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

By Arang Rhie, Shane A. McCarthy, O. Fedrigo, J. Damas, G. Formenti, Sergey Koren, Marcela Uliano-Silva, W. Chow, Arkarachai Fungtammasan, Juwan Kim and 117 more. Nature, 2020

2,673 citations recorded by the source corpus.

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1–4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. 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 assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences. The Vertebrate Genome Project has used an optimized pipeline to generate high-quality genome assemblies for sixteen species (representing all major vertebrate classes), which have led to new biological insights.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/176c091c0c02eb22912d4dd1305310df34b93807

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Citations in the corpus

Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs (2022, background): “Thanks to advancements in genome sequencing and assembly [4], these genomes tend to be highly accurate and contiguous.”
Haplotype-resolved assembly of diploid genomes without parental data (2022, background): “Statistical physicists often optimize an equation like equations (1) and (2) with stochastic algorithms.”
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads (2023, neutral): “The Earth Biogenome Project (EBP) [3] was founded to coordinate and promote biodiversity genomics through affiliated projects such as the Darwin Tree of Life project (DToL) [4], the Vertebrate Genomes Project (VGP) [5] and the Aquatic Symbiosis Genomics project (ASG) [6].”
Ensembl 2024 (2023, methodology): “We have continued to generate annotations for assemblies from global biodiversity initiatives, such as the Darwin Tree of Life project ( 4 , the Vertebrate Genomes Project ( 6 , and the Earth BioGenome Project ( 7 )) (EBP).”
Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing (2021, positive): “However, because genome maps are noisy and scaffolding methods are fallible, automated scaffolding usually results in incomplete or misassembled scaffolds and researchers often rely on laborious manual curation to correct these shortcomings [13,14].”
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update (2022, background): “The Vertebrate Genome Project (VGP) aims to change this using the latest sequencing technologies and developing new assembly tools, with the goal of assembling reference genomes for all 71,657 known vertebrate species (21).”
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies (2020, background): “This validation strategy is also not applicable to any species without a curated and complete reference [32].”
YaHS: yet another Hi-C scaffolding tool (2022, neutral): “…have been launched in the past few years, such as the Earth Biogenome Project (Lewin et al. , 2018), the Vertebrate Genomes Project (Rhie et al. , 2021) and the Darwin Tree of Life Project (DToL, Blaxter et al. , 2022) aiming to assemble high quality, chromosome-scale genomes for many…”
Ensembl 2022 (2021, background): “We created project specific pages for DToL and the VGP.”
Sequence locally, think globally: The Darwin Tree of Life Project (2022, background): “…to DToL goals and also to the goals of other major international projects, such as the Vertebrate Genomes Project (adding family and ordinal reference genomes) (11), the Insects 5k initiative (30% of the species in Britain and Ireland are arthropods) (12), and the 10k Plants Genomes Project (13).”