n the submitted manuscript, the authors performed genome assembly of two isolates of Phytophthora nicotianae.
They evaluated quality of each assembled genome sequence with different methods, finding that the hybrid method gave the best quality.
They performed annotation and revealed specific features of P. nicotianae genome in comparison with the published oomycete genomes.
One of the interesting observations is that the number of ABC transporter, which is potentially involved in exportation of toxins, expanded in the P. nicotianae lineage.

My comments are as follows.

The gene structure was predicted based on homology with other oomycete gene models together with de novo.
Should the authors include RNA-Seq data to construct more accurate gene model of P. nicotianae?
If the predicted gene model is incomplete, the result of CAFÉ is not reliable, is it?

Please include the list of RXLR effectors and other effector candidates with their amino acid sequences as a supplemental data.
In addition, please show the list of gene families with the gene ID and the 1604 single copy genes as supplemental data.
The above information is helpful for the community.

The authors identified RXLR effectors. How about Crinkler effectors?
Please make a list of Crinkler effectors too.

How about checking nucleotide differences between race 0 and race 1?
Is there any evidence of positive selection in the annotated genes?

In fig1, does CA Assembly mean Celera Assembler Assembly?
Please show the meaning of this abbreviation in the figure legend?

In fig2, is "pacBioToCA+ABySS" corresponding to the final assembly that was used for the annotation? Please clarify it.

The fig4 is fine, but if the authors use the conventional two dimensional bin plot (Haas et al. 2009 Nature 461:393-8 Figure 2) in the Phytophthora papers, readers can more easily compare the distribution of P. nicotianae with that of the published Phytophthora species. The method is available in Saunders et al. 2014. In "Plant-Pathogen Interactions: Methods and Protocols", P. Birch, J. Jones, and J. Bos, eds. Methods in Molecular Biology, 1127:29-51.

The authors have deposited the genome assembly, the annotation and the raw sequencing read data in NCBI. Please publish protein and gene fasta files together with them. Although it is easy to get these sequences from the genome sequence using the annotation, these fasta files are more accessible for any researchers.

Level of interest:
Please indicate how interesting you found the manuscript: An article of importance in its field

Quality of written English:
Please indicate the quality of language in the manuscript: Acceptable

Declaration of competing interests
Please complete a declaration of competing interests, considering the following questions:

1. Have you in the past five years received reimbursements, fees, funding, or salary from an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future?

2. Do you hold any stocks or shares in an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future?

3. Do you hold or are you currently applying for any patents relating to the content of the manuscript?

4. Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript?

5. Do you have any other financial competing interests?

6. Do you have any non-financial competing interests in relation to this paper?

If you can answer no to all of the above, write 'I declare that I have no competing interests' below. If your reply is yes to any, please give details below.

I declare that I have no competing interests

I agree to the open peer review policy of the journal. I understand that my name will be included on my report to the authors and, if the manuscript is accepted for publication, my named report including any attachments I upload will be posted on the website along with the authors' responses. I agree for my report to be made available under an Open Access Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments which I do not wish to be included in my named report can be included as confidential comments to the editors, which will not be published. I agree to the open peer review policy of the journal.

Authors' response to reviews: 

Response to Reviewers

The authors would like to thank all the reviewers for their time and comments. We have responded to each comment point-by-point as shown below in italics. The corresponding revision in the manuscript has been highlighted in yellow. The doc format of point-by-point response was attached as supplementary material.

1. Should the authors include RNA-Seq data to construct more accurate gene model of P. nicotianae?
If the predicted gene model is incomplete, the result of CAFÉ is not reliable, is it?

Response: We agree with the reviewer that inclusion of RNA-Seq data could improve the annotation results. Unfortunately, we do not have the RNA-Seq data for this study. As an alternative approach, we used publicly available ESTs from the appressorium [1] and mycelium [2, 3]of P. nicotianae to validate the annotation. We retrieved a total of 10,524 ESTs from the dbEST database. Using the threshold of match length >200 bp and E-value <1e-5, we aligned 8,043 ESTs to the race 0 genome and 7,618 ESTs to the race 1 genome. And 4,454 genes in race 0 and 3604 genes in race 1 were supported by at least 1 EST (Please see Lines 142 – 147 and Additional file 2). Since the gene structure in Oomycete was less complex than that of animals or plants, and the mean exon number per gene in Phytophthora genus varied from 2.2 to 2.8 (Additional file 1), we think the current annotation process provided a reliable result.

