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

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

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).

Original language	English
Pages (from-to)	260
Journal	Nature Communications
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41467-018-08260-0
Publication status	Published - 16 Jan 2019

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Chromosome-level assembly of the water buffalo genome ...
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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(1), 260. https://doi.org/10.1038/s41467-018-08260-0

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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).",

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 Paolo Ajmone-Marsan and Smith, {Timothy P L} and Williams, {John L}",

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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, no. 1, pp. 260. https://doi.org/10.1038/s41467-018-08260-0

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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

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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).

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DO - 10.1038/s41467-018-08260-0

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SN - 2041-1723

VL - 10

SP - 260

JO - Nature Communications

JF - Nature Communications

IS - 1

ER -

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

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