Genetic Diversity and Population Structure of Races of Fusarium oxysporum Causing Cotton Wilt.

G3 : Genes - Genomes - Genetics
Hannah C HalpernMarin Talbot Brewer

Abstract

To better understand the evolution of virulence we are interested in identifying the genetic basis of this trait in pathogenic fungi and in developing tools for the rapid characterization of variation in virulence among populations associated with epidemics. Fusarium oxysporum f. sp. vasinfectum (FOV) is a haploid fungus that causes devastating outbreaks of Fusarium wilt of cotton wherever it is grown. In the United States, six nominal races and eleven genotypes of FOV have been characterized based on the translation elongation factor (EF-1α) gene and intergenic spacer region (IGS), but it is unclear how race or genotype based on these regions relates to population structure or virulence. We used genotyping-by-sequencing to identify SNPs and determine genetic diversity and population structure among 86 diverse FOV isolates. Six individuals of Fusarium oxysporum closely related to FOV were genotyped and included in some analyses. Between 193 and 354 SNPs were identified and included in the analyses depending on the pipeline and filtering criteria used. Phylogenetic trees, minimum spanning networks (MSNs), principal components analysis (PCA), and discriminant analysis of principal components (DAPC) demonstrated that races and gen...Continue Reading

References

Jun 1, 1991·Research in Microbiology·E DenamurR Krishnamoorthy
Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Apr 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·K O'DonnellR C Ploetz
Jan 1, 1993·Annual Review of Phytopathology·J F Leslie
Oct 24, 2008·Phytopathology·Niklaus J GrünwaldWilliam E Fry
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Sep 1, 2009·Fungal Genetics and Biology : FG & B·Kerry O'DonnellBrice A J Sarver
May 17, 2011·PloS One·Robert J ElshireSharon E Mitchell
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
May 20, 2010·Functional Plant Biology : FPB·Jonathan P AndersonKaram B Singh
Sep 10, 2011·Bioinformatics·Tanja Magoč, Steven L Salzberg
Mar 3, 2012·G3 : Genes - Genomes - Genetics·Julian M CatchenJohn H Postlethwait
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
May 25, 2013·Molecular Ecology·Julian CatchenWilliam A Cresko
Jun 27, 2015·Frontiers in Genetics·Zhian N KamvarNiklaus J Grünwald
Oct 17, 2015·International Journal of Molecular Sciences·Mara de Sain, Martijn Rep
Jan 6, 2016·Nature Reviews. Genetics·Kimberly R AndrewsPaul A Hohenlohe
Mar 24, 2016·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura
Jun 15, 2016·Annual Review of Phytopathology·Niklaus J GrünwaldMichael G Milgroom
Jul 13, 2016·Molecular Ecology Resources·Brian J Knaus, Niklaus J Grünwald
Nov 22, 2018·Phytopathology·V Edel-Hermann, C Lecomte

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJNA632933
SRR11792269

Methods Mentioned

BETA
PCR
PCA

Software Mentioned

bowtie2
poppr
UGbS
DAPC
SAMtools
adegenet
R
Stacks
Picard
Geneious

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.