In the previous manuscript, we presented that ABC transporters gene family underwent expansion in P. nicotianae, but not in P. infestans, based on CAFÉ analysis. To confirm this finding, we also used Pfam to annotate the ABC transporter domains in P. nicotianae and P. infestans (Please see Lines 172 – 175 and Additional file 6).

2. Please include the list of RXLR effectors and other effector candidates with their amino acid sequences as a supplemental data. In addition, please show the list of gene families with the gene ID and the 1604 single copy genes as supplemental data.
The above information is helpful for the community.

Response: We have included the gene list of RxLR effector candidates as well as their amino acid sequences in Additional file 5. We also included the gene ID of gene families and 1,604 single copy genes in Additional file 6.

3. The authors identified RXLR effectors. How about Crinkler effectors?
Please make a list of Crinkler effectors too.

Response: We have annotated Crinkler effectors for races 0 and 1 (Please see Lines 201 – 206). A total of 32 and 26 Crinkler effectors were annotated in P. nicotianae races 0 and 1. The gene list of Crinkler effectors and their corresponding amino acid sequences were also included in the Additional file 7.

4. How about checking nucleotide differences between race 0 and race 1?
Is there any evidence of positive selection in the annotated genes?

Response: We performed whole genome comparison between race 0 and race 1. The average nucleotide identity was 99.35% for 1-to-1 alignment and 98.84% for m-to-m alignment as estimated using NUCmer [4]. We used KaKs_Calculator to calculate Ka/Ks between race 0 and race 1. Mean synonymous mutation ratio (Ks) between races 0 and 1 was 0.075. 4 genes were identified with Ka/Ks > 1, which were possibly under positive selection (Please see Lines 148 – 151 and Additional file 7).

5. In fig1, does CA Assembly mean Celera Assembler Assembly?
Please show the meaning of this abbreviation in the figure legend?

Response: CA Assembly means Celera Assembler Assembly. We have explained it in Figure 1 legend.

6. In fig2, is "pacBioToCA+ABySS" corresponding to the final assembly that was used for the annotation? Please clarify it.

Response: The assembly “pacBioToCA+ABySS" was used in constructing the final assembly together with assembly from ECTools corrected PacBio reads. We have clarified this in Figure 2 legend.

7. The fig4 is fine, but if the authors use the conventional two dimensional bin plot (Haas et al. 2009 Nature 461:393-8 Figure 2) in the Phytophthora papers, readers can more easily compare the distribution of P. nicotianae with that of the published Phytophthora species. The method is available in Saunders et al. 2014. In "Plant-Pathogen Interactions: Methods and Protocols", P. Birch, J. Jones, and J. Bos, eds. Methods in Molecular Biology, 1127:29-51.

Response: We have drawn a new Figure 4 based on 5’ and 3’ intergenic border lengths using advised method.

8. The authors have deposited the genome assembly, the annotation and the raw sequencing read data in NCBI. Please publish protein and gene fasta files together with them. Although it is easy to get these sequences from the genome sequence using the annotation, these fasta files are more accessible for any researchers.

Response: We agree with the reviewer that fasta files are convenient in practical research. We’d also like to upload original fasta files to NCBI. However, NCBI do not support direct upload of fasta files of annotated genes. We have uploaded the corresponding fasta, gff files to GigaDB and it should be available to public after the paper was published.


