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De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing

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Abstract

Garlic is widely used as a spice throughout the world for the culinary value of its flavor and aroma, which are created by the chemical transformation of a series of organic sulfur compounds. To analyze the transcriptome of Allium sativum and discover the genes involved in sulfur metabolism, cDNAs derived from the total RNA of Allium sativum buds were analyzed by Illumina sequencing. Approximately 26.67 million 90 bp paired-end clean reads were achieved in two libraries. A total of 127,933 unigenes were generated by de novo assembly and were compared with the sequences in public databases. Of these, 45,286 unigenes had significant hits to the sequences in the Nr database, 29,514 showed significant similarity to known proteins in the Swiss-Prot database and, 20,706 and 21,952 unigenes had significant similarity to existing sequences in the KEGG and COG databases, respectively. Moreover, genes involved in organic sulfur biosynthesis were identified. These unigenes data will provide the foundation for research on gene expression, genomics and functional genomics in Allium sativum.

Key message The obtained unigenes will provide the foundation for research on functional genomics in Allium sativum and its closely related species, and fill the gap of the existing plant EST database.

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Abbreviations

ACSO:

Sulfur-alk(en)yl cysteine sulfoxide

BLAST:

Basic local alignment search tool

COG:

Cluster of orthologous group

EST:

Expressed sequence tag

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

NCBI:

National Center for Biotechnology Information

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Acknowledgments

This study was supported by the Chinese National Department Public Benefit Research Foundation (No. 200903018).

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Authors and Affiliations

  1. State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China

    Xiudong Sun, Fanlu Meng & Shiqi Liu

  2. College of Life Science, Shandong Agricultural University, Taian, 271018, Shandong, China

    Shumei Zhou

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  1. Xiudong Sun
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  2. Shumei Zhou
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  4. Shiqi Liu
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Correspondence to Shiqi Liu.

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Communicated by C. Quiros.

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Sun, X., Zhou, S., Meng, F. et al. De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing. Plant Cell Rep 31, 1823–1828 (2012). https://doi.org/10.1007/s00299-012-1295-z

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  • DOI: https://doi.org/10.1007/s00299-012-1295-z

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