Abstract
Though grape transcriptomics has expanded dramatically over the last ten years, few additional novel genomic resources were developed since the release of the PN40024 reference genome in 2007. This is partly because of the difficulty associated with assembling grape genomes. Despite a relatively small genome size of ~500 Mb and modest repeat content, high sequence and structural heterozygosity makes assembling grape genomes particularly challenging. Without assemblies representative of the genetic diversity within the cultivated germplasm, identifying cultivar-specific functions not represented in the PN40024 genome has remained elusive. Now, third-generation sequencing technologies and long-range scaffolding methods have made it possible to relatively inexpensively and rapidly generate highly contiguous and complete grape genomes. This chapter will describe the challenges associated with the isolation of high-quality nucleic acids suitable for long-read sequencing and provide an overview of the sequencing and assembling approaches that can be used to successfully reconstruct grape genomes.
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References
Aigrain L, Gu Y, Quail MA (2016) Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays a systematic comparison of DNA library preparation kits for Illumina sequencing. BMC Genom 17:458
An D, Cao HX, Li C, Humbeck K, Wang W (2018) Isoform sequencing and state-of-art applications for unravelling complexity of plant transcriptomes. Genes 9(1):43. https://doi.org/10.3390/genes9010043
Aradhya MK, Dang GS, Prins BH et al (2003) Genetic structure and differentiation in cultivated grape Vitis vinifera L. Genet Res 81:179–192. https://doi.org/10.1017/s0016672303006177
Aranda PS, LaJoie DM, Jorcyk CL (2012) Bleach gel: a simple agarose gel for analyzing RNA quality. Electrophoresis 33(2):366–369
Argout X, Salse J, Aury JM et al (2011) The genome of Theobroma cacao. Nat Genet 43:101–108. https://doi.org/10.1038/ng.736
Ausubel FM, Brent R, Kingston et al (1994) Current protocols in molecular biology. Wiley, New York, pp 2.0.1–2.14.8
Bhattacharjee R, Kolesnikova-Allen M, Aikpokpodion P, Taiwo S, Ingelbrecht I (2004) A semi-automated rapid method of extracting genomic DNA for molecular marker analysis in cocoa, Theobroma cacao L. Plant Mol Biol Report 22:435a–435h458
Blanco-Ulate B, Hopfer H, Figueroa-Balderas R et al (2017) Red blotch disease alters grape berry development and metabolism by interfering with the transcriptional and hormonal regulation of ripening. J Exp Bot 68(5):1225–1238
Bradnam KR, Fass JN, Alexandrov A et al (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience 2:10
Braidot E, Zancani M, Petrussa E et al (2008) Transport and accumulation of flavonoids in grapevine (Vitis vinifera L.). Plant Signal Behav 3(9):626–632
Cardone MF, D’Addabbo P, Alkan C et al (2016) Inter-varietal structural variation in grapevine genomes. Plant J 88:648–661
Cheng SH, Moore BD, Seemann JR (2000) Purification of uncontaminated, intact plant RNA. In: Rapley R (ed) The nucleic acid protocols handbook. Humana Press, Totowa
Chin CS, Peluso P, Sedlazeck FJ et al (2016) Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 13:1050–1054. https://doi.org/10.1038/nmeth.4035
Chin CS, Alexander DH, Marks P et al (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10(6):563–569. https://doi.org/10.1038/nmeth.2474
Claros MG, Bautista R, Guerrero-Fernández D et al (2012) Why assembling plant genome sequences is so challenging. Biology (Basel) 1:439–459. https://doi.org/10.3390/biology1020439
Costello M, Pugh TJ, Fennell TJ et al (2013) Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation. Nucleic Acids Res 41(6):e67
Couch JA, Fritz PJ (1990) Isolation of DNA from plants high in polyphenolics. Plant Mol Biol Rep 8:8–12
