Genome-Wide Identification, Expansion, Evolution, and Expression Analysis Reveals ABCB Genes Important for Secondary Cell Wall Development in Moso Bamboo (Phyllostachys edulis)

Round 1

Reviewer 1 Report

Minor revision is required as per attachment 

Comments for author File: Comments.pdf

Author Response

06 Jul, 2023

Agronomy

Manuscript ID: agronomy-2481649

Genome-wide identification, expansion, evolution, and expression analysis reveals ABCB genes important for secondary cell wall development in Moso bamboo (Phyllostachys edulis)

 

Dear Professor,

 

Thank you and the reviewers very much for revising our manuscript ‘Genome-wide identification, expansion, evolution, and expression analysis reveals ABCB genes important for secondary cell wall development in Moso bamboo (Phyllostachys edulis)’ (Manuscript ID: agronomy-2481649). Your effort and time spent on our manuscript are greatly appreciated by all of us. We are delighted to all suggestion and review comments, which you and the reviewers made. Your revisions/suggestions have definitely improved the quality of our manuscript.

The manuscript was extensively edited according to your and reviewers’ comments. Please find the revised manuscript in Agronomy’s manuscript center. The changes were marked up using the“Track Changes” function. The responses to the reviewers are highlighted below.

 

Thank you again for your kind help and excellent suggestions for our manuscript. We hope these revisions will be satisfactory and will lead to acceptance for publication. We are looking forward to hearing from you soon.

 

Yours sincerely

 

Feng Que

---------------

Dr. Feng Que

Co-Innovation Center for Sustainable Forestry in Southern China

Bamboo Research Institute, Nanjing Forestry University

159 Longpan Road, Nanjing, 210037, Jiangsu China

Fax: 86 25 85427177

Email: [email protected]

 

 

 

------------------------

Reviewer's report:

The manuscript entitled " Analysis of genome-wide identification, evolution, and expression of the ABCB genes reveals their importance in the development of the secondary cell wall in Moso bamboo (Phyllostachys edulis) is very well managed. The article has explained the unique study about the ABCB gene family in Moso bamboo. However following minor revisions are required before final acceptance of the article.

 

1. In manuscript use the full scientific names of crop species following abbreviations. Also prefer scientific names instead of common names.

 

Response:

--We thank the reviewer for this comment.

--As suggested by the reviewer, we have all the common names into scientific names throughout the manuscript.

 

In order to classify and study the phylogeny of the ABCB gene family in Moso bamboo, this study also used the previously identified and analyzed ABCB gene families in Arabidopsis thaliana, Oryza sativa (O. sativa), and Z. mays. (Lines 100-102)

 

The collinearities between Moso bamboo and O. sativa, and between Moso bamboo and Z. mays were analyzed by the MCScan tool with the commands such as: jcvi.compara.synteny and jcvi.graphics.synteny [19]. (Lines 118-120)

 

Using the available information of the previously identified and analyzed the ABCB gene families in Arabidopsis, O. sativa, and Z. mays, our study aimed to classify the ABCB genes in Moso bamboo. To this end, we constructed a phylogenetic tree using the ABCB protein sequences of Arabidopsis, O. sativa, Z. mays, and Moso bamboo. Proteins with similar structures were grouped into clusters. Following the classification approach used in previous studies on Arabidopsis, O. sativa, and Z. mays, the ABCB genes in Moso bamboo were classified into five subgroups, I-V (Figure 2). (Lines 170-176)

 

The ABCB protein sequences from Arabidopsis, O. sativa, and Z. mays and the 37 PhABCBs were used to construct the phylogenetic tree. (Lines 195-196)

 

In comparison to Arabidopsis, O. sativa, and Z. mays, a larger number of ABCBs were identified in Moso bamboo genome. Arabidopsis, O. sativa, Z. mays and Moso bamboo had 28, 27, 31, and 37 ABCBs, respectively (Table 2). To investigate putative evolutionary events, a synteny analysis was performed among the ABCB genes of O. sativa, Z. mays, and Moso bamboo (Figure 4). (Lines 212-216)

 

Figure 4. The synteny analysis of the ABCB genes among O. sativa, Moso bamboo, and Z. mays. Each colored bar represents a chromosome, and the genes are labeled according to their position on the chromosomes. The green lines indicate collinear blocks of the ABCBs between O. sativa and Moso bamboo, while the red lines represent collinear blocks of the ABCBs between Moso bamboo and Z. mays. The gray lines in the background represent collinear blocks among different chromosomes. (Lines 226-230)

