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The Draft Genome of Eggplant

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

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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Fig. 6.1
Fig. 6.2

Literature Cited

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    CAS  CrossRef  Google Scholar 

  • Asamizu E, Ichihara H, Nakaya A, Nakamura Y, Hirakawa H, Ishii T, Tamura T, Fukami-Kobayashi K, Nakajima Y, Tabata S (2014) Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases. Plant Cell Physiol 55:e8

    CAS  CrossRef  Google Scholar 

  • Barchi L, Lanteri S, Portis E, Acquadro A, Valè G, Toppino L, Rotino GL (2011) Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genom 12:304

    CAS  CrossRef  Google Scholar 

  • Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J (2012) Hi-C: a comprehensive technique to capture the conformation of genomes. Methods 58:268–276

    CAS  CrossRef  Google Scholar 

  • Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W (2011) Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27:578–579

    CAS  CrossRef  Google Scholar 

  • Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jiménez-Goméz JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham RC, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JK, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR (2014) The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 6:1034–1038

    CrossRef  Google Scholar 

  • Bombarely A, Rosli HG, Vrebalov J, Moffett P, Mueller LA, Martin GB (2012) A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. Mol Plant Microbe Interact 25:1523–1530

    CAS  CrossRef  Google Scholar 

  • Cao G, Sofic E, Prior RL (1996) Antioxidant capacity of tea and common vegetables. J Agric Food Chem 44:3426–3431

    CAS  CrossRef  Google Scholar 

  • Ding Q, Liu J, Gao L (2016) The complete chloroplast genome of eggplant (Solanum melongena L.). Mitochondrial DNA Part B 1:843–844

    CrossRef  Google Scholar 

  • Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL (2017) De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356:92–95

    CAS  CrossRef  Google Scholar 

  • Eddy SR (2011) Accelerated profile HMM searches. PLoS Comput Biol 7:e1002195

    CAS  CrossRef  Google Scholar 

  • Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44(D1):D279–D285

    CAS  CrossRef  Google Scholar 

  • Fukuoka H, Yamaguchi H, Nunome T, Negoro S, Miyatake K, Ohyama A (2010) Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant (Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato. Gene 450:76–84

    CAS  CrossRef  Google Scholar 

  • Fukuoka H, Miyatake K, Nunome T, Negoro S, Shirasawa K, Isobe S, Asamizu E, Yamaguchi H, Ohyama A (2012) Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets. Theor Appl Genet 125:47–56

    CAS  CrossRef  Google Scholar 

  • Ghurye J, Pop M, Koren S, Bickhart D, Chin CS (2017) Scaffolding of long read assemblies using long range contact information. BMC Genom 18:527

    CrossRef  Google Scholar 

  • Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A, Yamaguchi H, Sato S, Isobe S, Tabata S, Fukuoka H (2014) Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world. DNA Res 21:649–660

    CAS  CrossRef  Google Scholar 

  • Huang X, Yang SP, Chinwalla AT, Hillier LW, Minx P, Mardis ER, Wilson RK (2006) Application of a superword array in genome assembly. Nucleic Acids Res 34:201–205

    CAS  CrossRef  Google Scholar 

  • Jurka J (1998) Repeats in genomic DNA: mining and meaning. Curr Opin Struct Biol 8:333–337

    CAS  CrossRef  Google Scholar 

  • Kim S, Park M, Yeom SI, Kim YM, Lee JM, Lee HA, Seo E, Choi J, Cheong K, Kim KT, Jung K, Lee GW, Oh SK, Bae C, Kim SB, Lee HY, Kim SY, Kim MS, Kang BC, Jo YD, Yang HB, Jeong HJ, Kang WH, Kwon JK, Shin C, Lim JY, Park JH, Huh JH, Kim JS, Kim BD, Cohen O, Paran I, Suh MC, Lee SB, Kim YK, Shin Y, Noh SJ, Park J, Seo YS, Kwon SY, Kim HA, Park JM, Kim HJ, Choi SB, Bosland PW, Reeves G, Jo SH, Lee BW, Cho HT, Choi HS, Lee MS, Yu Y, Do Choi Y, Park BS, van Deynze A, Ashrafi H, Hill T, Kim WT, Pai HS, Ahn HK, Yeam I, Giovannoni JJ, Rose JK, Sørensen I, Lee SJ, Kim RW, Choi IY, Choi BS, Lim JS, Lee YH, Choi D (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46:270–278

    CAS  CrossRef  Google Scholar 

  • Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40(Database issue):D1202–D1210

    CrossRef  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

    CAS  CrossRef  Google Scholar 

  • Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272

    CAS  CrossRef  Google Scholar 

  • Llorens C, Futami R, Covelli L, Domínguez-Escribá L, Viu JM, Tamarit D, Aguilar-Rodríguez J, Vicente-Ripolles M, Fuster G, Bernet GP, Maumus F, Munoz-Pomer A, Sempere JM, Latorre A, Moya A (2011) The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res 39(Database issue):D70–D74

    CrossRef  Google Scholar 

  • Nakaya A, Ichihara H, Asamizu E, Shirasawa S, Nakamura Y, Tabata S, Hirakawa H (2017) Plant Genome DataBase Japan (PGDBj). Methods Mol Biol 1533:45–77

    CAS  CrossRef  Google Scholar 

  • Nunome T, Ishiguro K, Yoshida T, Hirai M (2001) Mapping of fruit shape and color development traits in eggplant (Solanum melongena L.) based on RAPD and AFLP markers. Breed Sci 51:19–26

    CAS  CrossRef  Google Scholar 

  • Nunome T, Suwabe K, Iketani H, Hirai M (2003a) Identification and characterization of microsatellites in eggplant. Plant Breed 122:256–262

    CAS  CrossRef  Google Scholar 

  • Nunome T, Suwabe K, Ohyama A, Fukuoka H (2003b) Characterization of trinucleotide microsatellites in eggplant. Breed Sci 53:77–83

    CAS  CrossRef  Google Scholar 

  • Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 27:29–34

    CAS  CrossRef  Google Scholar 

  • Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes. Bioinformatics 21(Suppl 1):i351–i358

    CAS  CrossRef  Google Scholar 

  • Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33(Web Server issue):W116–W120

    CAS  CrossRef  Google Scholar 

  • Schmidt MH, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger AM, Usadel B (2017) De novo assembly of a new Solanum pennellii accession using Nanopore sequencing. Plant Cell 29:2336–2348

    CAS  CrossRef  Google Scholar 

  • Stanke M, Waack S (2003) Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19(Suppl 2):ii215–ii225

    CrossRef  Google Scholar 

  • Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41

    CrossRef  Google Scholar 

  • The Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29

    CrossRef  Google Scholar 

  • The Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195

    Google Scholar 

  • The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641

    CrossRef  Google Scholar 

  • Wu F, Eannetta NT, Xu Y, Tanksley SD (2009) A detailed synteny map of the eggplant genome based on conserved ortholog set II (COSII) markers. Theor Appl Genet 118:927–935

    CAS  CrossRef  Google Scholar 

  • Wu F, Tanksley SD (2010) Chromosomal evolution in the plant family Solanaceae. BMC Genom 11:182

    CrossRef  Google Scholar 

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Correspondence to Hideki Hirakawa .

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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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