Draft Assembly of Phytophthora capsici from Long-Read Sequencing Uncovers Complexity.
Mol Plant Microbe Interact
; 32(12): 1559-1563, 2019 Dec.
Article
in En
| MEDLINE
| ID: mdl-31479390
ABSTRACT
Resolving complex plant pathogen genomes is important for identifying the genomic shifts associated with rapid adaptation to selective agents such as hosts and fungicides, yet assembling these genomes remains challenging and expensive. Phytophthora capsici is an important, globally distributed plant pathogen that exhibits widespread fungicide resistance and a broad host range. As with other pathogenic oomycetes, P. capsici has a complex life history and a complex genome. Here, we leverage Oxford Nanopore Technologies and existing short-read resources to rapidly generate a low-cost, improved assembly. We generated 10 Gbp from a single MinION flow cell resulting in >1.25 million reads with an N50 of 13 kb. The resulting assembly is 95.2 Mbp in 424 scaffolds with an N50 length of 313 kb. This assembly is approximately 30 Mbp bigger than the current reference genome of 64 Mbp. We confirmed this larger genome size using flow cytometry, with an estimated size of 110 Mbp. BUSCO analysis identified 97.4% complete orthologs (19.2% duplicated). Evolutionary analysis supports a recent whole-genome duplication in this group. Our work provides a blueprint for rapidly integrating benchtop long-read sequencing with existing short-read data, to dramatically improve assembly quality and integrity of complex genomes and offer novel insights into pathogen genome function and evolution.
Key words
Full text:
1
Database:
MEDLINE
Main subject:
Phytophthora
/
Sequence Analysis, DNA
/
Genome, Protozoan
Type of study:
Prognostic_studies
Language:
En
Journal:
Mol Plant Microbe Interact
Journal subject:
BIOLOGIA MOLECULAR
/
BOTANICA
/
MICROBIOLOGIA
Year:
2019
Type:
Article
Affiliation country:
United States