Sequencing smart:<i>De novo</i>sequencing and assembly approaches for non-model mammals

Etherington, Graham; Heavens, Darren; Baker, David; Lister, Ashleigh; McNelly, Rose; Accinelli, Gonzalo Garcia; Clavijo, Bernardo; Macaulay, Iain C.; Haerty, Wilfried; Palma, Federica Di

doi:10.1101/723890

Cited by 4 publications

(3 citation statements)

References 29 publications

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“…Previous studies (e.g., Etherington et al., 2019; Paajanen et al., 2019) have assessed the efficiency of available sequencing technologies in genome assembly and genome completeness mainly through summary statistics such as scaffold N50 and BUSCO values. Scaffold N50 indicates the minimum scaffold size among the largest scaffolds making up half of the assembly, while BUSCO values measure the number of complete/incomplete/missing core genes in the assembly.…”

Section: Discussionmentioning

confidence: 99%

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Peona

Blom

et al. 2020

Molecular Ecology Resources

114

135

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Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat‐rich and GC‐rich regions (genomic “dark matter”) limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long‐read, linked‐read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC‐rich microchromosomes and the repeat‐rich W chromosome. Telomere‐to‐telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.

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Section: Discussionmentioning

confidence: 99%

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Peona

Blom

et al. 2020

Molecular Ecology Resources

114

135

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“…Such technical advantages and established recommendations and strategies have been widely applied in humans [3][4][5][6], terrestrial animals [7][8][9][10][11][12], and plants and crops [13][14][15][16][17][18]. Genomic applications in aquatic species that could be potentially important for aquaculture are slower compared with human, livestock, and crops [19][20][21], compounded by larger diversity, lack of reference genomes, and more novice aquaculture industries.…”

Section: Introductionmentioning

confidence: 99%

Twelve quick steps for genome assembly and annotation in the classroom

et al. 2020

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Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts. In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species. Herein, we state 12 steps to help researchers get started in genome projects by presenting guidelines that are broadly applicable (to any species), sustainable over time, and cover all aspects of genome assembly and annotation projects from start to finish. We review some commonly used approaches, including practical methods to extract high-quality DNA and choices for the best sequencing platforms and library preparations. In addition, we discuss the range of potential bioinformatics pipelines, including structural and functional annotations (e.g., transposable elements and repetitive sequences). This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable, and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community.

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“…These methods allow the assembly of pseudo‐long reads up to tens of kb from short‐read data, and with higher accuracy compared to true long‐read sequencing (Jiao & Schneeberger, 2017). Initially introduced by Illumina (Kuleshov et al, 2014; McCoy et al, 2014), there are few but increasing numbers of publications using linked‐read methods, particularly in the field of museomics (Etherington et al, 2019; Latorre et al, 2020; Lutgen et al, 2020). 10× Genomics (Zheng et al, 2016), a newer technology loosely based on innovations developed by the Illumina SLR technique, offers several advantages for museum science applications.…”

Section: Introductionmentioning

confidence: 99%

A linked‐read approach to museomics: Higher quality de novo genome assemblies from degraded tissues

Colella

Tigano

MacManes

2020

Molecular Ecology Resources

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A disconnect between the capabilities of high-throughput sequencing technologies and the quality, or lack thereof, of historical museum specimens has proven a major barrier to accessing molecular data from degraded samples. Natural history collections (NHCs) store a wide variety of species from across the globe, including those that are now difficult to collect or are extinct in the wild. Voucher specimens housed in NHCs are an invaluable source of morphological material as they provide a reference for measuring change across both space and time. Specimens have also been recognized as important repositories of genetic sequence data (Holmes et al., 2016;

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Sequencing smart:De novosequencing and assembly approaches for non-model mammals

Cited by 4 publications

References 29 publications

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Twelve quick steps for genome assembly and annotation in the classroom

A linked‐read approach to museomics: Higher quality de novo genome assemblies from degraded tissues

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