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. 2021 Jun 11;2021:gigabyte25. doi: 10.46471/gigabyte.25

In silico characterization of chitin deacetylase genes in the Diaphorina citri genome

Sherry Miller 1,2, Teresa D Shippy 1, Blessy Tamayo 3, Prashant S Hosmani 4, Mirella Flores-Gonzalez 4, Lukas A Mueller 4, Wayne B Hunter 5, Susan J Brown 1, Tom D’Elia 3, Surya Saha 4,6,*
PMCID: PMC9632012  PMID: 36824334

Abstract

Chitin deacetylases (CDAs) are one of the least understood components of insect chitin metabolism. The partial deacetylation of chitin polymers appears to be important for the proper formation of higher order chitin structures, such as long fibers and bundles, which contribute to the integrity of the insect exoskeleton and other structures. Some CDAs may also be involved in bacterial defense. Here, we report the manual annotation of four CDA genes from the Asian citrus psyllid, Diaphorina citri, laying the groundwork for future study of these genes.

Data Description

Introduction

Chitin deacetylases (CDAs) are metalloenzymes that partially deacetylate chitin polymers [1]. CDA activity in insects was first reported in the cabbage looper Trichoplusia ni [2]. In Drosophila melanogaster, several CDAs are involved in tracheal development [3, 4]. More recently, genomic and phylogenetic studies have shown that CDAs are present widely in insects and can be classified into five different groups [5, 6]. Most holometabolous insects have at least one representative of each of the five CDA groups, while the hemimetabolous insects that have been examined lack group II and group V genes [6]. The exact role of insect CDAs is not well understood, but they may play a role in organization of chitin molecules into higher order structures [7].

Context

Loss of function experiments indicate that some CDAs are essential for growth and development, making them a potential target for insect pest control [6, 8–12]. Here we describe the chitin deacetylase gene family in the Asian citrus psyllid, Diaphorina citri (Hemiptera: Liviidae; NCBI:txid121845). D. citri is the vector for Candidatus Liberibacter asiaticus (CLas), which is responsible for the global outbreak of Huanglongbing (citrus greening) disease. We identified four chitin deacetylase genes in the D. citri v3 genome, three of which have multiple isoforms. As in other hemipterans, only groups I, III and IV are represented [6].

Methods

Chitin deacetylase genes in D. citri genome v3 [13] were identified by BLAST (NCBI BLAST, RRID:SCR_004870) search of D. citri sequences with chitin deacetylase orthologs from other insects. Orthology was confirmed by reciprocal BLAST of the National Center for Biotechnology Information (NCBI) non-redundant protein database [14]. Genes were manually annotated in Apollo 2.1.0 (RRID:SCR_001936) [15] using available evidence, including RNA-seq reads, Iso-seq transcripts and de novo-assembled transcripts. A more detailed annotation protocol is available at protocols.io (Figure 1) [16].

Figure 1.

Figure 1.

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Protocols.io protocol outlining the annotation process of the D. citri genome [16]. https://www.protocols.io/widgets/doi?uri=dx.doi.org/10.17504/protocols.io.bniimcce

Domain analysis was performed with InterPro (InterPro, RRID:SCR_006695) [17]. Multiple alignments were performed using CLUSTALW (RRID:SCR_002909) [18] within MEGA X (MEGA software, RRID:SCR_000667) [19] followed by phylogenetic tree construction using the neighbor-joining method in MEGA X. Table 1 contains a list of orthologs used in the phylogenetic analysis. Expression data from the Citrus Greening Expression Network (CGEN) [20] (Table 2) was visualized using the pheatmap (pheatmap, RRID:SCR_016418) package of R (R Project for Statistical Computing, RRID:SCR_001905) [21, 22] or Microsoft Excel (Microsoft Excel, RRID:SCR_016137).

Table 1.

Orthologs used in phylogenetic analysis.

