Agriculture Science Report: Future Opportunities for Oilseed Rape

This report delves into the opportunities and challenges presented by Sclerotinia stem rot, a significant fungal pathogen affecting various crops, particularly oilseed rape. The study highlights the pathogen's broad host range and the mechanisms behind its virulence, including the role of effector proteins and the two-speed genome hypothesis. It discusses the latest research, including machine learning approaches and single-molecule sequencing, to understand fungal genomes and identify effector types. The analysis emphasizes the importance of understanding fungal genome architecture, repeat-induced point mutation (RIP), and transposable elements (TEs) in the context of effector and secreted proteins. The report references several key studies, including those by do Amaral et al. (2012), Amselem et al. (2015), Liang et al. (2013), and Lee et al. (2013), to provide a comprehensive overview of the current state of research and future directions in the field of plant pathology.

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Farming of oilseed rape
Control of Sclerotinia stem rot on oilseed rape has
great future opportunities
M. C. Derbyshire and M. Denton-Giles
March 3, 2016: A recent study has shown
that Sclerotinia stem rot has great future
opportunities for rapeseed oil. An article
was published in the journal of Plant
Pathology (DOI:
10.1111/ppa.12517), based on a survey of
495 experts on this topic. It has been found
that Sclerotinia is a type of pathogen, which
has a wide list of hosts, approximately 400
crop species are infected by this particular
fungus. The hosts include several such
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crops, which are significant to the farmers
economically. The above mentioned
pathogen is different from the others,
affecting the significant crops because
maximum others have only one or very thin
range of hosts. Some plant pathogen species
have alternating genes. One is called ‘Gene
Rich, Repeat Sparse’ and the other is called
‘Gene Poor, Repeat Rich’. Thus, they are
known as two-speed genome. Amselem,
Lebrun & Quesneville, (2015) said in the
article ‘Whole genome comparative analysis
of transposable elements provides new
insight into mechanisms of their inactivation
in fungal genomes.’ published in the
journal BMC genomics, 16(1), that the
repeat rich regions in the fungi are inclined
towards a procedure, called ‘Repeat Induced
Point Mutation (RIP)’. The repeat activity
and RIP play a significant role in the
development of secreted virulence proteins,
called Effectors.
Among top ten plant pathogenic
fungi eight of the fungi were has a narrow
range of pathogens, two of the fungi, Botryis
cinerea and Fusarium graminearum have a
broad range of hosts. Fusarium oxysporum
was also included in the list is a complex
species because it has a number of formae
specials with various host specificities.
According to do Amaral et al. (2012), there
is a limitation on the knowledge of the broad
range host fungi, most of the information
available and the knowledge the experts
have are related to the fungi that has a
narrow range of hosts.
Increased mutation rates in repeat-
rich regions of fungi arose from repeat
induced point mutation. This particular
activity is carried out in defense of excess
TE activity, which can be harmful if not
prevented or controlled. The analysis of the
fungal genome marks the beginning of the
investigation of the evolution of the
molecular activity of fungal effector genes.

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Many studies have been carried out and two
of the studies are on the S. Sclerotiorum to
identify the effector type or secreted proteins
that are responsible for the infection. The
studies focused on the difference between
the effector type and non effector type gene.
A recent development in this area is the
machine learning approach. This has been
highlighted by do Amaral et al. (2012), in
their article ‘Defining the predicted protein
secretome of the fungal wheat leaf pathogen
Mycosphaerella graminicola’, published in
the journal, PLoS One. They said that it is
based on a number of criteria that derive
from the features of the effectors already
known to predict and identify other effector.
Pacific Biosciences developed the
single molecule real time sequencing
platform that produce read of up to 60 kb.
The current S. sclerotiorum genome is of
high quality in comparison to other
functional genomes (Liang et al., 2013).
There is a number of procedures that
are used for growing S. Sclerotiorum and
extract and sequence nucleic acids for the
analysis, all the experiments were done by
the use of WT 1980 or a mutant derivative
thereafter. MHAP version was used to
generate a de novo genome assembly of S.
Sclerotiorum strain 1980. For the
assessment of contiguity of assembled
sequences, alignment of previously
generated optical map was done using the
Map solver version. For the assessment of
the amount of repetitive sequence in the new
S. sclerotiorum genome REPET pipeline
was run (Lee et al., 2013).
Oilseed rape
A new, complete and precise genome
with a wide range of nectrotrophic fungus,

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was produced through experiments. Along
with that, limited number of novel effectors
for future studies were acknowledged and
described. Lee et al. have mentioned in the
article ‘Mycosphaerella graminicola LysM
effector-mediated stealth pathogenesis
subverts recognition through both CERK1
and CEBiP homologues in wheat’, published
in the journal MolPlant Microbe Interact, in
2013, that the Genome architecture was also
illustrated in the experiments, in the context
of RIP, TEs, effector and secreted type
proteins. These are dissimilar to the three
most filamentous oomycetes and fungi,
hence, the two-speed hypothesis can be
confirmed. The findings have boundless
significance for future studies.

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References
do Amaral, A. M., Antoniw, J., Rudd, J. J., & Hammond-Kosack, K. E. (2012). Defining the
predicted protein secretome of the fungal wheat leaf pathogen Mycosphaerella
graminicola. PLoS One, 7(12), e49904.
Amselem, J., Lebrun, M. H., & Quesneville, H. (2015). Whole genome comparative analysis of
transposable elements provides new insight into mechanisms of their inactivation in
fungal genomes. BMC genomics, 16(1), 141.
Liang Y, YajimaW, Davis MR, Kav NNV & Strelkov SE. (2013). Disruption of a gene encoding
a hypothetical secreted protein from Sclerotinia sclerotiorumreduces its virulence on
canola (Brassica napus). Can J PlantPathol. 35:46–55.
Lee WS, Rudd JJ, Hammond-Kosack KE, & Kanyuka K. (2013). Mycosphaerella graminicola
LysM effector-mediated stealth pathogenesis subverts recognitionthrough both CERK1
and CEBiP homologues in wheat. MolPlant Microbe Interact. 27:236–243.