The Whole Mitochondrial Genome Sequence of Dendrobium loddigesii Rolfe, an Endangered Orchid Species in China, Reveals a Complex Multi-Chromosome Structure
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsDear Authors,
With great interest I have read Your manuscript titled „The Whole Mitochondrial Genome Sequence of Dendrobium loddigesii Rolfe, an Endangered Orchid Species in China, Reveals a complex multi-chromosome Structure”. Nevertheless, I have found some imperfections, which-in my opinion-should be improved or at least clarified before an eventual publication. I have listed them below:
1. In chapter reproduction I suggest to enlarge the background of investigations and present the other studies of mitochndrial genome in orchids. Moreover, the value of presented investigations and reasons to their conducting should be stronger justified.
2. Lines 49-51. Please, consider other investigations of orchids mitochondrial genome. I listed some publications below.
3. Lines 55-60. In my opinion this description should be moved into presentation of concise aims of investigations
4. Figure 1,5,6 are illegible. Their quality (including the font size) should be improved.
5. Discussion. I suggest to discuss the applicability of Your findings.
6. Please, look into the folowing papers. Perhaps some of them would be helpful in manuscript improvements:
· Shen, B., Shen, A., Liu, L. et al. 2024. Assembly and comparative analysis of the complete multichromosomal mitochondrial genome of Cymbidium ensifolium, an orchid of high economic and ornamental value. BMC Plant Biol 24, 255. https://doi.org/10.1186/s12870-024-04962-4
· Meng-Ting Wang, Zhen-Yu Hou, Chao Li, Jia-Peng Yang, Zhi-Tao Niu, Qing-Yun Xue, Wei Liu, Xiao-Yu Ding 2022. Rapid structural evolution of Dendrobium mitogenomes and mito-nuclear phylogeny discordances in Dendrobium (Orchidaceae). J. Syst. Evol. 61(5): 790-805. https://doi.org/10.1111/jse.12912
· Yang, J.-X.; Dierckxsens, N.; Bai, M.-Z.; Guo, Y.-Y. Multichromosomal Mitochondrial Genome of Paphiopedilum micranthum: Compact and Fragmented Genome, and Rampant Intracellular Gene Transfer. Int. J. Mol. Sci. 2023, 24, 3976. https://doi.org/10.3390/ijms24043976
· Kenneth M. Cameron, On the value of nuclear and mitochondrial gene sequences for reconstructing the phylogeny of vanilloid orchids (Vanilloideae, Orchidaceae), Annals of Botany, 104(3): 377–385, https://doi.org/10.1093/aob/mcp024
Author Response
Reviewer 1:
With great interest I have read Your manuscript titled The Whole Mitochondrial Genome Sequence of Dendrobium loddigesii Rolfe, an Endangered Orchid Species in China, Reveals a complex multi-chromosome Structure”. Nevertheless, I have found some imperfections, which-in my opinion-should be improved or at least clarified before an eventual publication. I have listed them below:
Comment 1: In chapter reproduction I suggest to enlarge the background of investigations and present the other studies of mitochndrial genome in orchids. Moreover, the value of presented investigations and reasons to their conducting should be stronger justified.
Response: Thank you for your suggestions, the manuscript added the published mitochondrial genome of Dendrobium. Please see paragraph 2 of the introduction.
Commented 2: Lines 49-51. Please, consider other investigations of orchids mitochondrial genome. I listed some publications below.
Response: Thank you for your suggestions, we have downloaded and read these kindly provided references, and some publications are added to the manuscript as references. Please see the revised manuscript.
Commented 3: Lines 55-60. In my opinion this description should be moved into presentation of concise aims of investigations.
Response: Thank you for your suggestions, the manuscript has adjusted this description for the aims of the investigations. Please see the revised manuscript.
Commented 4: Figure 1,5,6 are illegible. Their quality (including the font size) should be improved.
