Microbiology Resource of the Month: Improved Reference Genome for Fusarium oxysporum

Sept. 27, 2018

Announcement: Improved Assembly of Reference Genome Fusarium oxysporum f. sp. lycopersici Strain Fol4287
Resource: An improved reference genome for Fusarium oxysporum 

Why is it necessary to generate new iterations of reference genome sequences?

Fusarium oxysporum is a fungal plant pathogen, and the lycopersici strain was isolated from a tomato. Scientists study this microbe to better understand fungal evolution, pathogenesis, and disease prevention. 

There are many important purposes of an accurate and well-annotated reference genome: 
  • Identifying new isolates or strains of a species.
  • Deriving sequences for genes or genomic regions of interest.
  • Designing primers, CRISPR gRNAs, or siRNAs for genetic studies.
For these reasons and others, an accurate reference genome can be the foundation for additional scientific research. These sequences are loaded into databases such as GenBank and FungiDB that serve as important tools for the research community.

How did different technologies help better resolve single-nucleotide errors found in the previous sequence?

The previous F. oxysporum genome iteration, published in 2010, was generated using Sanger sequencing. While it provided a number of insights, low sequence coverage resulted in a number of single-nucleotide errors. 

In the new Microbiology Resource Announcement article, the same isolate was resequenced by combining Illumina and PacBio sequence technologies, with 66x coverage (compared to the previous 6x coverage).

Who will benefit from having an improved reference sequence?

Researchers who rely on a well-annotated reference genome will be able to use this new sequence with confidence. 
Additionally, F. oxysporum and other Fusarium species have lineage-specific (LS) chromosomes that play a part in determining pathogenic potential. The newly generated genome sequences were separated into their physically distinct chromosomes, including complete mitochondrial DNA and ribosomal DNA sequences. The 11 core chromosomes, 4 LS chromosomes, and some unmapped contigs were assembled into Genbank as a single assembly number. This will help scientists better study these LS chromosomes and their role during plant pathogenesis.

Why Microbiology Resource Announcements

“Scientific research has benefited from the resources developed and shared between scientists — from software published on Github to plasmids made available on Addgene. These resources facilitate our work and allow researchers to build on and extend the work of others. Indeed, some of the most impactful papers have been those describing resources — the E. coli Keio Knockout Collection manuscript, for example, has been cited nearly 5,000 times. Many resources are worth sharing. We hope your next submission will spur someone else’s work or, potentially, inspire collaboration in our community.” – Microbiology Resource Announcements Editor-in-Chief Irene Newton.

Author: Julie Wolf

Julie Wolf
Dr. Julie Wolf is in science communications at Indie Bio, and was a former ASM employee. Follow Julie on Twitter for more ASM and microbiology highlights at @JulieMarieWolf.