Abstract
The US Pacific Northwest is the primary production region of black raspberry, and this high-value specialty crop has been underutilized for several decades. Black raspberries contain high levels of anthocyanins and other bioactive compounds, which has sparked a renewed interest in breeding programs and cultivation. Despite this potential, black raspberry stands have seen a marked decline that many attribute to disease pressures and only three new cultivars have been released over the last 20 years. Here we discuss the available genomic resources for black raspberry, including the recently released draft genome. These resources will expedite marker-assisted improvement of raspberry with applications across the Rosaceae family. The 243 Mb black raspberry genome was sequenced using an Illumina-based whole genome shotgun sequencing approach, and a chromosome-scale assembly was generated using a high-density genetic map. Black raspberry is the sixth genome to be sequenced in the Rosaceae facilitating in-depth comparative genomics across the family. Black raspberry and the diploid wild strawberry (Fragaria vesca) are largely collinear with some lineage-specific structural rearrangements. The genome has 28,005 genes which is comparable to other Rosaceae species and includes a number of recently duplicated genes which may be related to domestication. Gene expression atlases during fruit ripening and Verticillium inoculation provide insights into ripening and disease resistance, respectively. Together the resources discussed here will provide tools for the improved understanding and breeding of Rosaceae crops.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Alice LA (2002) Evolutionary relationships in Rubus (Rosaceae) based on molecular data. Acta Horticu (ISHS) 585:79–83
Anonymous (2015) National statistics for Raspberries. In: National Agricultural Statistics Service
Ash MM, Wolford KA, Carden TJ, Hwang KT, Carr TP (2011) Unrefined and refined black raspberry seed oils significantly lower triglycerides and moderately affect cholesterol metabolism in male Syrian hamsters. J Med Food 14:1032–1038
Bennetzen JL (2000) Transposable element contributions to plant gene and genome evolution. Plant Mol Biol 42:251–269
Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433–438
Bushakra JM, Bryant DW, Dossett M, Vining KJ, VanBuren R, Gilmore BS, Lee J, Mockler TC, Finn CE, Bassil NV (2015a) A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag 4 conferring resistance to the aphid Amphorophora agathonica. Theor Appl Genet 128:1631–1646
Bushakra JM, Lewers KS, Staton ME, Zhebentyayeva T, Saski CA (2015b) Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.). BMC Plant Biol 15:1–11
Bushakra JM, Stephens MJ, Atmadjaja AN, Lewers KS, Symonds VV, Udall JA, Chagné D, Buck EJ, Gardiner SE (2012) Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach. Theor Appl Genet 125:311–327
Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB (2008) ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 18:810–820
Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Alvarado AS, Yandell M (2008) MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res 18:188–196
Castro P, Stafne ET, Clark JR, Lewers KS (2013) Genetic map of the primocane-fruiting and thornless traits of tetraploid blackberry. Theor Appl Genet 126:2521–2532
Chagné D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, Ireland H, Fiers M, Dzierzon H, Cestaro A, Fontana P, Bianco L, Lu A, Storey R, Knäbel M, Saeed M, Montanari S, Kim YK, Nicolini D, Larger S, Stefani E, Allan AC, Bowen J, Harvey I, Johnston J, Malnoy M, Troggio M, Perchepied L, Sawyer G, Wiedow C, Won K, Viola R, Hellens RP, Brewer L, Bus VGM, Schaffer RJ, Gardiner SE, Velasco R (2014) The draft genome sequence of European pear (Pyrus communis L. ‘Bartlett’). PLoS ONE 9:e92644
Cook DE, Lee TG, Guo X, Melito S, Wang K, Bayless AM, Wang J, Hughes TJ, Willis DK, Clemente TE, Diers BW, Jiang J, Hudson ME, Bent AF (2012) Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science 338:1206–1209
de Oliveira Dal’Molin CG, Quek L-E, Palfreyman RW, Brumbley SM, Nielsen LK (2010) AraGEM, a genome-scale reconstruction of the primary metabolic network in arabidopsis. Plant Physiol 152:579–589
Dossett M (2011) Evaluation of genetic diversity in wild populations of black raspberry (Rubus occidentalis L.). Doctor of Philosophy. Oregon State University
Dossett M, Bassil NV, Finn CE (2010a) Transferability of Rubus microsatellite markers to black raspberry. Acta Hort. (ISHS) 859:103–109
Dossett M, Bassil NV, Lewers KS, Finn CE (2012) Genetic diversity in wild and cultivated black raspberry (Rubus occidentalis L.) evaluated by simple sequence repeat markers. Genet Resour Crop Evol 59:1849–1865
Dossett M, Finn CE (2010) Identification of resistance to the large raspberry aphid in black raspberry. J Am Soc Hortic Sci 135:438–444
Dossett M, Lee J, Finn CE (2008) Inheritance of phenological, vegetative, and fruit chemistry traits in black raspberry. J Am Soc Hortic Sci 133:408–417
Dossett M, Lee J, Finn CE (2010b) Variation in anthocyanins and total phenolics of black raspberry populations. J Funct Foods 2:292–297
