evolution remain mysteries. Here we conducted a population genomic study to dissect the genetic distinction and connection of broad geographical DSIs. Despite DSI groups show diverse genetic makeup and large inter-area genetic differentiation, we identified a basal Asian ancestry (bASN) specifically shared by the Asian DSIs. Interestingly, bASN was relatively enriched in ancient Asian human genomes dated as early as ~50,000 years before present, and diminished in more recent history. Notably, bASN was not likely derived from archaic hominins but rather modeled as a survived lineage of the initial peopling of Asia. Shared adaptations associated with the bASN were identified among DSI groups (e.g., LIMS1 for hair morphology) and enriched in neurological functions at an identical locus (e.g., NKAIN3) or different loci in an identical gene (e.g., TENM4). It remains debatable whether the dark skin phenotype is an ancestral feature or a result of genetic convergence. We show that the phenotypic convergence of the dark skin in DSIs could have resulted from parallel evolution (e.g., DDB1), convergence driven by genetic admixture (e.g., MTHFD1 and RAD18) or novel mutations (e.g., STK11), as well as notably purifying selection (e.g., MC1R). Our results provided new insights into the initial peopling of Asia and
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