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The Draft Genome of Eggplant

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The Eggplant Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

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Abstract

The genome sequences of many plant species have been determined using next-generation sequencing (NGS) data. In the Solanaceae, the genome sequences of species such as potato, tomato, wild tomato, and pepper have been determined. To determine the genome sequence of eggplant, several kinds of linkage maps were constructed using random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), expressed sequence tag (EST), simple sequence repeat (SSR), single nucleotide polymorphism (SNP), and conserved ortholog set (COS) markers. To clarify the genome structure and complex traits, the draft genome sequence SME_r2.5.1 of the purebred cultivar Nakate-Shinkuro was determined in 2014. SME_r2.5.1 consisted of 33,873 sequences with a total length of 833.1 Mb. Gene prediction identified 85,446 coding sequences (CDSs) (SME_r2.5.1_cds). According to similarity and domain searches, 41,048 transposable elements, 1714 pseudogenes, and 649 short genes were excluded, and the remaining 42,035 CDSs constituted the final subset of genes (SME_r2.5.1_cds_ip). Annotation was performed by BLAST searches against NCBI’s NR and TAIR10 databases and InterProScan searches against the Pfam database. Genes related to the phenylpropanoid pathway producing the antioxidant chlorogenic acid (CGA) were searched by their annotation (hydroxycinnamoyl-CoA shikimate hydroxycinnamoyl transferase [HCT], hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase [HQT], and p-coumarate 3-hydroxylase [C3H]). The information about the genome, genes, and annotation is available at the Eggplant Genome Database (http://eggplant.kazusa.or.jp). The DNA markers of eggplant have been manually curated from the literature and deposited in the Plant Genome Database Japan (http://pgdbj.jp). Collectively, the use of this genomic information is expected to accelerate the breeding efficiency of eggplant.

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Authors and Affiliations

  1. Kazusa DNA Research Institute, Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan

    Hideki Hirakawa

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  1. Hideki Hirakawa
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Correspondence to Hideki Hirakawa .

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Editors and Affiliations

  1. Biological Sciences, University of Southampton, Southampton, UK

    Mark A. Chapman

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Hirakawa, H. (2019). The Draft Genome of Eggplant. In: Chapman, M. (eds) The Eggplant Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-99208-2_6

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