Species Accession Name in NCBI Name in Tree
Nilaparvata lugens AJQ20732.1 chitin deacetylase 1 Nl CDA1
Nilaparvata lugens AJQ20733.1 chitin deacetylase 2 Nl CDA2
Nilaparvata lugens AJQ20734.1 chitin deacetylase 3 Nl CDA3
Nilaparvata lugens AJQ20735.1 chitin deacetylase 4 Nl CDA4
Tribolium castaneum NP_001095946.1 chitin deacetylase 1 precursor Tc CDA1
Tribolium castaneum NP_001116303.1 chitin deacetylase 2 isoform B precursor Tc CDA2
Tribolium castaneum NP_001104011.1 chitin deacetylase 3 precursor Tc CDA3
Tribolium castaneum NP_001103903.1 chitin deacetylase 4 precursor Tc CDA4
Tribolium castaneum NP_001103739.1 chitin deacetylase 5 isoform A precursor Tc CDA5
Tribolium castaneum NP_001103905.1 chitin deacetylase 6 precursor Tc CDA6
Tribolium castaneum NP_001104012.1 chitin deacetylase 7 precursor Tc CDA7
Tribolium castaneum NP_001103906.1 chitin deacetylase 8 precursor Tc CDA8
Tribolium castaneum NP_001103904.1 chitin deacetylase 9 precursor Tc CDA9
Drosophila melanogaster NP_001262062.1 serpentine, isoform C Dm Serp
Drosophila melanogaster NP_730442.2 vermiform, isoform G Dm verm
Drosophila melanogaster NP_609806.1 ChLD3 Dm ChLD3
Drosophila melanogaster NP_728468.1 chitin deacetylase-like 4 Dm Cda4
Drosophila melanogaster NP_001245808.1 chitin deacetylase-like 5, isoform I Dm Cda5
Drosophila melanogaster NP_001286519.1 chitin deacetylase-like 9, isoform B Dm Cda9
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Species, accession number, full name and abbreviated name are provided for all orthologs used in phylogenetic analysis.

Table 2.

TPM expression values.