Da Silva C, Zamperin G, Ferrarini A et al (2013) The high polyphenol content of grapevine cultivar tannat berries is conferred primarily by genes that are not shared with the reference genome. Plant Cell 25:4777–4788. https://doi.org/10.1105/tpc.113.118810
Di Genova A, Almeida AM, Muñoz-Espinoza C et al (2014) Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants. BMC Plant Biol 14:7. https://doi.org/10.1186/1471-2229-14-7
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Earl D, Bradnam K, St. John JN et al (2011) Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res 21:2224–2241. https://doi.org/10.1101/gr.126599.111
Edwards D, Batley J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnol J 8:2–9. https://doi.org/10.1111/j.1467-7652.2009.00459.x
Ekblom R, Wolf JBW (2014) A field guide to whole-genome sequencing, assembly and annotation. Evol Appl. https://doi.org/10.1111/eva.12178
Endrullat C, Glökler J, Franke P, Frohme M (2016) Standardization and quality management in next-generation sequencing. Appl Transl Genom 10:2–9. https://doi.org/10.1016/j.atg.2016.06.001
Fang G, Hammar S, Grumet R (1992) A quick and inexpensive method for removing polysaccharides from plant genomic DNA. Biotechniques 13(1):52–54
Feuillet C, Leach JE, Rogers J et al (2011) Crop genome sequencing: lessons and rationales. Trends Plant Sci 16:77–88. https://doi.org/10.1016/j.tplants.2010.10.005
Gambino G, Dal Molin A, Boccacci P et al (2017) Whole-genome sequencing and SNV genotyping of ‘Nebbiolo’ (Vitis vinifera L.) clones. Sci Rep 7:17294
Goff SA, Ricke D, Lan T-H et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100. https://doi.org/10.1126/science.1068275
Green MR, Sambrook J (2016) Precipitation of DNA with ethanol. Cold Spring Harb Protoc. https://doi.org/10.1101/pdb.prot093377
Green MR, Sambrook J (2017) Precipitation of DNA with isopropanol. Cold Spring Harb Protoc. https://doi.org/10.1101/pdb.prot093385
Guzmán P, Ecker JR (1988) Development of large DNA methods for plants: molecular cloning of large segments of Arabidopsis and carrot DNA into yeast. Nucleic Acids Res 16(23):11091–11105
Hanania U, Velcheva M, Sahar N et al (2004) An improved method for isolating high-quality DNA vitis nuclei. Plant Mol Biol Rep 22:173–177
Healy A, Furtado A, Cooper T, Henry R (2014) Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods 10(1):1–8
Heptinstall J, Rapley R (2000) Spectrophotometric analysis of nucleic acids. In: Rapley R (ed) The Nucleic acid protocols handbook. Humana Press, Totowa
Hyma KE, Barba P, Wang M et al (2015) Heterozygous mapping strategy (HetMappS) for high resolution genotyping-by-sequencing markers: a case study in grapevine (N. A. Tinker, Ed.). PLoS ONE 10:e0134880
Iandolino AB, Goes da Silva F, Lim H, Choi H, Williams LE, Cook DR (2004) High-quality Rna, cDNA, and derived EST libraries from grapevine (Vitis vinifera L.). Plant Mol Biol Rep 22:269–278
Jaillon O, Aury J-M, Noel B et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467. https://doi.org/10.1038/nature06148
Japelaghi RH, Haddad R, Garoosi GA (2011) Rapid and efficient isolation of high quality nucleic acids from plant tissues rich in polyphenols and polysaccharides. Mol Biotechnol 49:129–137. https://doi.org/10.1007/s12033-011-9384-8
Jiao C, Gao M, Wang X, Fei Z (2015) Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes. BMC Genom 16:223
Kajitani R, Toshimoto K, Noguchi H et al (2014) Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 24:1384–1395. https://doi.org/10.1101/gr.170720.113
Kim CS, Lee CH, Shin JS, Chung YS, Hyung NI (1997) A simple and rapid method for isolation of high quality genomic DNA from fruit trees and conifers using PVP. Nucleic Acids Res 25:1085–1086
Knebelsberger T, Stöger I (2012) DNA extraction, preservation, and amplification. In: Kress W, Erickson D (eds) DNA Barcodes. Methods in molecular biology (methods and protocols). Humana Press, Totowa
Laucou V, Lacombe T, Dechesne F et al (2011) High throughput analysis of grape genetic diversity as a tool for germplasm collection management. Theor Appl Genet 122(6):1233–1245