 

Compared with Arabidopsis, O. sativa and Z. mays, Moso bamboo genome contained a larger number of the ABCB genes, especially in subgroup Ⅴ. The synteny analysis of the ABCB genes revealed more synteny between Moso bamboo and monocots (O. sativa and Z. mays), while less synteny was observed between Moso bamboo and dicots (Arabidopsis). In addition, the range of synteny between the ABCB gene family of O. sativa and Arabidopsis was also limited [24]. (Lines 386-391)

 

Extensive research and reports are available for Arabidopsis, O. sativa, Z. mays, and other species. In Arabidopsis, the abcb1 mutant exhibited decreased IAA transport, although the plant growth was only slightly affected. However, in Z. mays and sorghum, the abcb1 mutant had more pronounced effects and resulted in a significantly dwarfed phenotype. The lower stem internodes of Z. mays and sorghum mutants were significantly shortened [2, 10]. The function of the ABCB genes is thought to be conserved among all plant species. The remarkable difference between the abcb1 mutants of Arabidopsis and Z. mays may be due to their fundamentally different body shapes [10]. Moso bamboo belongs to the Poaceae family, similar to Z. mays and sorghum. (Lines 413-422)

 

 

2. Authors have used only "Arabidopsis" throughout the manuscript but not mentioned that which specie of Arabidopsis was used in the study. If it is Arabidopsis thaliana then make it clear.

 

Response:

--We thank the reviewer for this comment.

--The specie of Arabidopsis used in this study is “Arabidopsis thaliana”. As suggested by the reviewer, we have written it as Arabidopsis thaliana when it first appears. In addition, the full scientific name of Arabidopsis was also used in the “Materials and Methods” part.

 

ATP-binding cassette (ABC) family is one of the largest family of transporters in plants. More than 120 ABC transport proteins have been identified in the Arabidopsis thaliana genome [1]. (Lines 30-32)

 

In order to classify and study the phylogeny of the ABCB gene family in Moso bamboo, this study also used the previously identified and analyzed ABCB gene families in Arabidopsis thaliana, Oryza sativa (O. sativa), and Z. mays. (Lines 100-102)

 

3. Clearly mention the study objectives at the end of the introduction section.

 

Response:

--We thank the reviewer for this comment.

--As suggested by the reviewer, we have mentioned the study objective at the end of the instruction section.

 

Therefore, to study the potential roles of ABCBs in the growth and development of Moso bamboo, we identified the ABCB gene family and performed analyses of the conserved domains, duplication events, synteny, and expression profiles of PhABCBs. Furthermore, the potential functions of PhABCBs during internode development were investigated by using weighted gene co-expression network analysis (WGCNA). (Lines 76-81)

 

 

4. Mention the abbreviations used in table 1 at the end of table

 

Response:

--We thank the reviewer for this comment.

--As suggested by the reviewer, we have mentioned the abbreviations used in the Table 1 at the end of Table 1.

 

Table 1. Detailed information on PhABCB genes, including their properties and predicted protein characteristics in Moso bamboo.

