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).

Extensive genomic and transcriptomic variation defines the chromosome-scale assembly ofHaemonchus contortus, a model gastrointestinal worm

“…A key challenge to achieving this chromosomal assembly was the presence of extensive genetic diversity in the sequencing data. Although high-quality genome assemblies are becoming more prevalent through the use of long-read sequencing technologies [4,5,54] , a feature of these assemblies is that they are derived from a single, few, or clonal individual(s) in which the genetic diversity is low or absent; most of the genetic diversity present in a single diploid individual can be phased and separated into distinct haplotypes (for example, using software such as Falcon-Unzip [8] and Supernova [7] for PacBio and 10X Genomics data, respectively), and assembled separately. However, even under these scenarios, heterozygosity remains a key technical limitation towards achieving contiguous genome assemblies.…”

“…However, high-throughput sequencing has significantly impacted the rate at which draft genomes are produced and, together with the recent introduction of long-read sequencing from Pacific Biosciences (PacBio) and Oxford Nanopore, the quality and contiguity of assemblies of both large and small genomes has completely changed. Now, the ability to generate highly contiguous and closed prokaryote genomes is becoming routine, even from metagenomic samples containing multiple strains or species [2,3] , and high-quality chromosome-scale genomes for a number of eukaryotic species are rapidly becoming available [4][5][6] . These technologies generally require microgram quantities of high molecular weight DNA, and the success of a genome assembly is highly dependent on the degree of polymorphism present in the DNA that is sequenced.…”

A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System

“…An additional advantage to single-insect assemblies is that genome assembly for a diploid sample is algorithmically simpler than for a sample of many pooled individuals, each of which may contribute up to two unique haplotypes. Several de novo assembly methods are available for diploid samples [21,22,33], and have been broadly applied taxonomically [5,34]. Recent work indicates that assembly of high-heterozygosity samples is more accurate than for inbred samples when parental data can be used to partition long-read sequence data by haplotype, an approach called trio-binning [22,35].…”

Asian water buffalo: domestication, history and genetics

“…The array contains 89 988 SNPs, together with 5799 probes for Quality Control and 1784 probes for gender determination (Iamartino et al ). The candidate SNPs for the array design were selected to be evenly distributed genome‐wide with respect to the bovine UMD 3.1 genome, but have been recently remapped after the release of the current version of the buffalo reference genome (Low et al ). Also, SNP numbers were weighted with respect to the significance of the breeds included in the discovery panel as follows: Mediterranean, 30%; Murrah, 30%; Jafarabadi, 20%; Nili‐Ravi, 20%.…”