Assembly and annotation of an Ashkenazi human reference genome
Abstract Background Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very small sample of the human population. There is a need for reference genom...
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doaj-34b6a666474a481a80ed46ff3264dec42020-11-25T03:28:59ZengBMCGenome Biology1474-760X2020-06-0121111810.1186/s13059-020-02047-7Assembly and annotation of an Ashkenazi human reference genomeAlaina Shumate0Aleksey V. Zimin1Rachel M. Sherman2Daniela Puiu3Justin M. Wagner4Nathan D. Olson5Mihaela Pertea6Marc L. Salit7Justin M. Zook8Steven L. Salzberg9Center for Computational Biology, Johns Hopkins UniversityCenter for Computational Biology, Johns Hopkins UniversityCenter for Computational Biology, Johns Hopkins UniversityCenter for Computational Biology, Johns Hopkins UniversityNational Institute of Standards and TechnologyNational Institute of Standards and TechnologyCenter for Computational Biology, Johns Hopkins UniversityJoint Initiative for Metrology in Biology, Stanford UniversityNational Institute of Standards and TechnologyCenter for Computational Biology, Johns Hopkins UniversityAbstract Background Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very small sample of the human population. There is a need for reference genomes from multiple human populations to avoid potential biases. Results Here, we describe the assembly and annotation of the genome of an Ashkenazi individual and the creation of a new, population-specific human reference genome. This genome is more contiguous and more complete than GRCh38, the latest version of the human reference genome, and is annotated with highly similar gene content. The Ashkenazi reference genome, Ash1, contains 2,973,118,650 nucleotides as compared to 2,937,639,212 in GRCh38. Annotation identified 20,157 protein-coding genes, of which 19,563 are > 99% identical to their counterparts on GRCh38. Most of the remaining genes have small differences. Forty of the protein-coding genes in GRCh38 are missing from Ash1; however, all of these genes are members of multi-gene families for which Ash1 contains other copies. Eleven genes appear on different chromosomes from their homologs in GRCh38. Alignment of DNA sequences from an unrelated Ashkenazi individual to Ash1 identified ~ 1 million fewer homozygous SNPs than alignment of those same sequences to the more-distant GRCh38 genome, illustrating one of the benefits of population-specific reference genomes. Conclusions The Ash1 genome is presented as a reference for any genetic studies involving Ashkenazi Jewish individuals.http://link.springer.com/article/10.1186/s13059-020-02047-7 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Alaina Shumate Aleksey V. Zimin Rachel M. Sherman Daniela Puiu Justin M. Wagner Nathan D. Olson Mihaela Pertea Marc L. Salit Justin M. Zook Steven L. Salzberg |
spellingShingle |
Alaina Shumate Aleksey V. Zimin Rachel M. Sherman Daniela Puiu Justin M. Wagner Nathan D. Olson Mihaela Pertea Marc L. Salit Justin M. Zook Steven L. Salzberg Assembly and annotation of an Ashkenazi human reference genome Genome Biology |
author_facet |
Alaina Shumate Aleksey V. Zimin Rachel M. Sherman Daniela Puiu Justin M. Wagner Nathan D. Olson Mihaela Pertea Marc L. Salit Justin M. Zook Steven L. Salzberg |
author_sort |
Alaina Shumate |
title |
Assembly and annotation of an Ashkenazi human reference genome |
title_short |
Assembly and annotation of an Ashkenazi human reference genome |
title_full |
Assembly and annotation of an Ashkenazi human reference genome |
title_fullStr |
Assembly and annotation of an Ashkenazi human reference genome |
title_full_unstemmed |
Assembly and annotation of an Ashkenazi human reference genome |
title_sort |
assembly and annotation of an ashkenazi human reference genome |
publisher |
BMC |
series |
Genome Biology |
issn |
1474-760X |
publishDate |
2020-06-01 |
description |
Abstract Background Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very small sample of the human population. There is a need for reference genomes from multiple human populations to avoid potential biases. Results Here, we describe the assembly and annotation of the genome of an Ashkenazi individual and the creation of a new, population-specific human reference genome. This genome is more contiguous and more complete than GRCh38, the latest version of the human reference genome, and is annotated with highly similar gene content. The Ashkenazi reference genome, Ash1, contains 2,973,118,650 nucleotides as compared to 2,937,639,212 in GRCh38. Annotation identified 20,157 protein-coding genes, of which 19,563 are > 99% identical to their counterparts on GRCh38. Most of the remaining genes have small differences. Forty of the protein-coding genes in GRCh38 are missing from Ash1; however, all of these genes are members of multi-gene families for which Ash1 contains other copies. Eleven genes appear on different chromosomes from their homologs in GRCh38. Alignment of DNA sequences from an unrelated Ashkenazi individual to Ash1 identified ~ 1 million fewer homozygous SNPs than alignment of those same sequences to the more-distant GRCh38 genome, illustrating one of the benefits of population-specific reference genomes. Conclusions The Ash1 genome is presented as a reference for any genetic studies involving Ashkenazi Jewish individuals. |
url |
http://link.springer.com/article/10.1186/s13059-020-02047-7 |
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