Reviewer #3: The paper submitted by Liu and coauthors provides details of the sequencing and assembly of two Phytophthora nicotianae genomes.  This is not the first genomes of this species to be sequenced and publicly abvailable, with four strains sequenced by the Board Institute and which can be found at the FungiDB site with the synonym P. parasitica.  This work has not been published but the authors should refer to this work, indicating if the two genomes sequenced by the authors provides any additional knowledge about this important plant pathogen.  For example, I know that with the other four genomes there were problems with the assembly and annotation of large genes that contain many repeats.  Does the current study help to sort out such issues?  
Despite this omission, I feel that the manuscript is suitable for publication in GigaScience providing the authors address the above issue and make the following corrections.

Response: The work of Broad Institute provided great value to the community by sequencing five strains of Phytophthora parasitica. And we have included relevant information in the manuscript (Please see Lines 72 - 77). Compared with their work, we sought to investigate the mechanism that causing virulence differences between races 0 and 1 of P. nicotianae on Nicotiana tabacum. More importantly, the genomes of races 0 and 1 reported in this study were not previously available, and they complement currant database of Phytophthora genomes. We think a combination of the two may provide more information on questions such as host adaption and pathogenic polymorphism in the future.

A common shortcoming of Illumina-only sequencing method is the resolving of repeat regions due to the length of reads. Sequencing larger insert libraries may solve this issue. But with longer PacBio reads, we have the possibility to span whole repeat regions, which makes it easier to assemble repeat regions out. Compared with previous research, our work was the first use of PacBio SMRT sequencing technology in oomycetes.


1.     In the introduction the authors state that the limitation for the control of P.nicotianae is the production of chlamydospores.  Surely this is not restricted to P.nicotianae but to most oomycetes.  Other researchers argue that the production of motile zoospores is an important in the spread of infection.  However, it is the fact that oomycetes are not fungi, being more closely related to coloured algae and apicomplexans, rendering most if not all fungicides ineffectual in the control of Phytophthora and other oomycetes.

Response: We agree with the reviewer that besides chlamydospores, production of motile zoospores indeed makes black shank hard to eliminate. And the word fungicide was inappropriate when used in oomycetes. We have changed the corresponding statement in the context (Please see Lines 61 – 64).

2.     The authors should read their manuscript very carefully for grammatical and typographical errors.  
There are places where full stops are in the wrong place or missing and where spaces between words are missing. For example, p3 line 21, p6 line 48, p7 lines2, 48.  

Response: We have carefully checked the manuscript and corrected the missing space in Line 60, misplaced full stop in Line 162, misplaced space in Line 168 and a spelling error in Line 198.

3.     Please check the use of plural and singular.  For example, parameter on p4 should be parameters, p7 change to "effectors are important members of cytoplasmic effectors, which contain a special motif …".  

Response: We have carefully checked the manuscript and correct the mistakes in Line 104 and Line 185.


4.     There is a huge body of work in these type of effectors from Phytophthora species, yet the authors fail to include any of these references.  Inclusion of the numbers of RxLR effectors from other Phytohthora species could be included as a further comparison.  In addition, the RxLR is not part of the signal peptide for secretion as what seems to be suggested by the authors, otherwise it would cleaved upon entry to the secretion pathway.  Please alter this section to remove incorrect statements.  

Response: We have included recent research on the function and evolution of RxLR effectors in the context and removed the incorrect statements (Please see Lines 185 – 195). Comparison of numbers of RxLR effectors and Crinkler effectors with related species was also included in Additional file 8.

5.     The authors should check the manuscript for the incorrect usage abbreviated and unabbreviated species names.

Response: We have carefully checked the manuscript and ensured that only the first time species name used was unabbreviated. We have corrected the errors in Lines 88, 425 – 428.


6.     The authors show a complete disregard to the section on references in the Instructions to Authors.  
"Please ensure that the reference style is followed precisely; if the references are not in the correct style they may have to be retyped and carefully proofread.
All web links and URLs, including links to the authors' own websites, should be given a reference number and included in the reference list rather than within the text of the manuscript. They should be provided in full, including both the title of the site and the URL, as well as the date the site was accessed, in the following format: The Mouse Tumor Biology Database. http://tumor.informatics.jax.org/mtbwi/index.do. Accessed 20 May 2013. If an author or group of authors can clearly be associated with a web link, such as for weblogs, then they should be included in the reference.
Authors may wish to make use of reference management software to ensure that reference lists are correctly formatted. An example of such software is Papers, which is part of Springer Science+Business Media."
Apart from the fact that none of the references are formatted correctly, journal names appear in the abbreviated form or in full and in at least one case the journal name is partially missing.  Species names are not in italics.  It is obvious that the authors used a reference managing software but the failed to ensure that the citations had been entered correctly.