Gene name	Locus ID	Exon number	ORF (bp)	Length (aa)	pI	Mol wt (Da)	Predicted subcellular localization
PhABCB1	PH02Gene00141.t1	11	4236	1411	5.99	155634.53	Cell membrane; Cytoplasm
PhABCB2	PH02Gene02211.t1	10	3645	1214	8.87	132085.88	Cell membrane
PhABCB3	PH02Gene03263.t1	7	3519	1172	8.75	127481.14	Cell membrane
PhABCB4	PH02Gene04764.t1	6	3744	1247	8.17	134940.80	Cell membrane
PhABCB5	PH02Gene06566.t1	12	3759	1252	8.73	136018.67	Cell membrane
PhABCB6	PH02Gene06567.t1	12	3756	1251	8.73	135882.48	Cell membrane
PhABCB7	PH02Gene06568.t4	12	3780	1259	8.37	136947.38	Cell membrane
PhABCB8	PH02Gene09415.t1	18	2034	677	9.25	74684.40	Cell membrane
PhABCB9	PH02Gene12567.t1	10	3693	1230	6.12	134638.99	Cell membrane
PhABCB10	PH02Gene12568.t1	12	4461	1486	7.35	164030.94	Cell membrane
PhABCB11	PH02Gene15335.t1	9	3684	1227	8.82	134204.70	Cell membrane; Cytoplasm
PhABCB12	PH02Gene16857.t3	10	1917	638	9.50	68918.32	Cell membrane
PhABCB13	PH02Gene18579.t1	11	4236	1411	5.97	155590.64	Cell membrane; Cytoplasm
PhABCB14	PH02Gene18770.t1	9	3681	1226	8.73	133993.53	Cell membrane; Cytoplasm
PhABCB15	PH02Gene19306.t1	20	2211	736	9.07	80582.50	Cell membrane
PhABCB16	PH02Gene21697.t3	18	1986	661	7.21	71199.73	Cell membrane
PhABCB17	PH02Gene24334.t1	12	3699	1232	6.47	133393.92	Cell membrane
PhABCB18	PH02Gene24658.t1	10	2961	986	8.76	105842.05	Cell membrane
PhABCB19	PH02Gene28443.t1	11	4197	1398	6.39	154671.91	Cell membrane; Cytoplasm
PhABCB20	PH02Gene30805.t1	17	1944	647	9.08	69851.56	Cell membrane
PhABCB21	PH02Gene32020.t1	16	2094	697	9.02	75009.41	Cell membrane
PhABCB22	PH02Gene32243.t1	13	3789	1262	6.15	136558.88	Cell membrane
PhABCB23	PH02Gene33736.t1	9	3810	1269	8.32	137703.36	Cell membrane
PhABCB24	PH02Gene34468.t1	11	4194	1397	6.24	154407.53	Cell membrane
PhABCB25	PH02Gene34686.t1	12	3669	1222	8.04	132289.92	Cell membrane
PhABCB26	PH02Gene35123.t1	12	3699	1232	8.36	133356.57	Cell membrane; Cytoplasm
PhABCB27	PH02Gene35826.t1	11	3852	1283	8.20	138102.46	Cell membrane
PhABCB28	PH02Gene36577.t1	9	3798	1265	8.16	137402.93	Cell membrane
PhABCB29	PH02Gene37588.t2	12	3822	1273	8.45	137001.49	Cell membrane
PhABCB30	PH02Gene37590.t1	12	3921	1306	8.80	140773.87	Cell membrane
PhABCB31	PH02Gene37936.t1	5	4080	1359	7.90	147207.40	Cell membrane
PhABCB32	PH02Gene38406.t1	12	3798	1265	8.26	137425.05	Cell membrane
PhABCB33	PH02Gene40893.t1	10	4512	1503	9.48	162318.06	Cell membrane; Cytoplasm
PhABCB34	PH02Gene43132.t1	6	3996	1331	8.09	144115.40	Cell membrane
PhABCB35	PH02Gene43364.t1	13	3810	1269	8.24	137789.54	Cell membrane
PhABCB36	PH02Gene48283.t2	11	3879	1292	6.27	139920.60	Cell membrane
PhABCB37	PH02Gene48611.t1	9	3798	1265	9.24	138708.54	Cell membrane

Note:ORF, pI and Mol wt represent open reading frame, isoeletric point and molecular weight, respectively.

 

5. Italicize gene names throughout the manuscript

 

Response:

--We thank the reviewer for this comment.

--As suggested by the reviewer, we have checked and revised the gene name into italicize type throughout the manuscript.

Author Response File: Author Response.docx

Reviewer 2 Report

the practical aspect of this work must be highlighted in the conclusion.

Comments for author File: Comments.pdf

There are many grammatical issues all over the text.

Author Response

06 Jul, 2023

Agronomy

Manuscript ID: agronomy-2481649

Genome-wide identification, expansion, evolution, and expression analysis reveals ABCB genes important for secondary cell wall development in Moso bamboo (Phyllostachys edulis)

 

Dear Professor,

 

Thank you and the reviewers very much for revising our manuscript ‘Genome-wide identification, expansion, evolution, and expression analysis reveals ABCB genes important for secondary cell wall development in Moso bamboo (Phyllostachys edulis)’ (Manuscript ID: agronomy-2481649). Your effort and time spent on our manuscript are greatly appreciated by all of us. We are delighted to all suggestion and review comments, which you and the reviewers made. Your revisions/suggestions have definitely improved the quality of our manuscript.