Gene ID Dcitr04g03590.1.1 Dcitr04g03590.1.2 Dcitr04g03540.1.1 Dcitr04g03540.1.2 Dcitr02g03950.1.1 Dcitr01g12310.1.1 Dcitr01g12310.1.2 Dcitr01g12310.1.3 Dcitr01g12310.1.4 Dcitr01g12310.1.5
Gene/Transcript Name CDA1-RB CDA1-RA CDA2-RB CDA2-RA CDA4 CDA5-RD CDA5-RC partial CDA5-RA partial CDA5-RE CDA5-RB partial
Egg Citrus macrophylla CLas− Whole body 56.64 415.8 4.89 22.79 423.69 16.46 0 0 6.95 9.07
Nymph Citrus medica CLas+ Low infection Whole body 67.1 576.33 111.58 271.48 571.7 50.9 16.28 0 108.52 2.93
Nymph Citrus sinensis CLas+ High infection Whole body 71.33 513.82 100.65 247.03 374.09 78.16 3.45 0 145.78 3.22
Nymph C. sinensis CLas− Whole body 78.22 533.18 36.7 242.93 453.44 31.57 0 0 77.51 1.43
Nymph C. macrophylla CLas− Whole body 63.26 398.54 5.1 15.5 564.13 66.92 0 0 74.46 9.88
Nymph Citrus spp. CLas− Whole body 118.31 171.29 2.5 11.24 822.56 15.1 3.36 37.94 41.04 7.32
Nymph Citrus spp. CLas+ Whole body 58.83 343.75 0.36 8.66 260.62 13.61 0 33.96 6.56 8.04
Adult C. medica CLas− Gut 0.24 0.02 0 0.12 0.27 0 0 0.07 0.3 0
Adult C. medica CLas+ Gut 0.59 0.09 0.01 0.32 0.54 0.02 0 0.05 0.4 0
Adult C. medica CLas+ High infection Whole body 40.95 78.19 42.05 40.72 77.88 15 0 0 22.22 0.12
Adult C. medica CLas+ Low infection Whole body 35.92 94.71 97.78 9.81 99.09 9.59 0 0 27.89 0.07
Adult C. medica CLas− Whole body 46.28 171.94 125.69 78.25 193.02 29.12 4.81 0 48.75 0.2
Adult C. macrophylla CLas− Whole body 5.48 16.96 0 0.53 15.86 2.51 0 0 3.67 0
Adult Citrus spp. CLas− Whole body 14.83 0 0 1.41 66.18 2.36 0 0.39 1.78 0
Adult Citrus spp. CLas+ Whole body 8.49 9.2 0 3.78 9.23 0.66 1.12 1.98 2.62 0
Adult Citrus spp. CLas− midgut 0.73 0 0.03 0.5 3.13 0 0 0 0.17 0
Adult Citrus spp. CLas+ midgut 3.36 5.45 0.02 0.07 11.56 0.13 0.01 0.12 1.02 0
Adult Citrus reticulata CLas− Female abdomen 7.34 6.88 0 0.48 8.36 0.57 0 0 1.09 0
Adult C. reticulata CLas− Female antennae 9.65 31.14 0.14 0.75 30.31 1.7 0 0 2.81 0
Adult C. reticulata CLas− Female head 13.95 12.73 0.54 0.55 20.44 0 0 0.76 2.96 0
Adult C. reticulata CLas− Female leg 17.46 4.67 0.01 6.6 12.63 0 0 1.16 1.7 0.48
Adult C. reticulata CLas− Female terminal abdomen 14.73 36.64 0.08 1.27 16.78 0.53 0.08 0 3.73 0.76
Adult C. reticulata CLas− Female thorax 15.3 7.91 0.04 0.03 15.29 2.53 0 0.2 0.97 0
Adult C. reticulata CLas− Male abdomen 8.81 2.95 0 2.95 15.63 0.79 0 0.93 0.73 0
Adult C. reticulata CLas− Male antennae 11.9 36.52 0.79 2.06 30.78 2.14 0 0 4.56 0.13
Adult C. reticulata CLas− Male head 10.15 17.32 0.45 0.43 28.15 1.21 0 0 2.4 1.12
Adult C. reticulata CLas− Male leg 17.7 4.13 0.02 6.26 13.4 0.88 0 0.09 2.19 0.41
Adult C. reticulata CLas− Male terminal abdomen 17.41 20.3 1.29 0.75 25.87 1.9 0 0 5.19 0.16
Adult C. reticulata CLas− Male thorax 16.31 8.55 0 1.62 17.42 1.65 0 0 4.11 0.32
Adult C. reticulata CLas− Female antennae [23] 14.37 16.64 0.06 5.52 18.05 0.24 0.04 1.14 1.47 0
Adult C. reticulata CLas− Female terminal abdomen [23] 5.83 11.74 0 2.95 4.61 0.58 0 0.14 0.48 0.12
Adult C. reticulata CLas− Male antennae [23] 8.22 26.46 0.91 0.73 17.65 0.3 0 0 5.71 2.59
Adult C. reticulata CLas− Male terminal abdomen [23] 11.37 6.91 0 3.67 12.05 0.97 0.09 0 2.68 0.1
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Expression levels (transcripts per million, TPM) for annotated chitin deacetylase transcripts from available RNA-seq experiments used for Figure 2. All data are publicly available and were obtained from CGEN [20]. Developmental stage, citrus host, CLas (Candidatus Liberibacter asiaticus) infection status and tissue of each sample are provided in the first column.

Data validation and quality control

Chitin deacetylase genes in the D. citri v3 genome [13] were identified and manually annotated as described below. These genes were classified following the precedents established in other insects [5, 6].

Group I chitin deacetylases

Most insects have two group I genes named CDA1 and CDA2 (Table 3). The proteins encoded by these genes have an N-terminal chitin-binding domain (ChBD), a low-density lipoprotein receptor class A domain (LDLa), and a deacetylase catalytic domain [5]. RNA interference (RNAi) of group I CDAs in a variety of insects suggests that loss of function of CDA1 or CDA2 can result in lethality and therefore these genes could be potential targets for pest control methods [6–12]. Recent experiments in Tribolium suggest that TcCDA1 and TcCDA2 are required for organization of chitin into longer fibers that are important for cuticular strength [7].

Table 3.

