Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus.

BMC Biology
Sergio M LatorreHernán A Burbano

Abstract

Understanding the mechanisms and timescales of plant pathogen outbreaks requires a detailed genome-scale analysis of their population history. The fungus Magnaporthe (Syn. Pyricularia) oryzae-the causal agent of blast disease of cereals- is among the most destructive plant pathogens to world agriculture and a major threat to the production of rice, wheat, and other cereals. Although M. oryzae is a multihost pathogen that infects more than 50 species of cereals and grasses, all rice-infecting isolates belong to a single genetically defined lineage. Here, we combined the two largest genomic datasets to reconstruct the genetic history of the rice-infecting lineage of M. oryzae based on 131 isolates from 21 countries. The global population of the rice blast fungus consists mainly of three well-defined genetic groups and a diverse set of individuals. Multiple population genetic tests revealed that the rice-infecting lineage of the blast fungus probably originated from a recombining diverse group in Southeast Asia followed by three independent clonal expansions that took place over the last ~ 200 years. Patterns of allele sharing identified a subpopulation from the recombining diverse group that introgressed with one of the clonal li...Continue Reading

References

Oct 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·M Nei, W H Li
Oct 5, 2001·Trends in Genetics : TIG·A MiraN A Moran
Nov 25, 2003·Science·Michael Lynch, John S Conery
Feb 11, 2005·Molecular Biology and Evolution·A J DrummondO G Pybus
Mar 12, 2005·BMC Genomics·Lovisa LovmarAnn-Christine Syvänen
Apr 23, 2005·Nature·Ralph A DeanBruce W Birren
Oct 14, 2005·Molecular Biology and Evolution·Daniel H Huson, David Bryant
May 11, 2006·PLoS Biology·Alexei J DrummondAndrew Rambaut
Aug 10, 2007·Genome Biology·Ruth HershbergDmitri A Petrov
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Sep 26, 2009·Nature·David ReichLalji Singh
May 8, 2010·Science·Richard E GreenSvante Pääbo
Aug 17, 2010·The New Phytologist·Ryohei Terauchi, Kentaro Yoshida
Feb 18, 2011·Molecular Biology and Evolution·Eric Y DurandMontgomery Slatkin
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Aug 23, 2011·Systematic Biology·Joseph Heled, Alexei J Drummond
Nov 26, 2011·Genome Biology and Evolution·Yogeshwar D Kelkar, Howard Ochman
Mar 15, 2012·Molecular Plant-microbe Interactions : MPMI·Hendrik RietmanVivianne G A A Vleeshouwers
Mar 17, 2012·Molecular Biology and Evolution·David BryantArindam RoyChoudhury
Apr 5, 2012·Molecular Plant Pathology·Ralph DeanGary D Foster
Apr 14, 2012·Nature·Matthew C FisherSarah J Gurr
May 9, 2012·Nature Reviews. Microbiology·Sylvain Raffaele, Sophien Kamoun
Sep 11, 2012·Genetics·Nick PattersonDavid Reich
Nov 22, 2013·Nature·Maanasa RaghavanEske Willerslev
Jan 11, 2014·Molecular Plant-microbe Interactions : MPMI·Vivianne G A A Vleeshouwers, Richard P Oliver
Apr 12, 2014·PLoS Computational Biology·Remco BouckaertAlexei J Drummond
Aug 12, 2014·Bioinformatics·Julia Chifman, Laura Kubatko
Dec 3, 2014·Fungal Genetics and Biology : FG & B·Daniel P Bebber, Sarah J Gurr
Feb 28, 2015·Genome Biology·Amelia HubbardDiane G O Saunders
Jul 15, 2015·Genome Biology and Evolution·Evgeni Bolotin, Ruth Hershberg
Jul 22, 2015·Nature·Pontus SkoglundDavid Reich
Oct 10, 2015·Current Opinion in Genetics & Development·Suomeng DongSophien Kamoun

❮ Previous
Next ❯

Citations

Nov 18, 2020·Phytopathology·Pauline HessenauerRichard C Hamelin
Nov 20, 2020·Molecular Plant-microbe Interactions : MPMI·Daniel J EbboleZonghua Wang
Oct 10, 2021·Molecular Plant-microbe Interactions : MPMI

❮ Previous
Next ❯

Methods Mentioned

BETA
PCA

Software Mentioned

R package stats
R stats package
BEAST2
R package cluster
SplitsTree
vcftools
Python scikit - learn
BEAST
SAMtools
Plink

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.