Thursday, 27 September 2018 22:34

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

Written by 
Published in mBiosphere

The scope of the ASM Journal Genome Announcements has been expanded in a big way to create Microbiology Resource Announcements. The new journal publishes all resources that may be valuable to researchers in the microbial sciences.

Each month, we’ll highlight a new Microbiology Resource and how it will help researchers with their scientific endeavors.


Month: September 2018


Fusarium oxysporum growth on agar platesFusarium oxysporum growth on sabouraud agar. Source.

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





Last modified on Thursday, 27 September 2018 23:11
Julie Wolf

Julie Wolf is the ASM Science Communications Specialist. She contributes to the ASM social media and blog network and hosts the Meet the Microbiologist podcast. She also runs workshops at ASM conferences to help scientists improve their own communication skills. Follow Julie on Twitter for more ASM and microbiology highlights at @JulieMarieWolf.

Julie earned her Ph.D. from the University of Minnesota, focusing on medical mycology and infectious disease. Outside of her work at ASM, she maintains a strong commitment to scientific education and teaches molecular biology at the community biolab, Genspace. She lives in beautiful New York City.