Estimated number of chitin deacetylase homologs.

Species Group I Group II Group III Group IV Group V Total
D. melanogaster 2* 1 1 1* 1 6
A. gambiae 2* 1 1 1 0 5
T. castaneum 2* 1 1 1* 4 9
B. mori 2* 1 1 1 3 8
A. mellifera 2* 1 1 1* 0 5
N. vitripennis 2 1 1 1 0 5
R. prolixus 2 0 1 1 0 4
A. pisum 2 0 1 1 0 4
N. lugens 2 0 1 1 0 4
D. citri 2* 0 1 1* 0 4
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D. citri gene numbers were determined based on annotation of the D. citri genome v3. All other ortholog numbers were obtained from published sources [5, 6, 24–32]. An asterisk (*) indicates that isoforms have been found for at least one member of the group in that organism.

As expected, we identified two group I genes in D. citri, which we named CDA1 and CDA2. Both genes encode proteins with the typical group I domain structure (Figure 3). We identified two isoforms each for D. citri CDA1 and CDA2 (Table 4). CDA2 has previously been shown to have multiple isoforms in several holometabolous insect species, with the transcripts differing only in the use of one alternative exon [5, 10, 12]. This gene structure is conserved in D. citri CDA2 with alternate exons 3a and 3b. The two D. citri CDA1 isoforms differ in the presence or absence of a 24-bp exon upstream of the last exon. Expression data from RNA-seq datasets available through CGEN [20] suggest that, in general, expression of CDA1 and CDA2 is higher in nymphs and eggs than in adults (Figure 2A).

Figure 3.

Figure 3.

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Chitin deacetylase domain organization in D. citri. Chitin deacetylases are categorized by group based on phylogenetic analysis, sequence similarity, and domain organization. D. citri domain analysis was performed using InterPro [17]. CDA5 is represented by the protein encoded by the de novo-assembled transcript MCOT06229.1.CO [34] because a small portion of the CDA5 gene is missing from the v3 genome assembly.

Table 4.

Chitin deacetylase genes in D. citri.

Gene/ Isoform OGSv3 ID Gene model Evidence supporting annotation
Complete MCOT Iso-Seq RNA-Seq Ortholog
CDA1 (Group I) Dcitr04g03590.1.1 X MCOT00151.2.CO X X X
Dcitr04g03590.1.2 MCOT00151.1.CO
CDA2 (Group I) Dcitr04g03540.1.1 X X X X
Dcitr04g03540.1.2
CDA3 (Group III) Dcitr02g03950.1.1 X MCOT04789.0.CT X X
CDA5 (Group IV) Dcitr01g12310.1.1 MCOT14896.0.CT X X X
Dcitr01g12310.1.2 MCOT06229.1.CO
Dcitr01g12310.1.3 MCOT06229.3.CO
Dcitr01g12310.1.4 MCOT19482.0.CT
Dcitr01g12310.1.5 MCOT06229.2.CO
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MCOT: MAKER (MAKER, RRID:SCR_005309), Cufflinks (Cufflinks, RRID:SCR_014597), Oases (Oases, RRID:SCR_011896), Trinity (Trinity, RRID:SCR_013048) pipeline. Each manually annotated gene has been assigned an OGSv3.0 gene identifier. Genes not marked as complete were only able to be annotated as partial gene models. Evidence types used for manual annotation of each gene are indicated. More information on these evidence sources is available in [16].

Figure 2.

Figure 2.

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Expression of D. citri chitin deacetylase genes. (A) Heatmap displaying relative expression levels of all annotated chitin deacetylase genes in RNA-seq datasets from various life stages, tissues and CLas infection states. Expression levels were obtained from CGEN [20] and are reported in Table 2. The heatmap is scaled by row. (B) Expression levels (transcripts per million, TPM) of CDA3 (Dcitr02g03950.1.1) in tissues from CLas+ and CLas− psyllids fed on two different types of citrus plants. Standard error bars are shown for all expression values except those marked with an asterisk (*), which had only one replicate. Expression levels were obtained from CGEN [20].

