Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics

Mahsa Mousavi-Derazmahalleh, Steven Chang, Geoff Thomas, Mark Derbyshire, Phillip E. Bayer, David Edwards, Matthew N. Nelson, William Erskine, Francisco J. Lopez-Ruiz, Jon Clements, James K. Hane

Research output: Contribution to journalArticle

Abstract

BackgroundNarrow-leafed lupin is an emerging crop of significance in agriculture, livestock feed and human health food. However, its susceptibility to various diseases is a major obstacle towards increased adoption. Sclerotinia sclerotiorum and Botrytis cinerea - both necrotrophs with broad host-ranges - are reported among the top 10 lupin pathogens. Whole-genome sequencing and comparative genomics are useful tools to discover genes responsible for interactions between pathogens and their hosts.ResultsGenomes were assembled for one isolate of B. cinerea and two isolates of S. sclerotiorum, which were isolated from either narrow-leafed or pearl lupin species. Comparative genomics analysis between lupin-derived isolates and others isolated from alternate hosts was used to predict between 94 to 98 effector gene candidates from among their respective non-conserved gene contents.ConclusionsDetection of minor differences between relatively recently-diverged isolates, originating from distinct regions and with hosts, may highlight novel or recent gene mutations and losses resulting from host adaptation in broad host-range fungal pathogens.

Original languageEnglish
Article number385
Number of pages11
JournalBMC Genomics
Volume20
DOIs
Publication statusPublished - 17 May 2019

Cite this

@article{fdc9c30025fa4954949941efed3c4854,
title = "Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics",
abstract = "BackgroundNarrow-leafed lupin is an emerging crop of significance in agriculture, livestock feed and human health food. However, its susceptibility to various diseases is a major obstacle towards increased adoption. Sclerotinia sclerotiorum and Botrytis cinerea - both necrotrophs with broad host-ranges - are reported among the top 10 lupin pathogens. Whole-genome sequencing and comparative genomics are useful tools to discover genes responsible for interactions between pathogens and their hosts.ResultsGenomes were assembled for one isolate of B. cinerea and two isolates of S. sclerotiorum, which were isolated from either narrow-leafed or pearl lupin species. Comparative genomics analysis between lupin-derived isolates and others isolated from alternate hosts was used to predict between 94 to 98 effector gene candidates from among their respective non-conserved gene contents.ConclusionsDetection of minor differences between relatively recently-diverged isolates, originating from distinct regions and with hosts, may highlight novel or recent gene mutations and losses resulting from host adaptation in broad host-range fungal pathogens.",
keywords = "Sclerotinia sclerotiorum, Botrytis cinerea, Lupin, Comparative genomics, PROTEIN, VIRULENCE, SEQUENCE, ALGORITHM, EFFECTORS, DATABASE",
author = "Mahsa Mousavi-Derazmahalleh and Steven Chang and Geoff Thomas and Mark Derbyshire and Bayer, {Phillip E.} and David Edwards and Nelson, {Matthew N.} and William Erskine and Lopez-Ruiz, {Francisco J.} and Jon Clements and Hane, {James K.}",
year = "2019",
month = "5",
day = "17",
doi = "10.1186/s12864-019-5774-2",
language = "English",
volume = "20",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",

}

Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics. / Mousavi-Derazmahalleh, Mahsa; Chang, Steven; Thomas, Geoff; Derbyshire, Mark; Bayer, Phillip E.; Edwards, David; Nelson, Matthew N.; Erskine, William; Lopez-Ruiz, Francisco J.; Clements, Jon; Hane, James K.

In: BMC Genomics, Vol. 20, 385, 17.05.2019.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics

AU - Mousavi-Derazmahalleh, Mahsa

AU - Chang, Steven

AU - Thomas, Geoff

AU - Derbyshire, Mark

AU - Bayer, Phillip E.

AU - Edwards, David

AU - Nelson, Matthew N.

AU - Erskine, William

AU - Lopez-Ruiz, Francisco J.

AU - Clements, Jon

AU - Hane, James K.

PY - 2019/5/17

Y1 - 2019/5/17

N2 - BackgroundNarrow-leafed lupin is an emerging crop of significance in agriculture, livestock feed and human health food. However, its susceptibility to various diseases is a major obstacle towards increased adoption. Sclerotinia sclerotiorum and Botrytis cinerea - both necrotrophs with broad host-ranges - are reported among the top 10 lupin pathogens. Whole-genome sequencing and comparative genomics are useful tools to discover genes responsible for interactions between pathogens and their hosts.ResultsGenomes were assembled for one isolate of B. cinerea and two isolates of S. sclerotiorum, which were isolated from either narrow-leafed or pearl lupin species. Comparative genomics analysis between lupin-derived isolates and others isolated from alternate hosts was used to predict between 94 to 98 effector gene candidates from among their respective non-conserved gene contents.ConclusionsDetection of minor differences between relatively recently-diverged isolates, originating from distinct regions and with hosts, may highlight novel or recent gene mutations and losses resulting from host adaptation in broad host-range fungal pathogens.

AB - BackgroundNarrow-leafed lupin is an emerging crop of significance in agriculture, livestock feed and human health food. However, its susceptibility to various diseases is a major obstacle towards increased adoption. Sclerotinia sclerotiorum and Botrytis cinerea - both necrotrophs with broad host-ranges - are reported among the top 10 lupin pathogens. Whole-genome sequencing and comparative genomics are useful tools to discover genes responsible for interactions between pathogens and their hosts.ResultsGenomes were assembled for one isolate of B. cinerea and two isolates of S. sclerotiorum, which were isolated from either narrow-leafed or pearl lupin species. Comparative genomics analysis between lupin-derived isolates and others isolated from alternate hosts was used to predict between 94 to 98 effector gene candidates from among their respective non-conserved gene contents.ConclusionsDetection of minor differences between relatively recently-diverged isolates, originating from distinct regions and with hosts, may highlight novel or recent gene mutations and losses resulting from host adaptation in broad host-range fungal pathogens.

KW - Sclerotinia sclerotiorum

KW - Botrytis cinerea

KW - Lupin

KW - Comparative genomics

KW - PROTEIN

KW - VIRULENCE

KW - SEQUENCE

KW - ALGORITHM

KW - EFFECTORS

KW - DATABASE

U2 - 10.1186/s12864-019-5774-2

DO - 10.1186/s12864-019-5774-2

M3 - Article

VL - 20

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

M1 - 385

ER -