Dataset Information

De novo assembly of the cattle reference genome with single-molecule sequencing.

ABSTRACT: Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use. We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species.

SUBMITTER: Rosen BD

PROVIDER: S-EPMC7081964 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Publications

De novo assembly of the cattle reference genome with single-molecule sequencing.

Rosen Benjamin D BD Bickhart Derek M DM Schnabel Robert D RD Koren Sergey S Elsik Christine G CG Tseng Elizabeth E Rowan Troy N TN Low Wai Y WY Zimin Aleksey A Couldrey Christine C Hall Richard R Li Wenli W Rhie Arang A Ghurye Jay J McKay Stephanie D SD Thibaud-Nissen Françoise F Hoffman Jinna J Murdoch Brenda M BM Snelling Warren M WM McDaneld Tara G TG Hammond John A JA Schwartz John C JC Nandolo Wilson W Hagen Darren E DE Dreischer Christian C Schultheiss Sebastian J SJ Schroeder Steven G SG Phillippy Adam M AM Cole John B JB Van Tassell Curtis P CP Liu George G Smith Timothy P L TPL Medrano Juan F JF

GigaScience 20200301 3

<h4>Background</h4>Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.<h4>Results</h4>We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of resul ...[more]

PMID: 32191811

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Project description:A high-quality reference genome is a fundamental resource for functional genetics, comparative genomics, and population genomics, and is increasingly important for conservation biology. PacBio Single Molecule, Real-Time (SMRT) sequencing generates long reads with uniform coverage and high consensus accuracy, making it a powerful technology for de novo genome assembly. Improvements in throughput and concomitant reductions in cost have made PacBio an attractive core technology for many large genome initiatives, however, relatively high DNA input requirements (~5 µg for standard library protocol) have placed PacBio out of reach for many projects on small organisms that have lower DNA content, or on projects with limited input DNA for other reasons. Here we present a high-quality de novo genome assembly from a single Anopheles coluzzii mosquito. A modified SMRTbell library construction protocol without DNA shearing and size selection was used to generate a SMRTbell library from just 100 ng of starting genomic DNA. The sample was run on the Sequel System with chemistry 3.0 and software v6.0, generating, on average, 25 Gb of sequence per SMRT Cell with 20 h movies, followed by diploid de novo genome assembly with FALCON-Unzip. The resulting curated assembly had high contiguity (contig N50 3.5 Mb) and completeness (more than 98% of conserved genes were present and full-length). In addition, this single-insect assembly now places 667 (>90%) of formerly unplaced genes into their appropriate chromosomal contexts in the AgamP4 PEST reference. We were also able to resolve maternal and paternal haplotypes for over 1/3 of the genome. By sequencing and assembling material from a single diploid individual, only two haplotypes were present, simplifying the assembly process compared to samples from multiple pooled individuals. The method presented here can be applied to samples with starting DNA amounts as low as 100 ng per 1 Gb genome size. This new low-input approach puts PacBio-based assemblies in reach for small highly heterozygous organisms that comprise much of the diversity of life.

Dataset Information

De novo assembly of the cattle reference genome with single-molecule sequencing.

Publications

De novo assembly of the cattle reference genome with single-molecule sequencing.

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