Response: The reference style we used was out of date and we failed to notice that. We have corrected the style and carefully reviewed every reference to eliminate any possible mistakes. We have corrected the partially missing journal names in Line 288 and make sure that species names were in italic.



References

1. Le Berre J-Y, Engler G, Panabières F. Exploration of the late stages of the tomato-Phytophthora parasitica interactions through histological analysis and generation of expressed sequence tags. New Phytol. 2008;177:480–492.
2. Kebdani N, Pieuchot L, Deleury E, Panabieres F, Le Berre J-Y, Gourgues M. Cellular and molecular characterization of Phytophthora parasitica appressorium-mediated penetration. New Phytol. 2010;185:248–257.
3. Panabières F, Amselem J, Galiana E, Le Berre J-Y. Gene identification in the oomycete pathogen Phytophthora parasitica during in vitro vegetative growth through expressed sequence tags. Fungal Genet Biol. 2005;42:611–623.
4. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol. 2004;5:R12.

The authors sincerely replied to my requests.
The one I feel concerned is that the number of CRN effectors is smaller than that of other Phytophthora species
(See Stam et al. 2013 PLoS One 8:e59517, Figure 1 and Figure 3).
The number is similar to that of Hyaloperonospora arabidopsidis.
Is it possible to underestimate the number of CRN effectors?
If it is, please mention this possibility on the manuscript.

Level of interest:

Please indicate how interesting you found the manuscript: An article of importance in its field

Quality of written English:

Please indicate the quality of language in the manuscript: Acceptable

Declaration of competing interests

Please complete a declaration of competing interests, considering the following questions:

1. Have you in the past five years received reimbursements, fees, funding, or salary from an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future?

2. Do you hold any stocks or shares in an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future?

3. Do you hold or are you currently applying for any patents relating to the content of the manuscript?

4. Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript?

5. Do you have any other financial competing interests?

6. Do you have any non-financial competing interests in relation to this paper? If you can answer no to all of the above, write 'I declare that I have no competing interests' below. If your reply is yes to any, please give details below.

I declare that I have no competing interests'

I agree to the open peer review policy of the journal.

I understand that my name will be included on my report to the authors and, if the manuscript is accepted for publication, my named report including any attachments I upload will be posted on the website along with the authors' responses. I agree for my report to be made available under an Open Access Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments which I do not wish to be included in my named report can be included as confidential comments to the editors, which will not be published. I agree to the open peer review policy of the journal.

Authors' response to reviews:

In the submitted manuscript, the authors performed genome assembly of two isolates of Phytophthora nicotianae.
They evaluated quality of each assembled genome sequence with different methods, finding that the hybrid method gave the best quality.
They performed annotation and revealed specific features of P. nicotianae genome in comparison with the published oomycete genomes.
One of the interesting observations is that the number of ABC transporter, which is potentially involved in exportation of toxins, expanded in the P. nicotianae lineage.

My comments are as follows.

The gene structure was predicted based on homology with other oomycete gene models together with de novo.
Should the authors include RNA-Seq data to construct more accurate gene model of P. nicotianae?
If the predicted gene model is incomplete, the result of CAFÉ is not reliable, is it?

Please include the list of RXLR effectors and other effector candidates with their amino acid sequences as a supplemental data.
In addition, please show the list of gene families with the gene ID and the 1604 single copy genes as supplemental data.
The above information is helpful for the community.

The authors identified RXLR effectors. How about Crinkler effectors?
Please make a list of Crinkler effectors too.

How about checking nucleotide differences between race 0 and race 1?
Is there any evidence of positive selection in the annotated genes?

In fig1, does CA Assembly mean Celera Assembler Assembly?
Please show the meaning of this abbreviation in the figure legend?

