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Data Note

Draft genome sequencing of the sugarcane hybrid SP80-3280

[version 1; peer review: 2 approved]
Diego Mauricio Riaño-Pachón
https://orcid.org/0000-0001-9803-3465
1,2, Lucia Mattiello1,3
Diego Mauricio Riaño-Pachón
https://orcid.org/0000-0001-9803-3465
1,2, Lucia Mattiello1,3
PUBLISHED 09 Jun 2017
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Abstract

Sugarcane commercial cultivar SP80-3280 has been used as a model for genomic analyses in Brazil. Here we present a draft genome sequence employing Illumina TruSeq Synthetic Long reads. The dataset is available from NCBI BioProject with accession PRJNA272769.

Keywords

sugarcane, long reads, polyploid, genomics

Corresponding author: Diego Mauricio Riaño-Pachón
Competing interests: No competing interests were disclosed.
Grant information: This work was supported by institutional funds from CTBE/CNPEM to DMRP and a Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) grant to LM (2012/23345-0). The research was developed with support from CENAPAD-SP (Centro Nacional de Processamento de Alto Desempenho em São Paulo), project UNICAMP/FINEP-MCT.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Copyright:  © 2017 Riaño-Pachón DM and Mattiello L. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
How to cite: Riaño-Pachón DM and Mattiello L. Draft genome sequencing of the sugarcane hybrid SP80-3280 [version 1; peer review: 2 approved]. F1000Research 2017, 6:861 (https://doi.org/10.12688/f1000research.11859.1) First published: 09 Jun 2017, 6:861 (https://doi.org/10.12688/f1000research.11859.1) Latest published: 03 Jul 2017, 6:861 (https://doi.org/10.12688/f1000research.11859.2)

Introduction

Sugarcane is an economically important crop used as source of sugar, ethanol and electricity generation1. Sugarcane has a haploid genome of ~1Gpb, however, modern sugarcane cultivars are polyploids derived from interspecific hybridization between S. officinarum L. and S. spontaneum L., reaching up to 130 chromosomes distributed among ~12 homo(eo)logous groups2,3, with a total genome size reaching 10Gpb4. Its complex genome structure has hampered genome sequencing, assembly and annotation. Partial genomic sequences are available5–8, as well as transcriptome sequences9–11, but there are not whole genome assemblies available to date. Here we used the Illumina TruSeq Synthetic Long Read sequencing technology to survey the genome of cultivar SP80-3280. The generated long reads and their assembly have been made public and will provide useful information for functional genomics studies.

Materials and methods

The leaf rolls of greenhouse grown, two-month old plants of sugarcane cultivar SP80-3280 (provided by Centro de Tecnologia Canavieira, Piracicaba, São Paulo), were collected and immediately frozen in liquid nitrogen. The plant tissue was ground up to become fine powder, and high molecular weight DNA was extracted from 100 mg of fresh frozen tissue using CTAB (Sigma-Aldrich, USA) and chloroform:isoamyl alcohol (Sigma-Aldrich, USA) as previously described12. 6µg of DNA were sent to Illumina (CA, USA) for DNA sequencing using TruSeq Synthetic long read technology13, through their FastTrack Sequencing Service. Sequencing was performed on an Illumina HiSeq2000 system using paired-end chemistry. Nine long read libraries, each generating approx. 600Mbps, were generated, giving an estimated coverage between 4 and 5 of the monoploid genome. A total of 1,378,917 reads longer than 1.5Kbp, or 5,642,855,018 bases, were generated. The underlying 1,966,604,928 short reads amount to 393,320,985,600bp, which would translate to an estimated coverage of 393x of the haploid genome. The maximum read length was 20,918bp, with 36% of the reads being longer than 4.5Kbp. Possible contaminants were removed by comparison against the NCBI’s nucleotide database using BLAST14, keeping only the reads with best hits against Viridiplantae, resulting in 1,224,061 useful for assembly. Prior to assembly, reads originating from mitochondria (NC_008360.1) and chloroplast (NC_005878.2) were excluded using mirabait (http://mira-assembler.sourceforge.net/). Reads longer than 1.5Kbp were assembled using Celera’s WGS Assembler v8.2, using similar parameters as previously described13, except for some of the error parameters that were left in their default settings, i.e., ‘unitiger=bogart, merSize=31, ovlMinLen=100’, and the parameters ovlErrorRate, cnsErrorRate, cgwErrorRate, utgGraphErrorRate, utgGraphErrorLimit, utgMergeErrorRate, utgMergeErrorLimit. A non-redundant assembly was created using CD-HIT15, merging 100% identical sequences and sub-sequences.

Data availability

Raw sequencing data are available at NCBI SRA; the long reads with accession number SRX845504, and the underlying short reads with accessions SRX853961 to SRX853969. The SP80-3280 assembly is available with accession number GCA_002018215.1. All data can be found under the BioProject.

Competing interests

No competing interests were disclosed.