In Drosophila and Tribolium, the CDA1 and CDA2 orthologs are adjacent to one another in the genome [3, 5] on chromosomes 3 and 5, respectively. The conserved clustering of these genes suggests there may be evolutionary constraint on their physical location. We found that the D. citri CDA1 and CDA2 orthologs are also adjacent to one another on chromosome 4. In the D. citri v3 genome, these genes are separated by approximately 50 kilobase pairs (Kb), although this distance appears to be inflated by falsely duplicated fragments of both genes in this assembly.

Group III chitin deacetylases

We identified one group III CDA in the D. citri v3 genome (Tables 3 and 4). This gene has been previously described and was named CDA3 because of its orthology to Nilaparvata lugens CDA3 [33]. Like group III CDAs in other insects, D. citri CDA3 contains a ChBD and catalytic domain but lacks the low-density lipoprotein receptor class A (LDLa) domain found in group I CDAs (Figure 3). Improvements in the genome assembly mean that our curated CDA3 model from genome v3 has additional 3′ sequence than the previously reported model (GenBank accession number XM_008481889.1), which was based on genome v1.1 [33, 34]. The resulting predicted protein is almost 50 amino acids longer, with additional conserved sequence at the C-terminus.

Yu et al. [33] reported that RNAi knockdown of CDA3 had no effect on molting or wing development. Instead, their results implicated CDA3 in the D. citri bacterial immune response. Recombinant CDA3 showed antibacterial activity against gram-positive bacteria, but had no effect on gram-negative bacteria. Moreover, injection of either Escherichia coli (gram-negative) or Staphylococcus aureus (gram-positive) bacteria into D. citri increased CDA3 expression in the midgut and decreased its expression in the fat body, although the timeline of these effects is not certain. To determine whether infection by CLas, a gram-negative bacterium, might also affect CDA3 expression, we used CGEN [20] to compare expression of D. citri CDA3 in RNA-seq datasets from CLas+ and CLas− guts [35], midguts [36] and whole bodies ([37] and NCBI BioProject PRJNA609978). CDA3 expression was lower in CLas+ versus CLas− whole body tissue in data from two different RNA-Seq experiments (Figure 2B). Expression of CDA3 in midgut and gut tissues was low in all samples but there was a slight increase in CLas+ versus CLas− midgut expression (Figure 2B). While the significance of these expression differences is not clear, they may warrant further investigation.

Group IV chitin deacetylases

Most insects examined to date have one group IV CDA, typically called CDA5 (CDA4 in N. lugens) (Table 3). CDA5 has been shown to have multiple isoforms in Tribolium and Drosophila [5]. Consistent with these observations, we identified and annotated five different isoforms of CDA5 in D. citri (Table 4). Unfortunately, the annotated models are missing a small amount of 3′ sequence due to genome assembly issues. However, we identified a de-novo assembled transcript (MCOT06229.1.CO) that appears to encode the full-length protein (Figure 3). The missing genome sequence does not affect the conserved functional domains of CDA5. Four of the five transcript isoforms encode proteins containing both an N-terminal ChBD and a C-terminal catalytic domain, as seen in other insect CDA5 orthologs. The remaining isoform (CDA5-RB) differs at the 5′ end and apparently lacks a ChBD-encoding region.

Other chitin deacetylase groups

We did not find any group II or group V CDAs in the D. citri v3 genome (Figure 4). To our knowledge CDAs from these groups have not been found in any hemipteran insects examined to date [6], so their absence in D. citri was expected.

Figure 4.

Figure 4.

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Phylogenetic tree of chitin deacetylase family members. ClustalW was used to perform the multiple sequence alignment. The tree was constructed with MEGA X software [19] using neighbor-joining analysis with 100 bootstrap replications. Drosophila melanogaster (Dm), Tribolium castaneum (Tc), Nilaparvata lugens (Nl), and Diaphorina citri (Dc). D. citri protein branches are marked with a circle. Colors delineate established chitin deacetylase groups.

