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De novo assembly of kenaf (Hibiscus cannabinus) transcriptome using Illumina sequencing for gene discovery and marker identification

Molecular Breeding volume 35, Article number: 192 (2015) Cite this article

Abstract

Kenaf (Hibiscus cannabinus) is one of important nature fiber crops in the world. However, the EST sequence resources available for kenaf are still very limited. In this study, 131,262,686 clean reads (13.12 Gb) using Illumina paired-end sequencing were assembled. De novo assembly yielded 90,175 unigenes with an average length of 700 bp. By sequence similarity searching for known proteins, 46,165 (51.19 %) unigenes were annotated for their function. Out of these annotated unigenes, 37,080 (41.12 %) unigenes showed significant similarity to genes of a diploid cotton (Gossypium raimondii). Searching against the Kyoto encyclopedia of genes and genomes (KEGG) indicated that 23,051 unigenes were mapped to 254 KEGG pathways, and 317 genes were assigned to starch and sucrose metabolic pathway which was related with cellulose biosynthesis. Furthermore, a total of 52,521 putative gene-associated SNPs and 11,083 SSRs (designated as HcEMS) were identified from these assembled unigenes. Among these HcEMS markers, mono-, di-, and trinucleotide repeat types were the most abundant types (40.3, 22.3, and 34.7 %, respectively). The AG-rich nucleotide repeats, including (AG)n, (AAG)n, and (AAAG)n types, were the most abundant and could be considered as the dominant types in kenaf. A sample of 835 HcEMSs were used to survey polymorphisms with eight kenaf accessions. Of them, 753 (90.1 %) successfully amplified at least one fragment and 450 (53.9 %) detected polymorphism. All these results will accelerate the understanding of genetic basis of the fiber development and marker-assisted breeding in kenaf.

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Abbreviations

NGS:

Next-generation sequencing

CDS:

Coding sequence

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

EST:

Expressed sequence tag

nr:

Non-redundant protein sequences

KOG:

Eukaryotic ortholog groups

BLAST:

Basic local alignment search tool

SNP:

Single nucleotide polymorphisms

SSR:

Simple sequence repeat

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Acknowledgments

This project was sponsored by funds from the Distinguished Young Research Fund in Fujian Agriculture and Forestry University (xjq201401; 2012xjj01), China National Scholarship (201408350022), Introduction Breeding and Varieties Demonstration of Featured Crops between China and Benin (2015I0001), National Agri-Industry Technology Research System for Crops of Bast and Leaf Fiber, China (nycytx-19-E06), and Experiment Station of Kenaf and Kenaf of the Ministry of Agriculture in Southeast China (Nongkejiaofa 2011).

Author contributions

J.Q. and L.Z. conceived the project and its components. X.W. and L.Z. contributed to RNA isolation and cDNA library construction. X.W. and L.Z. performed SSR development and polymorphism evaluation. J.X., L.L., and J.Q. selected the germplasms. X.W. and L.Z. prepared figures and tables. L.Z. analyzed all the data and wrote the paper.

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Authors and Affiliations

  1. Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Science/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

    Liwu Zhang, Xuebei Wan, Jiantang Xu, Lihui Lin & Jianmin Qi

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  1. Liwu Zhang
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  2. Xuebei Wan
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  4. Lihui Lin
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Correspondence to Liwu Zhang or Jianmin Qi.

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The authors declare that they have no conflict of interest.

Ethical standard

The experiment conducted complies with the laws of China.

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Zhang, L., Wan, X., Xu, J. et al. De novo assembly of kenaf (Hibiscus cannabinus) transcriptome using Illumina sequencing for gene discovery and marker identification. Mol Breeding 35, 192 (2015). https://doi.org/10.1007/s11032-015-0388-0

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  • DOI: https://doi.org/10.1007/s11032-015-0388-0

Keywords

  • Kenaf (Hibiscus cannabinus L.)
  • Transcriptome sequencing
  • SNP
  • SSR