Review for "The rust fungus Melampsora larici-populina expresses a conserved genetic program and distinct sets of secreted protein genes during infection of its two host plants, larch and poplar"

Completed on 21 Dec 2017 by Benjamin Schwessinger . Sourced from https://www.biorxiv.org/content/early/2017/12/06/229971.

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Comments to author

I love this work. It is such a fundamental biological
question of how an obligate biotrophic fungus infects two highly distinct plant
species. Some real fascinating biology.

Here are some thoughts and comments on this
manuscript:

· Some active voice in the
abstract would make it more accessible.

· Line numbers would have been
great.

Intro:

· ‘is qualified of macrocyclic’
should read ‘as’ not ‘of’

· the citation for Germain et
al., 2017 needs to be corrected

MM:

· This also refers to the
results. It would be great to see how many of the RNAseq reads did not map to
the reference gene models. Could you identify novel genes that were previously
missed from the annotation as the adequate expression data for both hosts were
missing? Is this novel RNAseq data being incorporated to new rounds of
annotations? If you had poplar RNAseq data if would be great to compare the RNAseq
mapping rate overlapping with gene models poplar vs. larch.

· PLEASE deposit all analysis scripts
on github and NOT on demand. This would be great for people that want to
compare RNAseq and microarray data. I really liked your quantile comparison
approach. Scripts need not be perfect. Every little helps!

· do I understand correctly that
you only included genes in your diff analysis that were expressed both in
RNAseq and microarray analysis?

Results/Discussion:

· for the KOG enrichment analysis,
it would be nice to show how many genes miss any annotation. I guess this will
be around 50%. This reverse to the KOG analysis in ‘Secreted proteins is the
only overrepresented category among DEGs detected on larch’. I see that these
are mentioned later on.

· I was wondering if the increase
in specifically expressed SP genes on larch vs. poplar (Figure 6 B) could be an
artefact of the micro-array vs. RNAseq analysis. Were all these larch specific
genes expressed in the microarray at all? It would be much more convincing and
reassuring to see some qRT-PCR analysis of the differentially expressed SP in
poplar vs. larch. Using the identical technique would very much strengthen the
argument made.

· in addition to the SSP gene
family expression analysis (which could be really alleles of each other as
well) did you observe any allele specific expression using SNPs as markers.
E.g. only one of the SNPs is expressed in one host vs. the other.

· One important consideration for
comparing acieal vs telial phases of rusts is that in the acieal phase rusts
are mono-karyotic haploytes. Hence all genes required for this life-phase need
to be allelic aka have two copies in the diploid phase. In future, when fully
phase Mlp genomes are available, it would be interesting to see if some of the
poplar specific SSP are singletons with a corresponding allele in one haploid
genome.

And I forgot figure 4A would be better as an upset plot e.g. http://vcg.github.io/upset/....