The University of Southampton
University of Southampton Institutional Repository

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

Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
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 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).
1-11
Low, Wai Yee
a32d820b-2e59-41b4-aeec-f4e142ef56b5
Tearle, Rick
45850257-5056-4f6f-a5cf-d19f90f04b36
Bickhart, Derek M.
81abf625-7be4-4db9-85f3-5267723de344
Rosen, Benjamin D.
4f43a150-f118-4270-8023-7bbfc462581f
Kingan, Sarah B.
72904a57-8649-4590-9380-87dcef767a24
Swale, Thomas
b56956f7-c3a8-4d43-baef-981651272015
Thibaud-Nissen, Francoise
b5d674ce-ac33-4b13-ad80-4112dfc3bbd4
Murphy, Terence
2ed50910-9b35-43a2-b311-89a4ce2297e3
Young, Rachel
18d24e3c-4add-4435-87a2-3e42a1614f41
Lefevre, Lucas
b47167bb-e808-45a9-b6dc-375fbb68aca3
Hume, David A.
dd2085e5-83d3-454a-9e68-9391c09133a4
Collins, Andrew
7daa83eb-0b21-43b2-af1a-e38fb36e2a64
Ajmone-Marsan, Paolo
683a62f5-187f-4820-af0e-27ff99c34280
Smith, Timothy P.L.
eeea58e8-934d-462f-82c1-ca0159d36406
Williams, John L.
45e2017f-ffc2-4329-9675-2bc9cc3377e9
Low, Wai Yee
a32d820b-2e59-41b4-aeec-f4e142ef56b5
Tearle, Rick
45850257-5056-4f6f-a5cf-d19f90f04b36
Bickhart, Derek M.
81abf625-7be4-4db9-85f3-5267723de344
Rosen, Benjamin D.
4f43a150-f118-4270-8023-7bbfc462581f
Kingan, Sarah B.
72904a57-8649-4590-9380-87dcef767a24
Swale, Thomas
b56956f7-c3a8-4d43-baef-981651272015
Thibaud-Nissen, Francoise
b5d674ce-ac33-4b13-ad80-4112dfc3bbd4
Murphy, Terence
2ed50910-9b35-43a2-b311-89a4ce2297e3
Young, Rachel
18d24e3c-4add-4435-87a2-3e42a1614f41
Lefevre, Lucas
b47167bb-e808-45a9-b6dc-375fbb68aca3
Hume, David A.
dd2085e5-83d3-454a-9e68-9391c09133a4
Collins, Andrew
7daa83eb-0b21-43b2-af1a-e38fb36e2a64
Ajmone-Marsan, Paolo
683a62f5-187f-4820-af0e-27ff99c34280
Smith, Timothy P.L.
eeea58e8-934d-462f-82c1-ca0159d36406
Williams, John L.
45e2017f-ffc2-4329-9675-2bc9cc3377e9

Low, Wai Yee, Tearle, Rick, Bickhart, Derek M., Rosen, Benjamin D., Kingan, Sarah B., Swale, Thomas, Thibaud-Nissen, Francoise, Murphy, Terence, Young, Rachel, Lefevre, Lucas, Hume, David A., Collins, Andrew, Ajmone-Marsan, Paolo, Smith, Timothy P.L. and Williams, John L. (2019) Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nature Communications, 10, 1-11. (doi:10.1038/s41467-018-08260-0).

Record type: Article

Abstract

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).

Text
s41467-018-08260-0 - Version of Record
Available under License Creative Commons Attribution.
Download (2MB)
Text
Buffalo Genome Proof_030119 - Proof
Restricted to Repository staff only
Request a copy

More information

Accepted/In Press date: 21 December 2018
e-pub ahead of print date: 16 January 2019

Identifiers

Local EPrints ID: 427446
URI: https://eprints.soton.ac.uk/id/eprint/427446
PURE UUID: 9afd9094-b30a-40af-942e-7eb26db5216f
ORCID for Andrew Collins: ORCID iD orcid.org/0000-0001-7108-0771

Catalogue record

Date deposited: 16 Jan 2019 17:30
Last modified: 19 Jul 2019 01:19

Export record

Altmetrics

Contributors

Author: Wai Yee Low
Author: Rick Tearle
Author: Derek M. Bickhart
Author: Benjamin D. Rosen
Author: Sarah B. Kingan
Author: Thomas Swale
Author: Francoise Thibaud-Nissen
Author: Terence Murphy
Author: Rachel Young
Author: Lucas Lefevre
Author: David A. Hume
Author: Andrew Collins ORCID iD
Author: Paolo Ajmone-Marsan
Author: Timothy P.L. Smith
Author: John L. Williams

University divisions

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of https://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×