The manuscript was extensively edited according to your and reviewers’ comments. Please find the revised manuscript in Agronomy’s manuscript center. The changes were marked up using the“Track Changes” function. The responses to the reviewers are highlighted below.

 

Thank you again for your kind help and excellent suggestions for our manuscript. We hope these revisions will be satisfactory and will lead to acceptance for publication. We are looking forward to hearing from you soon.

 

Yours sincerely

 

Feng Que

---------------

Dr. Feng Que

Co-Innovation Center for Sustainable Forestry in Southern China

Bamboo Research Institute, Nanjing Forestry University

159 Longpan Road, Nanjing, 210037, Jiangsu China

Fax: 86 25 85427177

Email: [email protected]

 

 

 

------------------------

Reviewer's report:

1. The title is too long. Rewrite it please.

 

Response:

--We thank the reviewer for this comment.

--As suggested by the reviewer, we have rewritten the title.

 

Genome-wide identification, expansion, evolution, and expression analysis reveals ABCB genes important for secondary cell wall development in Moso bamboo (Phyllostachys edulis)

 

 

2. Check the grammatical issues of manuscript.

 

Response:

--We thank the reviewer for this comment.

--As suggested by the reviewer, we have checked the grammatical issues of the manuscript.

 

Overexpression of AtABCB4 in root hair cells increased the auxin efflux activities and inhibited the root hair elongation [6]. (Lines 43-45)

 

Using the available information of the previously identified and analyzed ABCB gene families in Arabidopsis, O. sativa, and Z. mays, our study aimed to classify the ABCB genes in Moso bamboo. (Lines 170-172)

 

All PhABCBs, except PhABCB32, PhABCB26, PhABCB18, PhABCB16, PhABCB20, PhABCB8, PhABCB21, PhABCB12, and PhABCB15, contain all eight motifs. (Lines 183-185)

 

The TD mode existed only in subgroups Ⅱ and Ⅴ (Figure 5A). In subgroup Ⅴ, all four duplication models existed, and WGD was the predominant mode. (Lines 242-243)

 

During the active formation stages of SCW, PhABCB4, PhABCB7, PhABCB11, PhABCB14, PhABCB15, and PhABCB21, exhibited strongly upregulated expression. (Lines 296-298)

 

Moso bamboo culms consist of multiple internodes, and the individual internodes are the basic units of shoot elongation and growth. (Lines 422-423)

 

During the rapid growth of Moso bamboo, the internodes are subjected to in-creasing mechanical pressure at a high rate. (Lines 433-434)

 

Genes involved in the biosynthesis pathways of lignin, cellulose, and xylan were found to be co-expressed with 13 PhABCB genes (Lines 443-445)

 

Genes such as PhABCB7, PhABCB11, PhABCB14, and PhABCB21 were found to regulate SCW biogenesis. (Lines 489-490)

 

 

3. ATP-binding cassette (ABC) family is one of the largest transport families in plants. More than 120 ABC transport proteins have been identified in the Arabidopsis genome [1]. Revise the “the largest transport families” into “the largest family of transporters”

 

Response:

--We thank the reviewer for this comment.

--As suggested by the reviewer, we have revised the sentence.

 

ATP-binding cassette (ABC) family is one of the largest family of transporters in plants. More than 120 ABC transport proteins have been identified in the Arabidopsis thaliana genome [1]. (Lines 30-32)

 

 

4. To date, a total of eight of ABCB gene family have been identified as auxin transporters in Arabidopsis. Some errors in this sentence.

 

Response:

--We thank the reviewer for this comment.

--As suggested by the reviewer, we have revised the sentence.

 

To date, a total of eight ABCB genes have been identified as auxin transporters in Arabidopsis thaliana. (Lines 40-41)

 

 

5. The last paragraph of the Instruction. The paragraph length should not exceed of 10 lines. delete the last line and rewrite the research objectives.

 

Response:

--We thank the reviewer for this comment.

--As suggested by the reviewer, we have deleted the last sentence of the paragraph and reorganized the paragraph. The last paragraph was divided into two paragraphs. The research objectives were also rewritten.