Re-use potential

This manual curation was carried out as a part of the Diaphorina citri community annotation project [38] with a goal to annotate gene families related to immune response, metabolism and other major functions [39–42]. Our manual annotations will be useful for researchers studying the chitin deacetylase genes in the future. We annotated multiple isoforms for three of the four genes, which will inform the design of experiments to determine the expression pattern and function of specific isoforms. Our annotations will be incorporated into an updated official gene set and will be publicly available for comparative expression profiling on the CGEN [20].

Acknowledgements

We thank Dr. Josh Benoit for assistance with data visualization.

Funding Statement

This research was funded by USDA-NIFA grant 2015-70016-23028, HSI 1300394, 2020-70029-33199 and an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103418.

Data availability

The Diaphorina citri genome assembly, gene sets, and transcriptome data are accessible via the Citrus Greening website [20]. All accessions for genes used for phylogenetic analysis are provided within this report, and all additional data is available via the GigaScience GigaDB repository [43].

Editor’s Note

This article is one of a series of Data Releases crediting the outputs of a student-focused and community-driven manual annotation project curating gene models and if required, correcting assembly anomalies, for the Diaphorina citri genome project [13].

Declarations

List of abbreviations

CDA: chitin deacetylase; CGEN: Citrus Greening Expression Network; ChBD: chitin binding domain; CLas: Candidatus Liberibacter asiaticus ; NCBI: National Center for Biotechnology Information; RNAi: RNA interference; TPM: transcripts per million.

Ethical approval

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Funding

This research was funded by USDA-NIFA grant 2015-70016-23028, HSI 1300394, 2020-70029-33199 and an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103418.

Authors’ contributions

WBH, SJB, TD and LAM conceptualized the study; TD, SS, TDS and SJB supervised the study; SJB, TD, SS, and LAM contributed to project administration; SM, TDS, and BT conducted investigation; PH, MF-G, and SS contributed to software development; SS, TDS, PH, and MF-G developed methodology; SJB, TD, WBH, and LAM acquired funding; SM and TDS prepared and wrote the original draft; SS, WBH and SJB reviewed and edited the draft.

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GigaByte. 2021 Jun 11;2021:gigabyte25.

Article Submission

Surya Saha
GigaByte.

Assign Handling Editor

Editor: Scott Edmunds
GigaByte.

Editor Assess MS

Editor: Scott Edmunds
GigaByte.

Review MS

Editor: Mary Ann Tuli
Reviewer name and names of any other individual's who aided in reviewer Mary Ann Tuli
Do you understand and agree to our policy of having open and named reviews, and having your review included with the published papers. (If no, please inform the editor that you cannot review this manuscript.) Yes
Is the language of sufficient quality? Yes
Please add additional comments on language quality to clarify if needed 1) Line 27. "Genomic" should be "genomic"
Are all data available and do they match the descriptions in the paper? No
Additional Comments 1) Line 137. "Multiple alignments were performed using MUSCLE " We need the output of MUSCLE (FASTA). 2) Line 137. "phylogenetic trees were constructed (figures 1 and 3) in MEGA7 or MEGAX." We need the files underlying the phylogenetic tree (newick). Please indicate which version of MEGA was used for each tree. 3) Line 139. "Expression data from CGEN was visualized using the pheatmap package of R or Microscoft Excel" Please can you provide a file of the raw data used to produce the heatmap (figures 2a ) and the TMP graph (figure 2b).
Are the data and metadata consistent with relevant minimum information or reporting standards? See GigaDB checklists for examples <a href="http://gigadb.org/site/guide" target="_blank">http://gigadb.org/site/guide</a> Yes
Additional Comments Nomenclature standards have been met. All cited INSDC accession numbers are publicly available.
Is the data acquisition clear, complete and methodologically sound? Yes
Additional Comments The curation workflow used for community annotation is available via protocols.io , nonetheless the manuscript includes a comprehensive summary which is appropriate.
Is there sufficient detail in the methods and data-processing steps to allow reproduction? No
Additional Comments See "Are all data available and do they match the descriptions in the paper?" above. Once the additional files are made available I believe reproduction will be possible.
Is there sufficient data validation and statistical analyses of data quality? Yes
Additional Comments
Is the validation suitable for this type of data? Yes
Additional Comments
Is there sufficient information for others to reuse this dataset or integrate it with other data? Yes
Additional Comments
Any Additional Overall Comments to the Author 1) Citation [23] MUSCLE. https://www.ebi.ac.uk/Tools/msa/muscle/. - the website suggests users of MUSCLE cite DOI:10.1093/nar/gkz268 Some of my comments/recommendations are pertinent to the other D. citri manuscripts currently under review. Please send the files to us via the FTP server details at the end of this email. Please note the following. We strongly recommend filenames are concise and meaningful (e.g. "gene_exp_cell_lines.csv" is better than "Supp1.txt"). Filenames should be unique. Filenames should not include spaces. We recommend using the underscore (_) in place of spaces in the filenames. Filenames should only include the following characters a-z,A-Z,0-9,_,-,+,. Text and tabular information must be in a non-proprietary and text-based format (e.g. CSV/TSV rather than PDF or XLS) Images must be in a lossless raster format (e.g. TIFF, PNG) or vector format (e.g. SVG). If you encounter any errors please send us the full context and error message to help us resolve the problem. username = user34 password = SahacitriChiD FTP server = parrot.genomics.cn For using tools like FileZilla use the standard FTP protocol (not sftp). If you are using command line FTP, you may need to use the passive mode (e.g. use epsv command): > ftp @parrot.genomics.cn Connected to parrot.genomics.cn. 220 (vsFTPd 2.0.5) 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> epsv EPSV/EPRT on IPv4 off. ftp> put local: remote: 227 Entering Passive Mode (218,188,108,76,126,77) 150 Ok to send data. 100% |************************************************************************| 12 137.86 KiB/s 00:00 ETA 226 File receive OK. 12 bytes sent in 00:00 (0.26 KiB/s)
Recommendation Minor Revision
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GigaByte.

