High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell.
Nat Commun
; 9(1): 541, 2018 02 07.
Article
em En
| MEDLINE
| ID: mdl-29416032
ABSTRACT
The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence the gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on the bench with the MinION sequencer, and assemble the genome using typical consumer computing hardware (4 Cores, 16 Gb RAM) into chromosome arms (62 contigs with an N50 length of 12.3 Mb). We validate the contiguity and quality of the assembly with two independent single-molecule technologies, Bionano optical genome maps and Pacific Biosciences Sequel sequencing. The new A. thaliana KBS-Mac-74 genome enables resolution of a quantitative trait locus that had previously been recalcitrant to a Sanger-based BAC sequencing approach. In summary, we demonstrate that even when the purpose is to understand complex structural variation at a single region of the genome, complete genome assembly is becoming the simplest way to achieve this goal.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Arabidopsis
/
Genoma de Planta
/
Genômica
/
Sequenciamento de Nucleotídeos em Larga Escala
Tipo de estudo:
Evaluation_studies
Idioma:
En
Ano de publicação:
2018
Tipo de documento:
Article