In fig2, is "pacBioToCA+ABySS" corresponding to the final assembly that was used for the annotation? Please clarify it.

The fig4 is fine, but if the authors use the conventional two dimensional bin plot (Haas et al. 2009 Nature 461:393-8 Figure 2) in the Phytophthora papers, readers can more easily compare the distribution of P. nicotianae with that of the published Phytophthora species. The method is available in Saunders et al. 2014. In "Plant-Pathogen Interactions: Methods and Protocols", P. Birch, J. Jones, and J. Bos, eds. Methods in Molecular Biology, 1127:29-51.

The authors have deposited the genome assembly, the annotation and the raw sequencing read data in NCBI. Please publish protein and gene fasta files together with them. Although it is easy to get these sequences from the genome sequence using the annotation, these fasta files are more accessible for any researchers.

Level of interest
Please indicate how interesting you found the manuscript:
An article of importance in its field

Quality of written English
Please indicate the quality of language in the manuscript:
Acceptable

Declaration of competing interests
Please complete a declaration of competing interests, considering the following questions:
Have you in the past five years received reimbursements, fees, funding, or salary from an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future?
Do you hold any stocks or shares in an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future?
Do you hold or are you currently applying for any patents relating to the content of the manuscript?
Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript?
Do you have any other financial competing interests?
Do you have any non-financial competing interests in relation to this paper?

If you can answer no to all of the above, write 'I declare that I have no competing interests' below. If your reply is yes to any, please give details below.

I declare that I have no competing interests.

I agree to the open peer review policy of the journal. I understand that my name will be included on my report to the authors and, if the manuscript is accepted for publication, my named report including any attachments I upload will be posted on the website along with the authors' responses. I agree for my report to be made available under an Open Access Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments which I do not wish to be included in my named report can be included as confidential comments to the editors, which will not be published. I agree to the open peer review policy of the journal
I agree to the open peer review policy of the journal.

Authors' response to reviews:

The authors would like to thank all the reviewers for their time and comments. We have responded to each comment point-by-point as shown below in italics. The corresponding revision in the manuscript has been highlighted in yellow. The doc format of point-by-point response was attached as supplementary material.

1. Should the authors include RNA-Seq data to construct more accurate gene model of P. nicotianae?
If the predicted gene model is incomplete, the result of CAFÉ is not reliable, is it?

Response: We agree with the reviewer that inclusion of RNA-Seq data could improve the annotation results. Unfortunately, we do not have the RNA-Seq data for this study. As an alternative approach, we used publicly available ESTs from the appressorium [1] and mycelium [2, 3]of P. nicotianae to validate the annotation. We retrieved a total of 10,524 ESTs from the dbEST database. Using the threshold of match length >200 bp and E-value <1e-5, we aligned 8,043 ESTs to the race 0 genome and 7,618 ESTs to the race 1 genome. And 4,454 genes in race 0 and 3604 genes in race 1 were supported by at least 1 EST (Please see Lines 142 – 147 and Additional file 2). Since the gene structure in Oomycete was less complex than that of animals or plants, and the mean exon number per gene in Phytophthora genus varied from 2.2 to 2.8 (Additional file 1), we think the current annotation process provided a reliable result.

In the previous manuscript, we presented that ABC transporters gene family underwent expansion in P. nicotianae, but not in P. infestans, based on CAFÉ analysis. To confirm this finding, we also used Pfam to annotate the ABC transporter domains in P. nicotianae and P. infestans (Please see Lines 172 – 175 and Additional file 6).

2. Please include the list of RXLR effectors and other effector candidates with their amino acid sequences as a supplemental data. In addition, please show the list of gene families with the gene ID and the 1604 single copy genes as supplemental data.
The above information is helpful for the community.

Response: We have included the gene list of RxLR effector candidates as well as their amino acid sequences in Additional file 5. We also included the gene ID of gene families and 1,604 single copy genes in Additional file 6.