 

 

Bamboos are the perennial plants belonging to the Poaceae family [11]. Among them, Moso bamboo (Phyllostachys edulis) is highly significant due to its economic, cultural, and environmental values [12]. The notable characteristic of Moso bamboo is its rapid growth rate, with a maximum growth of 114.5 cm per day [13]. The underlying mechanism for this rapid growth is complex and fascinating. Recent research suggests that several factors contribute to the rapid growth, including environmental temperature, endogenous hormone distribution, mechanical pressure, and so on [13]. In a recent report, it was found at the cellular level that a large number of cells in division and elongation status within the division and elongation zones are the main factors for the rapid growth of Moso bamboo internodes [13]. Auxin, a well-known hormone, plays a pivotal role in controlling cell division and elongation [14]. The spatial distribution of auxin is involved in regulating the developmental patterning of plants [15]. The proper concentration of auxin in specific parts of plants is regulated by the synthesis, metabolism, and transport of auxin [16].

In Moso bamboo shoots, the spatial distribution of auxin is not uniform across different parts [17]. As auxin transporters, ABCBs may play important roles in regulating the development of Moso bamboo. Therefore, to study the potential roles of ABCBs in the growth and development of Moso bamboo, we identified the ABCB gene family and performed analyses of the conserved domains, duplication events, synteny, and ex-pression profiles of PhABCBs. Furthermore, the potential functions of PhABCBs during internode development were investigated by using weighted gene co-expression net-work analysis (WGCNA). (Lines 61-81)

 

Author Response File: Author Response.docx

Reviewer 3 Report

^{This is an interesting study in the field of ABCB transporter proteins in plants. In the present study, the author attempted to identify ABCB genes in the Moso bamboo plant. Using transcriptomic and co expression analysis, the author has identified key ABCB genes involved in Moso bamboo development. Furthermore, using the pathway enrichment method, the author claimed to reveal closely associated ABCB genes putatively involved in auxin transport in Moso bamboo. This is an interesting finding, that could be used for the molecular breeding of medicinal plants with better agronomical values. However, there are a few points that need to be corrected.}

^{1, In table no. 1 legend should mention predicted properties of phABCB}

^{2, Figure no. 1 is too small, and labels are difficult to read.}

^{3, In figure no. 3 author has annotated different motifs. It would be great if the author could reveal the nature/predicted function of these motifs.}

^{4, In figure no. 6 and 9, several graphs lack statistical analysis.}

^{5, In the discussion section, over all it is very redundant. It could be organized more coherently. Line 374 to 387 could be included in the introduction part not in discussion.}

Author Response

06 Jul, 2023

Agronomy

Manuscript ID: agronomy-2481649

Genome-wide identification, expansion, evolution, and expression analysis reveals ABCB genes important for secondary cell wall development in Moso bamboo (Phyllostachys edulis)

 

Dear Professor,

 

Thank you and the reviewers very much for revising our manuscript ‘Genome-wide identification, expansion, evolution, and expression analysis reveals ABCB genes important for secondary cell wall development in Moso bamboo (Phyllostachys edulis)’ (Manuscript ID: agronomy-2481649). Your effort and time spent on our manuscript are greatly appreciated by all of us. We are delighted to all suggestion and review comments, which you and the reviewers made. Your revisions/suggestions have definitely improved the quality of our manuscript.

The manuscript was extensively edited according to your and reviewers’ comments. Please find the revised manuscript in Agronomy’s manuscript center. The changes were marked up using the“Track Changes” function. The responses to the reviewers are highlighted below.

 

Thank you again for your kind help and excellent suggestions for our manuscript. We hope these revisions will be satisfactory and will lead to acceptance for publication. We are looking forward to hearing from you soon.

 

Yours sincerely

 

Feng Que

---------------

Dr. Feng Que

Co-Innovation Center for Sustainable Forestry in Southern China

Bamboo Research Institute, Nanjing Forestry University

159 Longpan Road, Nanjing, 210037, Jiangsu China

Fax: 86 25 85427177

Email: [email protected]

 

 

 

------------------------

Reviewer's report:

This is an interesting study in the field of ABCB transporter proteins in plants. In the present study, the author attempted to identify ABCB genes in the Moso bamboo plant. Using transcriptomic and co expression analysis, the author has identified key ABCB genes involved in Moso bamboo development. Furthermore, using the pathway enrichment method, the author claimed to reveal closely associated ABCB genes putatively involved in auxin transport in Moso bamboo. This is an interesting finding, that could be used for the molecular breeding of medicinal plants with better agronomical values. However, there are a few points that need to be corrected.

 

1, In table no. 1 legend should mention predicted properties of phABCB

 

Response:

--We thank the reviewer for this comment.

--As suggested by the reviewer, we have revised the legend of Table 1 and revised the “Subcellular localization” into “Predicted subcellular localization”.

 

Table 1. Detailed information on PhABCB genes, including their properties and predicted protein characteristics in Moso bamboo.

Gene name	Locus ID	Exon number	ORF (bp)	Length (aa)	pI	Mol wt (Da)	Predicted subcellular localization
PhABCB1	PH02Gene00141.t1	11	4236	1411	5.99	155634.53	Cell membrane; Cytoplasm
PhABCB2	PH02Gene02211.t1	10	3645	1214	8.87	132085.88	Cell membrane
PhABCB3	PH02Gene03263.t1	7	3519	1172	8.75	127481.14	Cell membrane
PhABCB4	PH02Gene04764.t1	6	3744	1247	8.17	134940.80	Cell membrane
PhABCB5	PH02Gene06566.t1	12	3759	1252	8.73	136018.67	Cell membrane
PhABCB6	PH02Gene06567.t1	12	3756	1251	8.73	135882.48	Cell membrane
PhABCB7	PH02Gene06568.t4	12	3780	1259	8.37	136947.38	Cell membrane
PhABCB8	PH02Gene09415.t1	18	2034	677	9.25	74684.40	Cell membrane
PhABCB9	PH02Gene12567.t1	10	3693	1230	6.12	134638.99	Cell membrane
PhABCB10	PH02Gene12568.t1	12	4461	1486	7.35	164030.94	Cell membrane
PhABCB11	PH02Gene15335.t1	9	3684	1227	8.82	134204.70	Cell membrane; Cytoplasm
PhABCB12	PH02Gene16857.t3	10	1917	638	9.50	68918.32	Cell membrane
PhABCB13	PH02Gene18579.t1	11	4236	1411	5.97	155590.64	Cell membrane; Cytoplasm
PhABCB14	PH02Gene18770.t1	9	3681	1226	8.73	133993.53	Cell membrane; Cytoplasm
PhABCB15	PH02Gene19306.t1	20	2211	736	9.07	80582.50	Cell membrane
PhABCB16	PH02Gene21697.t3	18	1986	661	7.21	71199.73	Cell membrane
PhABCB17	PH02Gene24334.t1	12	3699	1232	6.47	133393.92	Cell membrane
PhABCB18	PH02Gene24658.t1	10	2961	986	8.76	105842.05	Cell membrane
PhABCB19	PH02Gene28443.t1	11	4197	1398	6.39	154671.91	Cell membrane; Cytoplasm
PhABCB20	PH02Gene30805.t1	17	1944	647	9.08	69851.56	Cell membrane
PhABCB21	PH02Gene32020.t1	16	2094	697	9.02	75009.41	Cell membrane
PhABCB22	PH02Gene32243.t1	13	3789	1262	6.15	136558.88	Cell membrane
PhABCB23	PH02Gene33736.t1	9	3810	1269	8.32	137703.36	Cell membrane
PhABCB24	PH02Gene34468.t1	11	4194	1397	6.24	154407.53	Cell membrane
PhABCB25	PH02Gene34686.t1	12	3669	1222	8.04	132289.92	Cell membrane
PhABCB26	PH02Gene35123.t1	12	3699	1232	8.36	133356.57	Cell membrane; Cytoplasm
PhABCB27	PH02Gene35826.t1	11	3852	1283	8.20	138102.46	Cell membrane
PhABCB28	PH02Gene36577.t1	9	3798	1265	8.16	137402.93	Cell membrane
PhABCB29	PH02Gene37588.t2	12	3822	1273	8.45	137001.49	Cell membrane
PhABCB30	PH02Gene37590.t1	12	3921	1306	8.80	140773.87	Cell membrane
PhABCB31	PH02Gene37936.t1	5	4080	1359	7.90	147207.40	Cell membrane
PhABCB32	PH02Gene38406.t1	12	3798	1265	8.26	137425.05	Cell membrane
PhABCB33	PH02Gene40893.t1	10	4512	1503	9.48	162318.06	Cell membrane; Cytoplasm
PhABCB34	PH02Gene43132.t1	6	3996	1331	8.09	144115.40	Cell membrane
PhABCB35	PH02Gene43364.t1	13	3810	1269	8.24	137789.54	Cell membrane
PhABCB36	PH02Gene48283.t2	11	3879	1292	6.27	139920.60	Cell membrane
PhABCB37	PH02Gene48611.t1	9	3798	1265	9.24	138708.54	Cell membrane

Note:ORF, pI and Mol wt represent open reading frame, isoeletric point and molecular weight, respectively.

 

2, Figure no. 1 is too small, and labels are difficult to read.

 

Response:

--We thank the reviewer for this comment.

--As suggested by the reviewer, we have revised the Figure 1.

 

Figure 1. Predicted transmembrane regions of PhABCB proteins. The purple peaks on the top represent the predicted transmembrane helices.

 

3, In figure no. 3 author has annotated different motifs. It would be great if the author could reveal the nature/predicted function of these motifs.

 

Response:

--We thank the reviewer for this comment.

-- As suggested by the reviewer, providing the nature/predicted function of these motifs is better to reveal the potential function of these genes. The motifs in this study were searched through MEME suite (https://meme-suite.org/tools/meme). However, we don’t find the descriptions of the function of these motifs. Therefore, we are unable to reveal the nature/predicted function of these motifs here. In addition, in many other published papers, the nature/predicted function of the motifs were not revealed, too.

 

4, In figure no. 6 and 9, several graphs lack statistical analysis.

 

Response:

--We thank the reviewer for this comment.

-- Some genes don’t show significantly different expression levels among different parts of bamboo shoots by statistical analysis. These graphs with no letters were these genes. As suggested by the reviewer, we have added explanations in the legends of Figure 6 and 9.

 

Figure 6. Expression profiles of PhABCBs in different parts of Moso bamboo shoots. SAM, shoot apical meristem; YIN, young internode; MIN, mature internode; YNO, young node; MNO, mature node. Differences were determined using a one-way ANOVA test, and columns with the same letter are not significantly different (p < 0.05). Graphs with no letters represent no significant difference among the different parts. Error bars represent standard deviation (SD).

 

Figure 9. Expression profiles of 12 PhABCBs in different parts of Moso bamboo internode. The 18^th internode was divided into three parts: D-stem (lower part), M-stem (middle part), and U-stem (upper part). Differences among the different parts were determined using a one-way ANOVA test, and columns with the same letter indicate no significant difference (p < 0.05). Graphs with no letters represent no significant difference among the different parts. Error bars represent the standard deviation (SD).

 

5, In the discussion section, over all it is very redundant. It could be organized more coherently. Line 374 to 387 could be included in the introduction part not in discussion.

 

Response:

--We thank the reviewer for this comment.

--As suggested by the reviewer, we have reorganized the content in the discussion (Line 374 to 387).

 

ABCB is the second largest subfamily of ABC transporters, and ABC family is one of the largest transporter families in plants [2]. Sessile organisms such as plants require complex metabolic processes for detoxification to adapt to their environment and stress conditions. Therefore, gene expansion has been observed in the ABC transporter family of plants [22, 23]. Here, to investigate the potential function of ABCB genes in the growth and development of Moso bamboo, we performed a search and identification of the ABCB genes in Moso bamboo genome, which led to the identification of 37 PhABCB genes. Based on phylogenetic and gene structure analyses, these 37 PhABCBs were classified into five subgroups, I-V (Figure 2). Compared with Arabidopsis, O. sativa and Z. mays, Moso bamboo genome contained a larger number of the ABCB genes, especially in subgroup Ⅴ. The synteny analysis of the ABCB genes revealed more synteny between Moso bamboo and monocots (O. sativa and Z. mays), while less synteny was observed between Moso bamboo and dicots (Arabidopsis). In addition, the range of synteny between the ABCB gene family of O. sativa and Arabidopsis was also limited [24]. Through synteny analysis, we detected both expansion and loss of genes in the ABCB gene family of Moso bamboo. Some OsABCBs and ZmABCBs had two orthologous genes, while some others had no orthologous genes in the Moso bamboo genome. These results suggest that gene duplications may have occurred during the evolution of the ABCB gene family in Moso bamboo. (Lines 378-384)

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