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

Paolo Ajmone Marsan, 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, Timothy P. L. Smith, John L. Williams

Risultato della ricerca: Contributo in rivistaArticolo in rivistapeer review

39 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 originaleEnglish
pagine (da-a)N/A-N/A
RivistaNature Communications
Volume10
DOI
Stato di pubblicazionePubblicato - 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

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