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Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
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Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
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Journal Article
Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
2019
Overview
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).
Despite technological advances, chromosome-level assemblies of mammalian genomes are still rare. Here, the authors use PacBio, Chicago and Hi-C approaches to generate a highly contiguous and partially-phased genome assembly for the water buffalo,
Bubalus bubalis
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
Subject
/ 45/23
/ 631/601
/ Animals
/ Assembly
/ Chromosomes, Mammalian - genetics
/ Female
/ Genomes
/ High-Throughput Nucleotide Sequencing
/ Humanities and Social Sciences
/ Humans
/ Major histocompatibility complex
/ Major Histocompatibility Complex - genetics
/ Mammals
/ Molecular Sequence Annotation - methods
/ Repetitive Sequences, Nucleic Acid - genetics
/ Science