Grant information

This work was supported by institutional funds from CTBE/CNPEM to DMRP and a Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) grant to LM (2012/23345-0). The research was developed with support from CENAPAD-SP (Centro Nacional de Processamento de Alto Desempenho em São Paulo), project UNICAMP/FINEP-MCT.

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Acknowledgements

The authors are grateful to Larissa Prado da Cruz (CTBE/CNPEM) for assistance with molecular biology procedures.

References

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  • 9.  Mattiello L, Riaño-Pachón DM, Martins MC, et al.: Physiological and transcriptional analyses of developmental stages along sugarcane leaf. BMC Plant Biol. 2015; 15: 300. PubMed Abstract | Publisher Full Text | Free Full Text
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  • 11.  Belesini AA, Carvalho FMS, Telles BR, et al.: De novo transcriptome assembly of sugarcane leaves submitted to prolonged water-deficit stress. Genet Mol Res. 2017; 16(2). PubMed Abstract | Publisher Full Text
  • 12.  Porebski S, Bailey LG, Baum BR: Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Rep. 1997; 15(1): 8–15. Publisher Full Text
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  • 14.  Altschul SF, Gish W, Miller W, et al.: Basic local alignment search tool. J Mol Biol. 1990; 215(3): 403–410. PubMed Abstract | Publisher Full Text
  • 15.  Fu L, Niu B, Zhu Z, et al.: CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28(23): 3150–3152. PubMed Abstract | Publisher Full Text | Free Full Text

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Riaño-Pachón DM and Mattiello L. Draft genome sequencing of the sugarcane hybrid SP80-3280 [version 1; peer review: 2 approved] F1000Research 2017, 6:861 (https://doi.org/10.12688/f1000research.11859.1)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
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ApprovedThe paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approvedFundamental flaws in the paper seriously undermine the findings and conclusions
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Reviewer Report 21 Jun 2017
Chakravarthi Mohan, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil 
Approved
VIEWS 46
https://doi.org/10.5256/f1000research.12814.r23667
The data note entitled 'Draft genome sequencing of the sugarcane hybrid SP80-3280' is perhaps the first report describing the whole genome of sugarcane, a complex polyploid and its availability in NCBI will be a boon to sugarcane researchers.

... Continue reading
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Mohan C. Reviewer Report For: Draft genome sequencing of the sugarcane hybrid SP80-3280 [version 1; peer review: 2 approved]. F1000Research 2017, 6:861 (https://doi.org/10.5256/f1000research.12814.r23667)
The direct URL for this report is:
https://f1000research.com/articles/6-861/v1#referee-response-23667
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
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  • Author Response 03 Jul 2017
    Diego Mauricio Riaño-Pachón, Current address: Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
    03 Jul 2017
    Author Response
    Dear Dr. Mohan,

    thanks you for your review of our data note. In version 2 of the note we have added links for the genome annotation in addition to ... Continue reading
    Report a concern
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COMMENTS ON THIS REPORT
  • Author Response 03 Jul 2017
    Diego Mauricio Riaño-Pachón, Current address: Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
    03 Jul 2017
    Author Response
    Dear Dr. Mohan,

    thanks you for your review of our data note. In version 2 of the note we have added links for the genome annotation in addition to ... Continue reading
    Report a concern
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Reviewer Report 15 Jun 2017
Jason Miller, J. Craig Venter Institute, Rockville, MD, USA 
Approved
VIEWS 58
https://doi.org/10.5256/f1000research.12814.r23398
Summary:

The Data Note, "Draft genome sequencing of the sugarcane hybrid SP80-3280", describes a sugarcane genome assembly that is available at NCBI. The TruSeq method was applied to a monoploid sugarcane cultivar to generate a 1.2 gigabase assembly ... Continue reading
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Miller J. Reviewer Report For: Draft genome sequencing of the sugarcane hybrid SP80-3280 [version 1; peer review: 2 approved]. F1000Research 2017, 6:861 (https://doi.org/10.5256/f1000research.12814.r23398)
The direct URL for this report is:
https://f1000research.com/articles/6-861/v1#referee-response-23398
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
Report a concern
  • Author Response 03 Jul 2017
    Diego Mauricio Riaño-Pachón, Current address: Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
    03 Jul 2017
    Author Response
    Dear Dr. Miller,

    thank you very much for your review of our data note. We have followed your main suggestions, and they are available as version 2 of the ... Continue reading
    Report a concern
  • Respond or Comment
COMMENTS ON THIS REPORT
  • Author Response 03 Jul 2017
    Diego Mauricio Riaño-Pachón, Current address: Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
    03 Jul 2017
    Author Response
    Dear Dr. Miller,

    thank you very much for your review of our data note. We have followed your main suggestions, and they are available as version 2 of the ... Continue reading
    Report a concern

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VERSION 2 PUBLISHED 09 Jun 2017
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The paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations
A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approved
Fundamental flaws in the paper seriously undermine the findings and conclusions

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  1. Jason Miller, J. Craig Venter Institute, Rockville, USA
  2. Chakravarthi Mohan, Federal University of São Carlos, São Carlos, Brazil

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    Alongside their report, reviewers assign a status to the article:
    Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested
    Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
    Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions
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