3. The authors identified RXLR effectors. How about Crinkler effectors?
Please make a list of Crinkler effectors too.

Response: We have annotated Crinkler effectors for races 0 and 1 (Please see Lines 201 – 206). A total of 32 and 26 Crinkler effectors were annotated in P. nicotianae races 0 and 1. The gene list of Crinkler effectors and their corresponding amino acid sequences were also included in the Additional file 7.

4. How about checking nucleotide differences between race 0 and race 1?
Is there any evidence of positive selection in the annotated genes?

Response: We performed whole genome comparison between race 0 and race 1. The average nucleotide identity was 99.35% for 1-to-1 alignment and 98.84% for m-to-m alignment as estimated using NUCmer [4]. We used KaKs_Calculator to calculate Ka/Ks between race 0 and race 1. Mean synonymous mutation ratio (Ks) between races 0 and 1 was 0.075. 4 genes were identified with Ka/Ks > 1, which were possibly under positive selection (Please see Lines 148 – 151 and Additional file 7).

5. In fig1, does CA Assembly mean Celera Assembler Assembly?
Please show the meaning of this abbreviation in the figure legend?

Response: CA Assembly means Celera Assembler Assembly. We have explained it in Figure 1 legend.

6. In fig2, is "pacBioToCA+ABySS" corresponding to the final assembly that was used for the annotation? Please clarify it.

Response: The assembly “pacBioToCA+ABySS" was used in constructing the final assembly together with assembly from ECTools corrected PacBio reads. We have clarified this in Figure 2 legend.

7. The fig4 is fine, but if the authors use the conventional two dimensional bin plot (Haas et al. 2009 Nature 461:393-8 Figure 2) in the Phytophthora papers, readers can more easily compare the distribution of P. nicotianae with that of the published Phytophthora species. The method is available in Saunders et al. 2014. In "Plant-Pathogen Interactions: Methods and Protocols", P. Birch, J. Jones, and J. Bos, eds. Methods in Molecular Biology, 1127:29-51.

Response: We have drawn a new Figure 4 based on 5’ and 3’ intergenic border lengths using advised method.

8. The authors have deposited the genome assembly, the annotation and the raw sequencing read data in NCBI. Please publish protein and gene fasta files together with them. Although it is easy to get these sequences from the genome sequence using the annotation, these fasta files are more accessible for any researchers.

Response: We agree with the reviewer that fasta files are convenient in practical research. We’d also like to upload original fasta files to NCBI. However, NCBI do not support direct upload of fasta files of annotated genes. We have uploaded the corresponding fasta, gff files to GigaDB and it should be available to public after the paper was published.


Reviewer #3: The paper submitted by Liu and coauthors provides details of the sequencing and assembly of two Phytophthora nicotianae genomes.  This is not the first genomes of this species to be sequenced and publicly abvailable, with four strains sequenced by the Board Institute and which can be found at the FungiDB site with the synonym P. parasitica.  This work has not been published but the authors should refer to this work, indicating if the two genomes sequenced by the authors provides any additional knowledge about this important plant pathogen.  For example, I know that with the other four genomes there were problems with the assembly and annotation of large genes that contain many repeats.  Does the current study help to sort out such issues?  
Despite this omission, I feel that the manuscript is suitable for publication in GigaScience providing the authors address the above issue and make the following corrections.

Response: The work of Broad Institute provided great value to the community by sequencing five strains of Phytophthora parasitica. And we have included relevant information in the manuscript (Please see Lines 72 - 77). Compared with their work, we sought to investigate the mechanism that causing virulence differences between races 0 and 1 of P. nicotianae on Nicotiana tabacum. More importantly, the genomes of races 0 and 1 reported in this study were not previously available, and they complement currant database of Phytophthora genomes. We think a combination of the two may provide more information on questions such as host adaption and pathogenic polymorphism in the future.

A common shortcoming of Illumina-only sequencing method is the resolving of repeat regions due to the length of reads. Sequencing larger insert libraries may solve this issue. But with longer PacBio reads, we have the possibility to span whole repeat regions, which makes it easier to assemble repeat regions out. Compared with previous research, our work was the first use of PacBio SMRT sequencing technology in oomycetes.