Response: Thank you for your suggestions, figure 1,5, and 6 are relatively large. Due to the limitation of word size, the pictures are too small, so we put the clear pictures in the compressed file. We also adjust the figure 1,5, and 6 in the manuscript. Please see the revised manuscript.
Commented 5: Discussion. I suggest to discuss the applicability of Your findings.
Response: Thank you for your suggestions, the ‘discuss’ has added the applicability of our findings. Please see the revised manuscript.
Commented 6: Please, look into the following papers. Perhaps some of them would be helpful in manuscript improvements:
Response: Thank you for your suggestions, we have downloaded and read these kindly provided papers, and improved our manuscript. Please see the revised manuscript.
Reviewer 2 Report
Comments and Suggestions for Authors
The manuscript by Tong, et al. entitled “The Whole Mitochondrial Genome Sequence of Dendrobium loddigesii Rolfe, an Endangered Orchid Species in China, Reveals a complex multi-chromosome Structure.” report Dendrobium loddigesii mitogenome consisted of 17 circular subgenomes, contained 70 genes (36 protein-coding genes, 31 tRNA genes, and 3 rRNA genes) are analyzed using sequencing and phylogenetic methods. The authors claim that ‘the outcomes will significantly augment the orchid mitochondrial genome database, offering profound insights into Dendrobium's intricate mitochondrial genome architecture’. The work is technically sound piece of research, and within the scope of Gene, it could be published after minor modifications.
1. The authors need provide excises support information/references about ‘genomic DNA isolation’ and ‘mitochondria DNA from purified mitochondria’.
2. Mega software updated to version 11, the authors may run the NJ-tree on it
3. The authors may verify the predicted ‘70 genes’ is true.
4. To confirm the predicted ‘circular’ DNA (based on the contigs), the authors could run inverse PCR to verify.
5. Need check misused terminologies, for example 'These gene sequences' in lane 108.
Comments on the Quality of English Language
generally OK
Author Response
The manuscript by Tong, et al. entitled “The Whole Mitochondrial Genome Sequence of Dendrobium loddigesii Rolfe, an Endangered Orchid Species in China, Reveals a complex multi-chromosome Structure.” report Dendrobium loddigesii mitogenome consisted of 17 circular subgenomes, contained 70 genes (36 protein-coding genes, 31 tRNA genes, and 3 rRNA genes) are analyzed using sequencing and phylogenetic methods. The authors claim that ‘the outcomes will significantly augment the orchid mitochondrial genome database, offering profound insights into Dendrobium's intricate mitochondrial genome architecture’. The work is technically sound piece of research, and within the scope of Gene, it could be published after minor modifications.
Comment 1: The authors need provide excises support information/references about ‘genomic DNA isolation’ and ‘mitochondria DNA from purified mitochondria’.
Response: Thank you for your suggestions, the manuscript has modified the ' genomic DNA isolation’ and ‘mitochondria DNA from purified mitochondria’. Please see the revised manuscript.
Commented 2: Mega software updated to version 11, the authors may run the NJ-tree on it.
Response: Thank you for your suggestions, the manuscript has added Mega 11. Please see the revised manuscript.
Commented 3: The authors may verify the predicted ‘70 genes’ is true.
Response: Thank you for your suggestions, yes, we have predicted ‘70 genes’, including 36 PCGs, 31 tRNA genes, and 3 rRNA genes. Please see the revised manuscript.
Commented 3: To confirm the predicted ‘circular’ DNA (based on the contigs), the authors could run inverse PCR to verify.
Response: Thank you for your suggestions, the ring genome was assembled using three generations of data comparison and visualized using Mummer. All the sequences were completely covered from beginning to end by reads, and there were reads linking the end and beginning sequences, so the ring sequence could be determined. Please see below the picture.
Commented 4: Need check misused terminologies, for example 'These gene sequences' in lane 108.
Response: Thank you for your suggestions, we have revised misused terminologies. Please see the revised manuscript.
Author Response File: 
Author Response.pdf
