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Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity

Rapid innovation in sequencing technologies and improvement in assembly algorithms have enabled the creation of highly contiguous mammalian genomes. Here we report a chromosome-level assembly of the water buffalo (Bubalus bubalis) genome using single-molecule sequencing and chromatin conformation ca...

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Autores principales: Low, Wai Yee, Tearle, Rick, Bickhart, Derek M., Rosen, Benjamin D., Kingan, Sarah B., Swale, Thomas, Thibaud-Nissen, Françoise, Murphy, Terence D., Young, Rachel, Lefevre, Lucas, Hume, David A., Collins, Andrew, Ajmone-Marsan, Paolo, Smith, Timothy P. L., Williams, John L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335429/
https://www.ncbi.nlm.nih.gov/pubmed/30651564
http://dx.doi.org/10.1038/s41467-018-08260-0
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author Low, Wai Yee
Tearle, Rick
Bickhart, Derek M.
Rosen, Benjamin D.
Kingan, Sarah B.
Swale, Thomas
Thibaud-Nissen, Françoise
Murphy, Terence D.
Young, Rachel
Lefevre, Lucas
Hume, David A.
Collins, Andrew
Ajmone-Marsan, Paolo
Smith, Timothy P. L.
Williams, John L.
author_facet Low, Wai Yee
Tearle, Rick
Bickhart, Derek M.
Rosen, Benjamin D.
Kingan, Sarah B.
Swale, Thomas
Thibaud-Nissen, Françoise
Murphy, Terence D.
Young, Rachel
Lefevre, Lucas
Hume, David A.
Collins, Andrew
Ajmone-Marsan, Paolo
Smith, Timothy P. L.
Williams, John L.
author_sort Low, Wai Yee
collection PubMed
description Rapid innovation in sequencing technologies and improvement in assembly algorithms have enabled the creation of highly contiguous mammalian genomes. Here we report a chromosome-level assembly of the water buffalo (Bubalus bubalis) genome using single-molecule sequencing and chromatin conformation capture data. PacBio Sequel reads, with a mean length of 11.5 kb, helped to resolve repetitive elements and generate sequence contiguity. All five B. bubalis sub-metacentric chromosomes were correctly scaffolded with centromeres spanned. Although the index animal was partly inbred, 58% of the genome was haplotype-phased by FALCON-Unzip. This new reference genome improves the contig N50 of the previous short-read based buffalo assembly more than a thousand-fold and contains only 383 gaps. It surpasses the human and goat references in sequence contiguity and facilitates the annotation of hard to assemble gene clusters such as the major histocompatibility complex (MHC).
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spelling pubmed-63354292019-01-18 Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity Low, Wai Yee Tearle, Rick Bickhart, Derek M. Rosen, Benjamin D. Kingan, Sarah B. Swale, Thomas Thibaud-Nissen, Françoise Murphy, Terence D. Young, Rachel Lefevre, Lucas Hume, David A. Collins, Andrew Ajmone-Marsan, Paolo Smith, Timothy P. L. Williams, John L. Nat Commun Article Rapid innovation in sequencing technologies and improvement in assembly algorithms have enabled the creation of highly contiguous mammalian genomes. Here we report a chromosome-level assembly of the water buffalo (Bubalus bubalis) genome using single-molecule sequencing and chromatin conformation capture data. PacBio Sequel reads, with a mean length of 11.5 kb, helped to resolve repetitive elements and generate sequence contiguity. All five B. bubalis sub-metacentric chromosomes were correctly scaffolded with centromeres spanned. Although the index animal was partly inbred, 58% of the genome was haplotype-phased by FALCON-Unzip. This new reference genome improves the contig N50 of the previous short-read based buffalo assembly more than a thousand-fold and contains only 383 gaps. It surpasses the human and goat references in sequence contiguity and facilitates the annotation of hard to assemble gene clusters such as the major histocompatibility complex (MHC). Nature Publishing Group UK 2019-01-16 /pmc/articles/PMC6335429/ /pubmed/30651564 http://dx.doi.org/10.1038/s41467-018-08260-0 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Low, Wai Yee
Tearle, Rick
Bickhart, Derek M.
Rosen, Benjamin D.
Kingan, Sarah B.
Swale, Thomas
Thibaud-Nissen, Françoise
Murphy, Terence D.
Young, Rachel
Lefevre, Lucas
Hume, David A.
Collins, Andrew
Ajmone-Marsan, Paolo
Smith, Timothy P. L.
Williams, John L.
Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
title Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
title_full Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
title_fullStr Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
title_full_unstemmed Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
title_short Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
title_sort chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335429/
https://www.ncbi.nlm.nih.gov/pubmed/30651564
http://dx.doi.org/10.1038/s41467-018-08260-0
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