Towards complete and error-free genome assemblies of all vertebrate species

Abstract

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species 1-4 . To address this issue, the international Genome 10K (G10K) consortium 5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling the most accurate and complete reference genomes to date. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from sequencing and assembling 16 species representing major vertebrate lineages (mammals, birds, reptiles, amphibians, teleost fishes and cartilaginous fishes). We confirm that long-read sequencing technologies are essential for maximizing genome quality and that unresolved complex repeats and haplotype heterozygosity are major sources of error in assemblies. Our new assemblies identify and correct substantial errors in some of the best historical reference genomes. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.

HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding

“…We further advocate for the use of the hill climbing feature in HapSolo, because the computational cost is relatively small but the gains -while not always substantive -can be large (Figure 3). We believe HapSolo can be used to further improve assemblies that use heterozygous samples and employ HiC scaffolding, such as the data being created by the Vertebrate Genome Project [32].…”

“…The data were all based on the Pacific Biosciences (PacBio) sequencing platform and either provided by authors or downloaded from public databases. The chromosome number for each species were found in various sources [20,32,33] Contig Alignments: For each genome, the pre-processing step prior to application of HapSolo was to perform pairwise contig alignments, as described above. For this study, we used Blat v35 [27], although in principle other aligners, like minimap2 [34] could be used.…”

Significantly improving the quality of genome assemblies through curation

“…Despite the advances in sequencing and mapping technologies and the ever-increasing number of sophisticated algorithms and pipelines available, generating error-free eukaryotic genome assemblies in a purely automated fashion is currently not possible [1,2]. Assembly software designed to generate continuous sequence from raw reads is confused by heterozygous or repeat-rich regions, introducing erroneous duplications, collapses and misjoins.…”

“…We therefore also provide detailed recommendations on how to create similar analyses that do not use gEVAL to promote the core, proven design concepts in gEVAL.. This is especially timely in the context of emerging projects that aim to assemble the genomes of very large numbers of species to highest quality possible, including the Vertebrate Genomes Project (VGP), the Darwin Tree of Life Project (DToL, darwintreeoflife.org) and the overarching Earth Biogenome Project (EBP) [1,11].…”

“…A major source of remaining technical error in assemblies is the retention of duplicated regions that result from failure to recognise that two sequences are in fact allelic. These false duplications have wide-ranging negative consequences for subsequent research, for example causing prediction of erroneous gene duplications [1]. False duplications are caused by either incorrect resolution of assembly graphs or failures in detection of haplotypic variation.…”