Identification and Comparative Analysis of Conserved and Species-Specific microRNAs in Four Populus Sections

Round 1

Reviewer 1 Report

The manuscript presents a miRNA identification analysis of four different species of Populus. The authors used public available deep sequencing small RNA libraries for de novo miRNA identification and also an homolog-based approach. Also, by using genomic variant information of more than 600 individuals from P. trichocarpa and P. deltoides the authors performed an SNP analysis to identify sequence variation of the miRNAs and pre-miRNAs. The paper reads well for the most part and adresses an important and relevant problem. I believe it is suitable for publication after minor revision.   

Minor review:

line 42.  "...resequencing knowledge are available.[9-11]...". The dot is not placed correctly.

line 92. What is the meaning of miRNA*s? If it is miRNA-star please chose miRNA-star, as stated in the line 87, or miRNA* and use only one in the manuscript to not confuse the reader. miRNA* is also used in the Discussion section.   

lines 257-259. "All 143 miRNA families identified in this study, and each species contained at least 100 miRNA families, which was consistent with previous prediction". I could not understand the meaning of this sentence, please rewrite.

lines 266-268. "Additionally, we found that multiple unique sequences of miRNA in some shared miRNA families could promote the specific post-transcriptional regulation of miRNAs [39].". Why did the authors used "we found" and then used as reference the work of another group? I do not know if this observation came from the present work or from the one used as reference.

line 274. "Some views showed that most novel miRNA family members were likely to lack any function and that they would soon be lost through neutral selection [40].". I do not think that "views" is an appropriate word for this sentence. Maybe, studies, authors, groups.. etc.  

lines 281-283. "Researchers discovered that if a SNP in pre-miRNA decreased the hairpin structure stability, it could reduce the product of mature miRNA, otherwise increased the product". The lower stability of the hairpin increases or decreases the production of the mature miRNA?

lines 286-287. "We found that miR858 was absent in P. deltoides and P. tremula because of no hairpin sequence and P. trichocarpa due to hairpin structural failure". I believe that it reads better if the word "no" is substituted by "the lack of" or other similar sentence. Also, add an "in" before P. trichocarpa.

lines 289-290. "The target gain and loss information caused by these SNPs will be a potentially useful clue for Populus trees to study miRNA function and find SNP-associated phenotypes.". I did not understand the meaning of "target gain and loss information". Please rewrite this sentence.

Figures 1, 3, 4b, S1 and S2b should have the font size of the words improved to be easier to read.

Please state in the legend of figure S3 the species of Populus used in the analysis.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

 

The manuscript title “Identification and comparative analysis of conserved and species-specific microRNAs in four Populus sections” presents novel and important information.

 

The authors provided comprehensive analyzes on identifying miRNA loci in species of the genus Populus, revealing the interspecific variation of miRNAs, and the discovery of multiple miRNA-related SNPs.

 

Were the authors able to identify microRNAs in large-leaved poplars from the Leucoides section, which is perhaps the most ancient?

 

The Introduction section can be supplemented with information on the use of microRNAs for the genetic transformation of poplar.

 

L.35-62. This paragraph on the study of microRNAs on Populus should preferably be supplemented with information on the use of microRNAs for the genetic transformation of poplar.

 

References. Journal names should be abbreviated.

 

Ref.1, 2, 3, 31, 34. There is no complete description.

 

 

Ref.12, 38. Volume and page numbers are missing.

 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf