Comparative Genomics of Eight Complete Chloroplast Genomes of Phyllostachys Species

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The manuscript described on the characterisation and genome comparison analysis of eight Phyllostachys species. My general comments are as follows:

1. genus names are not in italicised form

2. numerical values less than 10 should be spelled in words.

3. There should be a space between the value and SI unit.

4. abbreviations should be spelled out in full at their first occurrence. (e.g. L26, etc)

5. The first half of the first paragraph in the introduction is only supported by one citation. While the work emphasised more on the chloroplast genome of Bamboo species, the authors wrote three long paragraphs in the introduction on chloroplast genome, but did not describe anything about previous molecular efforts in Phyllostachys in the fourth paragraph.

6. In 2.1, there is no information on the total genome DNA step. Also, Why is RNA seq transcriptome library conducted here? including the TruSeq RNA sample prep kit and the cDNA synthesis kit used.

7. Softwares and programmes used for the analyses should be indicated for their versions.

8. Plenty of hanging sentences. (e.g. 154, 166, 176, etc)

9. authors should avoid including Discussion materials in the Result section. (e.g. L239, etc)

10. authors should avoid including Materials and Method materials in the Result section (e.g. 275, etc)

11. I suppose the authors did not format the references based on the requirement of the Journal

Comments on the Quality of English Language

Plenty of grammar mistakes and misuse of symbols. This manuscript requires an English proofreading.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

   The manuscript by Li and colleagues reports on the sequencing, annotation and analysis of the chloroplast genomes of 8 strains of bamboo in the same genus. There are lots of useful and interesting information presented but a number of critical scientific points require addressing.

 Specific scientific points

1.       Title and throughout. Are these really 8 different species or 8 different isolates in a smaller number of species, as some appear different vars of the same species?

2.       The authors use RNAseq to generate the genome sequence. It is unclear whether this approach results in completely closed genomes or not, as some regions are likely to be non transcribed.

3.       The GenBank accessions are not given in the main manuscript.

4.       In section 2.5, the authors indicate that they removed sequences of protein coding sequences that were less than 300 bp. Why was this done? Some of the ribosomal proteins are less than 100aa so their genes will be less than 300 bp.

5.       There are many instances where the genus and species are not italicized.

6.       Some of the Figure legends require expanding and some axis require labelling (Fig 4) or larger font to be able to read.

7.       All factual statements should be clearly linked to a reference. L47 L51 L240 L297 L484

8.       All software should be referenced L171 L180

9.       Fig 3 has a label with contigs. Does this mean that the genomes are not fully assembled? If not complete, mapping to a reference will prevent the authors from knowing whether there have been rearrangements

10.   What x coverage was obtained for each genome?

11.   L299 Is this true? Please add a reference for transposons being the only dispersed repeat. The authors examples of dispersed repeats (L351) are too small (<100 bp) to be transposons

12.   L453 Are there chromosome assemblies available for bamboo, that may show that petB is present within them?

13.   L496 Two of the listed genes are not protein encoding, but encode a tRNA and a rRNA. Appropriate spacing around the commas used in the list, is required.

 

 

      Minor comments—there are many language revisions required. Provided below are a few examples

14.   Title, L8, 12 and throughout. Please use italics for genus and species names

15.   L14 There are several instances of absent periods. L44 L47 L144 L157

16.   L18 conserved (also L547)

17.   L22 SSR should be defined on first use rather than later in sentence

18.   L23 mono

19.   L25 the codons preferentially end with

20.   L26 and L27 These two sentences are unclear in meaning; please rephrase

21.   L33 The chloroplast

22.   L34 the main site for

23.   L39 which is the place

24.   L43 The chloroplast is an organelle

25.   L48 than the nuclear

26.   L54 in the chloroplast

27.   L56 Please avoid starting sentences with “and” or “but”

28.   L57 the chloroplast

29.   L58 sequences

30.   L58 the chloroplast (also L60, L69, L71, L79

31.   L78 chloroplasts show unique codon

32.   L98 of the forest

33.   L98 Bamboo is the general

34.   L103 countries with wide

35.   L103 habitats, encompassing about 40

36.   L105 why is less investment an advantage?

37.   L114 punctata and

38.   L115 in the early stage, by our research group, found

39.   L124 species is available [20-26], but this genome

40.   L125 in the bamboo genome have not been studied

41.   L129 chloroplast genomes, identified the nucleotide

42.   L127 please rephrase “chloroplast gene Is not involved in leaves”

43.   L131 provided a molecular foundation for phenotypic

44.   L135 Some sections of the methods switch to reading in a different person ands are provided as a set of instructions. L166 L176 L189

45.   L141 The specific steps were

46.   L141 vs L151 RNA seq or RNA-seq

47.   L142 kit instructions from Illumina (San Diego, CA, USA)

48.   L143 In short (?)

49.   L143 sorted by a polyA

50.   L144 fragmented in fragmentation

51.   L146 Please add city

52.   L150 location of NEB

53.   L150 what is the TBS380?

54.   L150 After quantification

55.   L151 location of Illumina is already given

56.   L155 all low quality reads resulting I high

57.   L156 de novo?

58.   L159 vs 169 Use the in full and italics version on first use. L169 P. (italics)

59.   L163 This sentence has no verb

60.   L176 The first sentence can be deleted as it is repeated -please add [39} after  v4.09

61.   L152 vs L181 different styles of spacing between numbers and units are used

62.   L200 GenBank numbers should be provided; also L573

63.   L218 what is the smallest protein coding sequence (since those <300 bp have been removed)?

64.   L229 italics for gene names

65.   L233 Please add a space after genome.

66.   L243 Have JLB, JSA, JLA and JSB been defined?

67.   L245 gene. The boundary

68.   L256 “of eight bamboo species in the Phyllostachys” can be deleted.

69.   L263 Please avoid using “etc” as the reader will not know what the authors had in their minds

70.   L270, L273 Please add spaces after periods

71.   L277 MAFFT? To match style used in methods

72.   L294 Please add what A and B refer to in an expanded legend

73.   L299 elements. Misa online analysis software was used to statistically  

74.   L185 vs L300 MISA or Misa

75.   L302 Among the eight chloroplast genomes, the maximum number

76.   L310 in the eight

77.   L313, L314, L315, L321 Please use lower case after the semi-colons

78.   L321 italics for taxa, also L339, L342-344, L492

79.   L365 at the three

80.   L445 (two instances) b/f or b6/f?

81.   L449 habitat. Meanwhile

82.   L495 [61]. Nine

83.   L498-L499 and L510-511 This is repeated information

84.   L520 and L521 (and elsewhere) Please use one style of capitalization for amino acids

85.   L546 should this be 76 based on the information in Table 1

86.   Various different styles are used in the references. For example, Ref 1 and ref 25, Ref 7 and Ref 21. Some are capitalized (e.g. 9 and 10, plus others)

 

Comments on the Quality of English Language

Please see main file for examples

Author Response

Please see the attachment.

Author Response File: Author Response.pdf