Lodhi MA, Ye G-N, Weeden NF, Reisch BI (1994) A simple and efficient method for DNA extraction from grapevine cultivars and Vitis species. Plant Mol Biol Rep 12:6–13
Lutz KA, Wang W, Zdepski A, Michael TP (2011) Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing. BMC Biotechnol 11:54. https://doi.org/10.1186/1472-6750-11-54
Maliyakal JE (1992) An efficient method for isolation of RNA and DNA from plants containing polyphenolics. Nucleic Acids Res 20:2381
Marsal G, Baiges I, Canals JM, Zamora F, Fort F (2013) Comparison of the efficiency of some of the most usual DNA extraction methods for woody plants in different tissues of Vitis vinifera L. J Int Sci Vigne Vin 47:227–237
Massonnet M, Fasoli M, Tornielli GB et al (2017) Ripening transcriptomic program in red and white grapevine varieties correlates with berry skin anthocyanin accumulation. Plant Physiol 174(4):2376–2396
Mayjonade B, Gouzy J, Donnadieu C et al (2016) Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules. Biotechniques 61:203–205. https://doi.org/10.2144/000114460
Michael TP, Jackson S (2013) The first 50 plant genomes. Plant Genome 6:1–7
Minio A, Lin J, Gaut BS, Cantu D (2017) How single molecule real-time sequencing and haplotype phasing have enabled reference-grade diploid genome assembly of wine grapes. Front Plant Sci 8:1–6. https://doi.org/10.3389/fpls.2017.00826
Minio A, Massonnet M, Figueroa-Balderas R et al (2019a) Iso-seq allows genome-independent transcriptome profiling of grape berry development. G3 Genes Genomes Genet 9:755–767
Minio A, Massonnet M, Figueroa-Balderas R et al (2019b) Diploid genome assembly of the wine grape carmenere. G3 Genes Genomes Genet 9:1331–1337
Morrell PL, Buckler ES, Ross-Ibarra J (2012) Crop genomics: advances and applications. Nat Rev Genet 13(2):85–96. https://doi.org/10.1038/nrg3097
Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight DNA. Nucleic Acids Res 8:4321–4325
Myles S, Chia J-M, Hurwitz B et al (2010) Rapid genomic characterization of the genus Vitis. PLoS ONE 5:e8219. https://doi.org/10.1371/journal.pone.0008219
Nakayama Y, Yamaguchi H, Einaga N, Esumi M (2016) Pitfalls of DNA quantification using DNA-binding fluorescent dyes and suggested solutions. PLoS ONE 11(3):e0150528. https://doi.org/10.1371/journal.pone.0150528
Newbury HJ, Possingham JV (1977) Factors affecting the extraction of intact ribonucleic acid from plant tissues containing interfering phenolic compounds. Plant Physiol 60:543–547
Pendleton M, Sebra R, Pang AWC et al (2015) Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods 12:780–786
Peterson DG, Boehm KS, Stack SM (1997) Isolation of milligram quantities of nuclear DNA from tomato (Lycopersicon esculentum), a plant containing high levels of polyphenolic compounds. Plant Mol Biol Rep 15(2):148–153
Pryszcz LP, Gabaldón T (2016) Redundans: An assembly pipeline for highly heterozygous genomes. Nucleic Acids Res 44:e113. https://doi.org/10.1093/nar/gkw294
Reid KE, Olsson N, Schlosser J, Peng F, Lund ST (2006) An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development. BMC Plant Biol 6:27. https://doi.org/10.1186/1471-2229-6-27
Rezadoost MH, Kordrostami M, Kumleh HH (2016) An efficient protocol for isolation of inhibitor-free nucleic acids even from recalcitrant plants. 3 Biotech 6(1):61
Ribeiro RA, Lovato MB (2007) Comparative analysis of different DNA extraction protocols in fresh and herbarium specimens of the genus Dalbergia. Gen Mol Res 6:173–187
Roach MJ, Johnson DL, Bohlmann J et al (2018) Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. PLoS Genet 14:e1007807. https://doi.org/10.1371/journal.pgen.1007807
Romieu C (2010) RNA extraction from young, acidic berries and other organs from Vitis vinifera L. In: Delrot S, Medrano H, Or E, Bavaresco L, Grando S (eds) Methodologies and results in grapevine research. Springer, Dordrecht
