Patchwork sequencing of tomato San Marzano and Vesuviano varieties highlights genome-wide variations

BMC Genomics

Luigi Frusciante³  Massimo Delledonne¹  Genny Buson¹  Maria Luisa Chiusano³  Elisa Zago¹  Amalia Barone³  Alessandra Traini²  Paola Tononi¹  Raffaella D’Alessandro³  Francesca Ferriello³  Adriana Sacco³  Maria Raffaella Ercolano³ 

[1] Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie, 15, 37134 Verona, Italy;Present address: East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK;Department of Agriculture Sciences, University of Naples Federico II, Via Universita’ 100, 80055 Portici, Italy

关键词: Solanum lycopersicum;    SNPs;    NGS sequencing;    Fruit quality;    Combined assembling;   

Others  :  1217858
DOI  :  10.1186/1471-2164-15-138

 received in 2013-07-24, accepted in 2014-01-24,  发布年份 2014

【 摘 要 】

Background

Investigation of tomato genetic resources is a crucial issue for better straight evolution and genetic studies as well as tomato breeding strategies. Traditional Vesuviano and San Marzano varieties grown in Campania region (Southern Italy) are famous for their remarkable fruit quality. Owing to their economic and social importance is crucial to understand the genetic basis of their unique traits.

Results

Here, we present the draft genome sequences of tomato Vesuviano and San Marzano genome. A 40x genome coverage was obtained from a hybrid Illumina paired-end reads assembling that combines de novo assembly with iterative mapping to the reference S. lycopersicum genome (SL2.40). Insertions, deletions and SNP variants were carefully measured. When assessed on the basis of the reference annotation, 30% of protein-coding genes are predicted to have variants in both varieties. Copy genes number and gene location were assessed by mRNA transcripts mapping, showing a closer relationship of San Marzano with reference genome. Distinctive variations in key genes and transcription/regulation factors related to fruit quality have been revealed for both cultivars.

Conclusions

The effort performed highlighted varieties relationships and important variants in fruit key processes useful to dissect the path from sequence variant to phenotype.