Review MS

Editor: Xingtan Zhang
Reviewer name and names of any other individual's who aided in reviewer Xingtan Zhang and Yingying Gao
Do you understand and agree to our policy of having open and named reviews, and having your review included with the published papers. (If no, please inform the editor that you cannot review this manuscript.) Yes
Is the language of sufficient quality? Yes
Please add additional comments on language quality to clarify if needed
Are all data available and do they match the descriptions in the paper? Yes
Additional Comments
Are the data and metadata consistent with relevant minimum information or reporting standards? See GigaDB checklists for examples <a href="http://gigadb.org/site/guide" target="_blank">http://gigadb.org/site/guide</a> Yes
Additional Comments
Is the data acquisition clear, complete and methodologically sound? No
Additional Comments
Is there sufficient detail in the methods and data-processing steps to allow reproduction? Yes
Additional Comments
Is there sufficient data validation and statistical analyses of data quality? No
Additional Comments
Is the validation suitable for this type of data? No
Additional Comments
Is there sufficient information for others to reuse this dataset or integrate it with other data? No
Additional Comments
Any Additional Overall Comments to the Author
Recommendation Reject (Unsound or Unusuable)
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GigaByte.

Editor Decision

Editor: Scott Edmunds
GigaByte. 2021 Jun 11;2021:gigabyte25.

Minor Revision

Surya Saha
GigaByte.

Assess Revision

Editor: Scott Edmunds
GigaByte.

Re-Review MS

Editor: Mary Ann Tuli
Comments on revised manuscript I am satisfied that the issues I raised have been addressed. Thank you.
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Editor Decision

Editor: Scott Edmunds
GigaByte.

Final Data Preparation

Editor: Mary-Ann Tuli
GigaByte.

Editor Decision

Editor: Scott Edmunds
GigaByte.

Accept

Editor: Scott Edmunds
Comments to the Author Good to see another one of these accepted.
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Export to Production

Editor: Scott Edmunds

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Data Availability Statement

    The Diaphorina citri genome assembly, gene sets, and transcriptome data are accessible via the Citrus Greening website [20]. All accessions for genes used for phylogenetic analysis are provided within this report, and all additional data is available via the GigaScience GigaDB repository [43].

    Articles from GigaByte are provided here courtesy of Gigascience Press

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