Ruan J, Li H (2019) Fast and accurate long-read assembly with wtdbg2. BioRxiv, 530972. https://doi.org/10.1101/530972
Safonova Y, Bankevich A, Pevzner PA (2015) dipSPAdes: assembler for highly polymorphic diploid genomes. J Comput Biol A J Comput Mol Cell Biol 22:528–545. https://doi.org/10.1089/cmb.2014.0153
Sahu SK, Thangaraj M, Kathiresan K (2012) DNA extraction protocol for plants with high levels of secondary metabolites and polysaccharides without using liquid nitrogen and phenol. ISRN Mol Biol 2012:205049. https://doi.org/10.5402/2012/205049
Sharma AD, Gill PK, Singh P (2002) DNA isolation from dry and fresh samples of polysaccharide-rich plants. Plant Mol Biol Rep 20:415. https://doi.org/10.1007/BF02772129
Simão FA, Waterhouse RM, Ioannidis P et al (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. https://doi.org/10.1093/bioinformatics/btv351
Tan ZJ, Chen SJ (2005) Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length. Biophys J 90(4):1175–1190
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
Thottathil GP, Jayasekaran K, Othman AS (2016) Sequencing crop genomes: a gateway to improve tropical agriculture. Trop Life Sci Res. https://doi.org/10.1111/evo.12191.1
Tuskan GA, Difazio S, Jansson S et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793):1596–1604
VanBuren R, Bryant D, Edger PP et al (2015) Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature 527:508–511
Varma A, Padh H, Shrivastava N (2007) Plant genomic DNA isolation: an art or a science. Biotechnol J 2:386–392
Velasco R, Zharkikh A, Troggio M et al (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2:e1326. https://doi.org/10.1371/journal.pone.0001326
Venturini L, Ferrarini A, Zenoni S et al (2013) De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity. BMC Genom 14:41. https://doi.org/10.1186/1471-2164-14-41
Walenz BP, Koren S, Bergman et al (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27(5):722–736. https://doi.org/10.1101/gr.215087.116
Xiao H, Kim WS, Meng B (2015) A highly effective and versatile technology for the isolation of RNAs from grapevines and other woody perennials for use in virus diagnostics. Virol J 12:171. https://doi.org/10.1186/s12985-015-0376-3
Yang C, Li F, Ji X, Wang J (2011) An effective method for RNA extraction from grapevine berry skins. Afr J Biotechnol 10(45):9032–9035
Yang S, Fresnedo-Ramírez J, Wang M et al (2016) A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine. Hortic Res 3:16002. https://doi.org/10.1038/hortres.2016.2
Yockteng R, Almeida AM, Yee S, Andre T, Hill C, Specht CD (2013) A method for extracting high-quality RNA from diverse plants for next-generation sequencing and gene expression analyses. Appl Plant Sci. https://doi.org/10.3732/apps.1300070
Yu J, Wang J, Lin W et al (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3:e38. https://doi.org/10.1371/journal.pbio.0030038
Zhou Y, Massonnet M, Sanjak JS et al (2017) Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication. Proc Natl Acad Sci USA 114:11715–11720. https://doi.org/10.1073/pnas.1709257114
Zhou Y, Minio A, Massonnet M, et al (2018) Structural variants, clonal propagation, and genome evolution in grapevine (Vitis vinifera). bioRxiv 508119; doi:https://doi.org/10.1101/508119
Acknowledgements
This work was supported by J. Lohr Vineyards and Wines, E. & J. Gallo Winery, Dolce Winery, the Louis P. Martini Endowment in Viticulture, and the NSF Grant #1741627. Part of this work was carried out in collaboration with UC Davis Chile and funded by the Chilean Economic Development Agency (CORFO).
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Figueroa-Balderas, R., Minio, A., Morales-Cruz, A., Vondras, A.M., Cantu, D. (2019). Strategies for Sequencing and Assembling Grapevine Genomes. In: Cantu, D., Walker, M. (eds) The Grape Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-18601-2_5
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