【 授权许可】

   
2014 Ercolano et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Bai Y, Lindhout P: Domestication and breeding of tomatoes: what have we gained and what can we gain in the future? Ann Bot-London 2007, 100:1085-1094.
• [2]Grandillo S, Chetelat R, Knapp SK, Spooner DM, Peralta I, Cammareri M, Perez O, Termolino P, Tripode P, Chiusano ML, Ercolano MR, Fruschiante L, Monte L, Pignone D: Solanum section Lycopersicon. In Wild crop relatives: Genomic and breeding resources, Volume 5. Edited by Kole C. Berlin, Heidelberg: Springer-Verlag; 2011:129-216.
• [3]Zago F: Buone varietà di pomodoro. L'Italia Agricola 1912, 44:110-456.
• [4]Zago F: Varietà per la preparazione dei pelati. L'Italia Agricola 1929, 66:360-362.
• [5]Ercolano MR, Carli P, Soria A, Cascone A, Fogliano V, Frusciante L, Barone A: Biochemical sensorial and genomic profiling of Italian tomato traditional varieties. Euphytica 2008, 164:571-582.
• [6]Carli P, Barone A, Fogliano V, Frusciante L, Ercolano MR: Dissection of genetic and environmental factors involved in tomato organoleptic quality. BMC Plant Biol 2011, 11:58. BioMed Central Full Text
• [7]Garcia-Martinez S, Corrado G, Ruiz-Martinez JJ, Rao R: Diversity and structure of a sample of traditional Italian and Spanish tomato accessions. Genet Resour Crop Evol 2013, 60:789-798.
• [8]The Tomato Genome Consortium: The tomato genome sequence provides insights into fleshy fruit evolution. Nature 2012, 485:635-641.
• [9]Todd PM, Alba R: The tomato genome fleshed out. Nat Biotechnol 2012, 30:765-767.
• [10]The 1000 Genomes Project Consortium: An integrated map of genetic variation from 1092 human genomes. Nature 2012, 491:56-65.
• [11]Cao J, Schneeberger K, Ossowski S, Günther T, Bender S, Fitz1 J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Müller J, Alonso-Blanco C, Borgwardt K, Schmid KJ, Weigel D: Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 2011, 43:956-963.
• [12]Treangen TJ, Salzberg SL: Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 2011, 13:36-46.
• [13]Schneeberger K, Ossowski S, Ott F, Klein JD, Wang X, Lanz C, Smith LM, Cao J, Fitz J, Warthmann N, Henz SR, Huson DH, Weigel D: Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc Natl Acad Sci USA 2011, 108:10249-10254.
• [14]Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Rätsch G, Mott R: Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 2011, 477:419-423.
• [15]Bevan M: Genomics: endless variation most beautiful. Nature 2011, 477:415-416.
• [16]Jiménez-Gómez JM, Maloof JN: Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol 2009, 9:85. BioMed Central Full Text
• [17]Lunter G, Goodson M: Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 2011, 21:936-939.
• [18]Gremme G, Brendel V, Sparks ME, Kurtz S: Engineering a software tool for gene structure prediction in higher organisms. Inf Softw Technol 2005, 47:965-978.
• [19]Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones S, Marra M: Circos: an information aesthetic for comparative genomics. Genome Res 2009, 19:1639-1645.
• [20]Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of_Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 2012, 6:80-92.
• [21]Choi Y, Sims GE, Murphy S, Miller JR, Chan AP: Predicting the functional effect of amino acid substitutions and indels. PLOSOne 2012, 7:e46688.
• [22]Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, and 1000 Genome Project Data Processing Subgroup: The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 2009, 25:2078-2079.
• [23]Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26(6):841-842.
• [24]Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
• [25]Conesa A, Götz S, García-Gómez JM, Teroll J, Talónl M, Roblesl M: Blast2GO: a universal tool for annotation visualization and analysis in functional genomics research. Bioinformatics 2005, 21:3674-3676.
• [26]Du Z, Zhou X, Ling Y, Zhang Z, Su Z: agriGO: a GO analysis toolkit for the agricultural community. Nucl Acids Res 2012, 38:W64-W70.
• [27]Tipney H, Hunter L: An introduction to effective use of enrichment analysis software. Hum Genomics 2010, 4:202-206. BioMed Central Full Text
• [28]Hamilton JP, Sim SC, Stoffel K: Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. The Plant Genome 2012, 5:17-29.
• [29]Sim SC, Robbins MD, Van Deynze A, Michel AP, Francis DM: Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L). Heredity 2011, 106:927-935.
• [30]Sim SC, Van Deynze A, Stoffel K, Douches DS, Zarka D, Ganal MW, Chetelat RT, Hutton SF, Scott JW, Gardner RG, Panthee DR, Mutschler M, Myers JR, Francis DM: High-density SNP genotyping of tomato (Solanum lycopersicum L) reveals patterns of genetic variation due to breeding. PLOSOne 2012, 7:e45520.
• [31]Blanca J, Cañizares J, Cordero L, Pascual L, Diez MJ, Nuez F: Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato. PLOSOne 2012, 7:e48198.
• [32]Hirakawa H, Shirasawa K, Ohyama A, Fukuoka H, Aoki K, Rothan C, Sato S, Isobe S, Tabata S: Genome-wide SNP genotyping to infer the effects on Gene functions in tomato. DNA Res 2013, 20(3):221-233. doi:10.1093/dnares/dst005
• [33]McHale LK, Haun WJ, Xu WW, Bhaskar PB, Anderson JE, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM: Structural variants in the soybean genome localize to clusters of biotic stress-response genes. Plant Physiol 2012, 159:1295-1308.
• [34]Pavlidis P, Metzler D, Stephan W: Selective sweeps in multilocus models of quantitative traits. Genetics 2012, 192:225-239.
• [35]Zhong S, Fei Z, Chen YR, Zheng Y, Huang M, Vrebalov J, McQuinn R, Gapper N, Liu B, Xiang J, Shao Y, Giovannoni JJ: Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol 2013, 31:154-159.
• [36]Klee HJ, Giovannoni JJ: Genetics and control of tomato fruit ripening and quality attributes. Annu Rev Genet 2011, 45:41-59.
• [37]Tsuchisaka A, Yu G, Jin H, Alonso JM, Ecker JR, Zhang X, Gao S, Theologis A: A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana. Genetics 2009, 183:979-1003.
• [38]Matas A, Gapper N, Chung M, Giovannoni J, Rose JKC: Biology and genetic engineering of fruit maturation for enhanced quality and shelf-life. Curr Opin Biotech 2009, 20:197-203.
• [39]Ng PC, Henikoff S: Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 2006, 7:61-80.