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De novo assembly and characterization of the Welsh onion (Allium fistulosum L.) transcriptome using Illumina technology

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Abstract

Welsh onion (Allium fistulosum L.) has long been cultivated as a vegetable and spice for its flavor and aroma. However, transcriptomic and genomic data for A. fistulosum remain scarce. The goal of this study was to generate transcript sequences for functional genomic analyses, and identify genes potentially involved in sulfur, selenium, and vitamin metabolism. In total, 53,378,674 high-quality reads were generated, and de novo assembly resulted in 103,286 contigs and 53,837 unigenes. The average unigene length was 619 bp with an N50 of 832 bp. Similarity searches revealed that 36,155 sequences were similar to those of known proteins in public databases. Of these, 35,250 unigenes sequences were significantly similar to sequences in the NCBI non-redundant protein database and 22,804 were annotated in the Swiss-Prot database. Additionally, 13,125 and 26,660 unigenes were annotated in the Cluster of Orthologous Group and Gene Ontology databases, respectively. A total of 20,680 unigenes were classified into 128 pathways via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database. Key enzymes involved in sulfur and selenium metabolism were also identified. Additionally, our transcriptome revealed a number of unigenes encoding important enzymes involved in vitamin metabolism. We also identified 2014 simple sequence repeats in 1892 unigenes. This transcriptome analysis provides valuable information to further our understanding of the molecular mechanisms regulating the biosynthesis of organic sulfur compounds. The detected simple sequence repeats may facilitate marker-assisted selection in Welsh onion breeding experiments.

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Authors and Affiliations

  1. State Key Laboratory of Crop Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, 271018, Shandong, China

    Xiu-Dong Sun, Xin-Hui Yu & Shi-Qi Liu

  2. State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai’an, Shandong, China

    Shu-Mei Zhou

Authors
  1. Xiu-Dong Sun
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  2. Xin-Hui Yu
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  3. Shu-Mei Zhou
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  4. Shi-Qi Liu
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Correspondence to Shi-Qi Liu.

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We declare that we have no financial or personal relationships with other people or organizations that can inappropriately influence our work. There is no professional or other personal interest of any nature or kind in any product, service and/or company that could be construed as influencing the position presented in our manuscript.

Funding

This study was funded by the National Natural Science Foundation of China (31372084) and by the Chinese National Department Public Benefit Research Foundation (201303108).

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The authors declare that they have no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Informed consent was obtained from all individual participants included in the study.

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Communicated by S. Hohmann.

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Sun, XD., Yu, XH., Zhou, SM. et al. De novo assembly and characterization of the Welsh onion (Allium fistulosum L.) transcriptome using Illumina technology. Mol Genet Genomics 291, 647–659 (2016). https://doi.org/10.1007/s00438-015-1131-6

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  • DOI: https://doi.org/10.1007/s00438-015-1131-6

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