Draft genome sequencing of the sugarcane hybrid SP80-3280

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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.

Introduction

Sugarcane is an economically important crop used as source of sugar, ethanol and electricity generation ¹. 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 groups ^{2, 3}, with a total genome size reaching 10Gpb ⁴. Its complex genome structure has hampered genome sequencing, assembly and annotation. Partial genomic sequences are available ^{5– 8}, as well as transcriptome sequences ^{9– 11}, but there are no whole genome assemblies available to date. Here we used the Illumina TruSeq Synthetic Long Read sequencing technology to survey the genome of the polyploid cultivar SP80-3280. The generated long reads, their assembly and genome annotation 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 described ¹². 6µg of DNA were sent to Illumina (CA, USA) for DNA sequencing using TruSeq Synthetic long read technology ¹³, 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 BLAST ¹⁴, keeping only the long reads with best hits against Viridiplantae, resulting in 1,224,061 useful for assembly. Prior to assembly, long 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 ¹⁵, using similar parameters as previously described ¹³, 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-HIT ¹⁶, merging 100% identical sequences and sub-sequences. RNASeq data previously generated in our group ¹⁷ for the same cultivar was exploited for gene prediction using BRAKER1 ¹⁸ and PASA ¹⁹, as well as sugarcane transcript data (ESTs), and Sorghum bicolor proteins using Exonerate ²⁰, all gene evidence was integrated to generate a high quality gene prediction set with Evidence Modeller ²¹, leading to 153,078 predicted protein-coding genes.

Data availability

The data referenced by this article are under copyright with the following copyright statement: Copyright: © 2017 Riaño-Pachón DM and Mattiello L

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 PRJNA272769. Genome annotation is available from https://figshare.com/projects/Sugarcane_SP80-3280_draft_genome_annotation/22327

Funding Statement

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.