Genome-Wide Identification and Characterization of Heat-Shock Transcription Factors in Rubber Tree
, Wencai Yu 4, Yueyi Chen 2,3, Shuguang Yang 2,3, Shaohua Wu 2,3, Jinquan Chao 2,3, Xinlong Wang 2,3 and Wei-Min Tian 2,3,*Round 1
Reviewer 1 Report
The manuscript describes the heat shock transcription factor family in Rubber tree (Hevea brasiliensis Muell. Arg.). The manuscript is generally scientifically sound. However, there are numerous spelling and grammatical errors, and this should be carefully checked by a competent proofreader.
The manuscript reports the identification and phylogenetic analysis of 30 heat shock transcription factors, their expression levels in 2 clones, the expression levels of 6 gene in 6 clones, and the subcellular localization of 3 genes.
This information will be useful for further research on cold tolerance in rubber tree, as well as in comparative studies of genomic organisation and stress responses.
Comments:
The subcellular localization of the three analysed genes was confirmed to be in the nucleus. As the genes are transcription factors, they all would be expected to be localized in the nucleus. Some discussion about the aim of the subcellular localization experiment could be included – e.g. are some TFs localized outside the nucleus, or was this done to confirm the location etc.
The phylogenetic analysis indicates that many of the genes are clustering in pairs. However, the expression patterns of these structurally similar genes are often not similar. Some discussion about these contrasts could be interesting. For example, is the pairwise clustering of these genes the result of a genome duplication, or specific family expansion? Is the differential expression of similar genes a result of specialization after duplication? If there are no results from this study (or the genome sequence paper of Tang et al 2016), perhaps there are some examples from other species that could be presented in the discussion, and indicate possible future research directions in the rubber tree.
Minor comments:
File S4 – in genes where 2 introns are found, only 1 intron length is given (HbHSFA9b, HbHSFB4d). Also, additional entry in row 18.
Author Response
-Response to the reviewer1's comments
Comment 1: “The manuscript describes the heat shock transcription factor family in Rubber tree (Hevea brasiliensis Muell. Arg.). The manuscript is generally scientifically sound. However, there are numerous spelling and grammatical errors, and this should be carefully checked by a competent proofreader.”
Response 1: We have carefully checked and revised such issues in the revised version.
Comment 2: Some discussion about the aim of the subcellular localization experiment could be included – e.g. are some TFs localized outside the nucleus, or was this done to confirm the location etc.
Response 2: We have included the subcellular localization of their homlogs in other plants.
Comment 3: “The phylogenetic analysis indicates that many of the genes are clustering in pairs. However, the expression patterns of these structurally similar genes are often not similar. Some discussion about these contrasts could be interesting. For example, is the pairwise clustering of these genes the result of a genome duplication, or specific family expansion? Is the differential expression of similar genes a result of specialization after duplication? If there are no results from this study (or the genome sequence paper of Tang et al 2016), perhaps there are some examples from other species that could be presented in the discussion, and indicate possible future research directions in the rubber tree. ”
Response 3: We have discussed the contrasts according to the reviewer’s suggestion.
Comment 4: “File S4 – in genes where 2 introns are found, only 1 intron length is given (HbHSFA9b, HbHSFB4d). Also, additional entry in row 18.”
Response 4: We have revised in the context and File S4.
Reviewer 2 Report
Li et al. The authors characterized the Hsf gene family in the rubber tree, including gene expression analysis under a variety of conditions. The heat and cold treatments have important biological significance for this plant and it is clear why they would choose this family and those treatments. The authors also show that Hsf family members have different expression patterns that likely corresponds to the tissue specific roles of homologs.
The gene family analysis would be much more convincing if it were placed in context of the rest of the plant family. For example, in Figure 1, there is no outgroup and there are no other taxa represented on the phylogeny. The absence of an outgroup is problematic because it is impossible to place when the family members diverged. However, missing the additional taxa is problematic as Fig 1 misleadingly implies that all of the Hsf divergence occurred within the rubber tree which is not the case. Please include Hsf members from plum, rice, or apple? The authors cited these taxa in the discussion and they likely have many overlapping family members. Figure 2 appears to resolve this problem, but Ficus and Arabidopsis are highly diverged (over 100 million years) and it is possible that phylogenetic signal has been lost due to convergence or high divergence in at least some of these family members. It should include a closer comparison. In Figure 4, please change for red/green colorblind individuals.
Please describe the phylogenetic methods. They are completely absent.
Author Response
-Response to the reviewer2's comments
Comment 1: “in Figure 1, there is no outgroup and there are no other taxa represented on the phylogeny. The absence of an outgroup is problematic because it is impossible to place when the family members diverged. However, missing the additional taxa is problematic as Fig 1 misleadingly implies that all of the Hsf divergence occurred within the rubber tree which is not the case. Please include Hsf members from plum, rice, or apple? The authors cited these taxa in the discussion and they likely have many overlapping family members. Figure 2 appears to resolve this problem, but Ficus and Arabidopsis are highly diverged (over 100 million years) and it is possible that phylogenetic signal has been lost due to convergence or high divergence in at least some of these family members. It should include a closer comparison.”
Response 1: It is a similar question to the academic editor’s comment 3. We have revised.
Comment 2: “In Figure 4, please change for red/green colorblind individuals. ”
Response 2: We have changed the color.
Comment 3: “Please describe the phylogenetic methods. They are completely absent. ”
Response 3: We have amended in the revised version and marked in red color.
Author Response File: 
Author Response.doc
