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

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

doi:10.1038/s41467-018-08260-0

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

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

Risultato della ricerca: Contributo in rivista › Articolo in rivista › peer review

43 Citazioni (Scopus)

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).

Lingua originale	English
pagine (da-a)	N/A-N/A
Rivista	Nature Communications
Volume	10
DOI	https://doi.org/10.1038/s41467-018-08260-0
Stato di pubblicazione	Pubblicato - 2019

Keywords

Animals
Biochemistry, Genetics and Molecular Biology (all)
Buffaloes
Chemistry (all)
Chromatin
Chromosomes, Mammalian
Contig Mapping
Female
Genome
Genomics
Goats
Haplotypes
High-Throughput Nucleotide Sequencing
Humans
Major Histocompatibility Complex
Molecular Sequence Annotation
Multigene Family
Physics and Astronomy (all)
Repetitive Sequences, Nucleic Acid
Whole Genome Sequencing

Accesso al documento

10.1038/s41467-018-08260-0

Altri file e collegamenti

Cita questo

Low, W. Y., Tearle, R., Bickhart, D. M., Rosen, B. D., Kingan, S. B., Swale, T., Thibaud-Nissen, F., Murphy, T. D., Young, R., Lefevre, L., Hume, D. A., Collins, A., Ajmone Marsan, P., Smith, T. P. L., & Williams, J. L. (2019). Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nature Communications, 10, N/A-N/A. https://doi.org/10.1038/s41467-018-08260-0

@article{aeaba4e2ccc54048abd61e90d79e581f,

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

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).",

keywords = "Animals, Biochemistry, Genetics and Molecular Biology (all), Buffaloes, Chemistry (all), Chromatin, Chromosomes, Mammalian, Contig Mapping, Female, Genome, Genomics, Goats, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, Major Histocompatibility Complex, Molecular Sequence Annotation, Multigene Family, Physics and Astronomy (all), Repetitive Sequences, Nucleic Acid, Whole Genome Sequencing, Animals, Biochemistry, Genetics and Molecular Biology (all), Buffaloes, Chemistry (all), Chromatin, Chromosomes, Mammalian, Contig Mapping, Female, Genome, Genomics, Goats, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, Major Histocompatibility Complex, Molecular Sequence Annotation, Multigene Family, Physics and Astronomy (all), Repetitive Sequences, Nucleic Acid, Whole Genome Sequencing",

author = "Low, {Wai Yee} and Rick Tearle and Bickhart, {Derek M.} and Rosen, {Benjamin D.} and Kingan, {Sarah B.} and Thomas Swale and Fran{\c c}oise Thibaud-Nissen and Murphy, {Terence D.} and Rachel Young and Lucas Lefevre and Hume, {David A.} and Andrew Collins and {Ajmone Marsan}, Paolo and Smith, {Timothy P. L.} and Williams, {John L.}",

year = "2019",

doi = "10.1038/s41467-018-08260-0",

language = "English",

volume = "10",

pages = "N/A--N/A",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

}

Low, WY, Tearle, R, Bickhart, DM, Rosen, BD, Kingan, SB, Swale, T, Thibaud-Nissen, F, Murphy, TD, Young, R, Lefevre, L, Hume, DA, Collins, A, Ajmone Marsan, P, Smith, TPL & Williams, JL 2019, 'Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity', Nature Communications, vol. 10, pagg. N/A-N/A. https://doi.org/10.1038/s41467-018-08260-0

TY - JOUR

T1 - Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity

AU - Low, Wai Yee

AU - Tearle, Rick

AU - Bickhart, Derek M.

AU - Rosen, Benjamin D.

AU - Kingan, Sarah B.

AU - Swale, Thomas

AU - Thibaud-Nissen, Françoise

AU - Murphy, Terence D.

AU - Young, Rachel

AU - Lefevre, Lucas

AU - Hume, David A.

AU - Collins, Andrew

AU - Ajmone Marsan, Paolo

AU - Smith, Timothy P. L.

AU - Williams, John L.

PY - 2019

Y1 - 2019

N2 - 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).

AB - 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).

KW - Animals

KW - Biochemistry, Genetics and Molecular Biology (all)

KW - Buffaloes

KW - Chemistry (all)

KW - Chromatin

KW - Chromosomes, Mammalian

KW - Contig Mapping

KW - Female

KW - Genome

KW - Genomics

KW - Goats

KW - Haplotypes

KW - High-Throughput Nucleotide Sequencing

KW - Humans

KW - Major Histocompatibility Complex

KW - Molecular Sequence Annotation

KW - Multigene Family

KW - Physics and Astronomy (all)

KW - Repetitive Sequences, Nucleic Acid

KW - Whole Genome Sequencing

KW - Animals

KW - Biochemistry, Genetics and Molecular Biology (all)

KW - Buffaloes

KW - Chemistry (all)

KW - Chromatin

KW - Chromosomes, Mammalian

KW - Contig Mapping

KW - Female

KW - Genome

KW - Genomics

KW - Goats

KW - Haplotypes

KW - High-Throughput Nucleotide Sequencing

KW - Humans

KW - Major Histocompatibility Complex

KW - Molecular Sequence Annotation

KW - Multigene Family

KW - Physics and Astronomy (all)

KW - Repetitive Sequences, Nucleic Acid

KW - Whole Genome Sequencing

UR - http://hdl.handle.net/10807/133488

UR - http://www.nature.com/ncomms/index.html

U2 - 10.1038/s41467-018-08260-0

DO - 10.1038/s41467-018-08260-0

M3 - Article

SN - 2041-1723

VL - 10

SP - N/A-N/A

JO - Nature Communications

JF - Nature Communications

ER -

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

Abstract

Keywords

Accesso al documento

Altri file e collegamenti

Fingerprint

Cita questo