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A draft human pangenome reference.

ABSTRACT: Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals¹. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

SUBMITTER: Liao WW

PROVIDER: S-EPMC10172123 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature

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A draft human pangenome reference.

Liao Wen-Wei WW Asri Mobin M Ebler Jana J Doerr Daniel D Haukness Marina M Hickey Glenn G Lu Shuangjia S Lucas Julian K JK Monlong Jean J Abel Haley J HJ Buonaiuto Silvia S Chang Xian H XH Cheng Haoyu H Chu Justin J Colonna Vincenza V Eizenga Jordan M JM Feng Xiaowen X Fischer Christian C Fulton Robert S RS Garg Shilpa S Groza Cristian C Guarracino Andrea A Harvey William T WT Heumos Simon S Howe Kerstin K Jain Miten M Lu Tsung-Yu TY Markello Charles C Martin Fergal J FJ Mitchell Matthew W MW Munson Katherine M KM Mwaniki Moses Njagi MN Novak Adam M AM Olsen Hugh E HE Pesout Trevor T Porubsky David D Prins Pjotr P Sibbesen Jonas A JA Sirén Jouni J Tomlinson Chad C Villani Flavia F Vollger Mitchell R MR Antonacci-Fulton Lucinda L LL Baid Gunjan G Baker Carl A CA Belyaeva Anastasiya A Billis Konstantinos K Carroll Andrew A Chang Pi-Chuan PC Cody Sarah S Cook Daniel E DE Cook-Deegan Robert M RM Cornejo Omar E OE Diekhans Mark M Ebert Peter P Fairley Susan S Fedrigo Olivier O Felsenfeld Adam L AL Formenti Giulio G Frankish Adam A Gao Yan Y Garrison Nanibaa' A NA Giron Carlos Garcia CG Green Richard E RE Haggerty Leanne L Hoekzema Kendra K Hourlier Thibaut T Ji Hanlee P HP Kenny Eimear E EE Koenig Barbara A BA Kolesnikov Alexey A Korbel Jan O JO Kordosky Jennifer J Koren Sergey S Lee HoJoon H Lewis Alexandra P AP Magalhães Hugo H Marco-Sola Santiago S Marijon Pierre P McCartney Ann A McDaniel Jennifer J Mountcastle Jacquelyn J Nattestad Maria M Nurk Sergey S Olson Nathan D ND Popejoy Alice B AB Puiu Daniela D Rautiainen Mikko M Regier Allison A AA Rhie Arang A Sacco Samuel S Sanders Ashley D AD Schneider Valerie A VA Schultz Baergen I BI Shafin Kishwar K Smith Michael W MW Sofia Heidi J HJ Abou Tayoun Ahmad N AN Thibaud-Nissen Françoise F Tricomi Francesca Floriana FF Wagner Justin J Walenz Brian B Wood Jonathan M D JMD Zimin Aleksey V AV Bourque Guillaume G Chaisson Mark J P MJP Flicek Paul P Phillippy Adam M AM Zook Justin M JM Eichler Evan E EE Haussler David D Wang Ting T Jarvis Erich D ED Miga Karen H KH Garrison Erik E Marschall Tobias T Hall Ira M IM Li Heng H Paten Benedict B

Nature 20230510 7960

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals<sup>1</sup>. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new allel ...[more]

PMID: 37165242

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Project description:BackgroundIndia harbors the world's largest cattle population, encompassing over 50 distinct Bos indicus breeds. This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle. To comprehensively characterize the genomic variation within Bos indicus and, specifically, dairy breeds, we aim to identify non-reference sequences and construct a comprehensive pangenome.ResultsFive representative genomes of prominent dairy breeds, including Gir, Kankrej, Tharparkar, Sahiwal, and Red Sindhi, were sequenced using 10X Genomics 'linked-read' technology. Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb, comparable to the Bos indicus Brahman reference genome. A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods, revealing 8 Mb and 17.7 Mb of novel sequence respectively. A confident set of 6,844 Non-reference Unique Insertions (NUIs) spanning 7.57 Mb was identified through both methods, representing the pangenome of Indian Bos indicus breeds. Comparative analysis with previously published pangenomes unveiled 2.8 Mb (37%) commonality with the Chinese indicine pangenome and only 1% commonality with the Bos taurus pangenome. Among these, 2,312 NUIs encompassing ~ 2 Mb, were commonly found in 98 samples of the 5 breeds and designated as Bos indicus Common Insertions (BICIs) in the population. Furthermore, 926 BICIs were identified within 682 protein-coding genes, 54 long non-coding RNAs (lncRNA), and 18 pseudogenes. These protein-coding genes were enriched for functions such as chemical synaptic transmission, cell junction organization, cell-cell adhesion, and cell morphogenesis. The protein-coding genes were found in various prominent quantitative trait locus (QTL) regions, suggesting potential roles of BICIs in traits related to milk production, reproduction, exterior, health, meat, and carcass. Notably, 63.21% of the bases within the BICIs call set contained interspersed repeats, predominantly Long Interspersed Nuclear Elements (LINEs). Additionally, 70.28% of BICIs are shared with other domesticated and wild species, highlighting their evolutionary significance.ConclusionsThis is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India. The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.

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A draft human pangenome reference.

Publications

A draft human pangenome reference.

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