1.     In the introduction the authors state that the limitation for the control of P.nicotianae is the production of chlamydospores.  Surely this is not restricted to P.nicotianae but to most oomycetes.  Other researchers argue that the production of motile zoospores is an important in the spread of infection.  However, it is the fact that oomycetes are not fungi, being more closely related to coloured algae and apicomplexans, rendering most if not all fungicides ineffectual in the control of Phytophthora and other oomycetes.

Response: We agree with the reviewer that besides chlamydospores, production of motile zoospores indeed makes black shank hard to eliminate. And the word fungicide was inappropriate when used in oomycetes. We have changed the corresponding statement in the context (Please see Lines 61 – 64).

2.     The authors should read their manuscript very carefully for grammatical and typographical errors.  
There are places where full stops are in the wrong place or missing and where spaces between words are missing. For example, p3 line 21, p6 line 48, p7 lines2, 48.  

Response: We have carefully checked the manuscript and corrected the missing space in Line 60, misplaced full stop in Line 162, misplaced space in Line 168 and a spelling error in Line 198.

3.     Please check the use of plural and singular.  For example, parameter on p4 should be parameters, p7 change to "effectors are important members of cytoplasmic effectors, which contain a special motif …".  

Response: We have carefully checked the manuscript and correct the mistakes in Line 104 and Line 185.


4.     There is a huge body of work in these type of effectors from Phytophthora species, yet the authors fail to include any of these references.  Inclusion of the numbers of RxLR effectors from other Phytohthora species could be included as a further comparison.  In addition, the RxLR is not part of the signal peptide for secretion as what seems to be suggested by the authors, otherwise it would cleaved upon entry to the secretion pathway.  Please alter this section to remove incorrect statements.  

Response: We have included recent research on the function and evolution of RxLR effectors in the context and removed the incorrect statements (Please see Lines 185 – 195). Comparison of numbers of RxLR effectors and Crinkler effectors with related species was also included in Additional file 8.

5.     The authors should check the manuscript for the incorrect usage abbreviated and unabbreviated species names.

Response: We have carefully checked the manuscript and ensured that only the first time species name used was unabbreviated. We have corrected the errors in Lines 88, 425 – 428.


6.     The authors show a complete disregard to the section on references in the Instructions to Authors.  
"Please ensure that the reference style is followed precisely; if the references are not in the correct style they may have to be retyped and carefully proofread.
All web links and URLs, including links to the authors' own websites, should be given a reference number and included in the reference list rather than within the text of the manuscript. They should be provided in full, including both the title of the site and the URL, as well as the date the site was accessed, in the following format: The Mouse Tumor Biology Database. http://tumor.informatics.jax.org/mtbwi/index.do. Accessed 20 May 2013. If an author or group of authors can clearly be associated with a web link, such as for weblogs, then they should be included in the reference.
Authors may wish to make use of reference management software to ensure that reference lists are correctly formatted. An example of such software is Papers, which is part of Springer Science+Business Media."
Apart from the fact that none of the references are formatted correctly, journal names appear in the abbreviated form or in full and in at least one case the journal name is partially missing.  Species names are not in italics.  It is obvious that the authors used a reference managing software but the failed to ensure that the citations had been entered correctly.

Response: The reference style we used was out of date and we failed to notice that. We have corrected the style and carefully reviewed every reference to eliminate any possible mistakes. We have corrected the partially missing journal names in Line 288 and make sure that species names were in italic.



References

1. Le Berre J-Y, Engler G, Panabières F. Exploration of the late stages of the tomato-Phytophthora parasitica interactions through histological analysis and generation of expressed sequence tags. New Phytol. 2008;177:480–492.
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The authors sincerely replied to my requests.
The one I feel concerned is that the number of CRN effectors is smaller than that of other Phytophthora species
(See Stam et al. 2013 PLoS One 8:e59517, Figure 1 and Figure 3).
The number is similar to that of Hyaloperonospora arabidopsidis.
Is it possible to underestimate the number of CRN effectors?
If it is, please mention this possibility on the manuscript.

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