Dossett M, Lee J, Finn CE (2011) Characterization of a novel anthocyanin profile in wild black raspberry mutants: an opportunity for studying the genetic control of pigment and color. J Funct Foods 3:207–214
Freialdenhoven A, Peterhansel C, Kurth J, Kreuzaler F, Schulze-Lefert P (1996) Identification of genes required for the function of non-race-specific mlo resistance to powdery mildew in barley. Plant Cell 8:5–14
Galletta GJ, Maas JL, Enns JM (1998) ‘Earlysweet’ black raspberry. Fruit Varieties J 52:123–124
Hedrick UP, Taylor OM, Berger A, Slate GL, Einset O (1925) The small fruits of New York. NY, J.B, Lyon Company, Printers, Albany
Hitchcock CL, Cronquist A (1973) Flora of the Pacific Northwest. University of Washington Press, Seattle
Ibarra-Laclette E, Lyons E, Hernández-Guzmán G, Pérez-Torres CA, Carretero-Paulet L, Chang T-H, Lan T, Welch AJ, Juárez MJA, Simpson J (2013) Architecture and evolution of a minute plant genome. Nature 498:94–98
International Rice Genome Sequencing Consortium (2005) The map-based sequence of the rice genome. Nature 436:793–800
Jennings DL (1988) Raspberries and blackberries: their breeding, diseases and growth. Academic Press, San Diego, CA
Jung S, Main D (2013) Genomics and bioinformatics resources for translational science in Rosaceae. Plant Biotechnol Rep 1–16
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645
Mayer KF, Rogers J, Doležel J, Pozniak C, Eversole K, Feuillet C, Gill B, Friebe B, Lukaszewski AJ, Sourdille P (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345:1251788
Mayes S, Massawe FJ, Alderson PG, Roberts JA, Azam-Ali SN, Hermann M (2011) The potential for underutilized crops to improve security of food production. J Exp Bot
Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, Sebra R, Peluso P, Eid J, Rank D (2013) Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol 14:R10
Melters DP, Paliulis LV, Korf IF, Chan SWL (2012) Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis. Chromosome Res 20:579–593
Meng R, Finn C (2002) Determining ploidy level and nuclear DNA content in Rubus by flow cytometry. J Am Soc Hortic Sci 127:767–775
Michael TP, VanBuren R (2015) Progress, challenges and the future of crop genomes. Curr Opin Plant Biol 24:71–81
Millen RS, Olmstead RG, Adams KL, Palmer JD, Lao NT, Heggie L, Kavanagh TA, Hibberd JM, Gray JC, Morden CW (2001) Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 13:645–658
Montrose DC, Horelik NA, Madigan JP, Stoner GD, Wang L-S, Bruno RS, Park HJ, Giardina C, Rosenberg DW (2011) Anti-inflammatory effects of freeze-dried black raspberry powder in ulcerative colitis. Carcinogenesis 32:343–350
Moyer RA, Hummer KE, Finn CE, Frei B, Wrolstad RE (2001) Anthocyanins, Phenolics, and Antioxidant capacity in diverse small fruits: Vaccinium, Rubus, and Ribes. J Agric Food Chem 50:519–525
Murray SL, Ingle RA, Petersen LN, Denby KJ (2007) Basal resistance against Pseudomonas syringae in Arabidopsis involves WRKY53 and a protein with homology to a nematode resistance protein. Mol Plant Microbe Interact 20:1431–1438
Naithani S, Partipilo CM, Raja R, Elser JL, Jaiswal P (2016) FragariaCyc: a metabolic pathway database for woodland strawberry Fragaria vesca. Front Plant Sci 7:242
Nakashima M, Hirano K, Nakashima S, Banno H, Nishihama R, Machida Y (1998) The expression pattern of the gene for NPK1 protein kinase related to mitogen-activated protein kinase kinase kinase (MAPKKK) in a tobacco plant: correlation with cell proliferation. Plant Cell Physiol 39:690–700
Ohno S (1970) Evolution by gene duplication. Springer, New York
Ourecky DK (1975) Brambles. In: Janick J, Moore JN (eds) Advances in fruit breeding. Purdue University Press, West Lafayette, IN, pp 98–129
Seeram NP, Momin RA, Nair MG, Bourquin LD (2001) Cyclooxygenase inhibitory and antioxidant cyanidin glycosides in cherries and berries. Phytomedicine 8:362–369
Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton J-M, Rees DJG, Williams KP, Holt SH, Rojas JJR, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman T-L, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Girona EL, Zdepski A, Wang W, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arús P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43:109–116
Stoner GD, Sardo C, Apseloff G, Mullet D, Wargo W, Pound V, Singh A, Sanders J, Aziz R, Casto B, Sun X (2005) Pharmacokinetics of anthocyanins and ellagic acid in healthy volunteers fed freeze-dried black raspberries daily for 7 days. J Clin Pharmacol 45:1153–1164
Straub S, Fishbein M, Livshultz T, Foster Z, Parks M, Weitemier K, Cronn R, Liston A (2011) Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing. BMC Genom 12:211
Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M (2011) Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics 12:1–11
Tennessen JA, Govindarajulu R, Ashman T-L, Liston A (2014) Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps. Genome Biol Evol 6:3295–3313
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796
Thomma BPHJ, Cammue BPA, Thevissen K (2002) Plant defensins. Planta 216:193–202
Thompson MM (1995) Chromosome numbers of Rubus cultivars at the national clonal germplasm repository. HortScience 30:1447–1456
Tulio AZ, Reese RN, Wyzgoski FJ, Rinaldi PL, Fu R, Scheerens JC, Miller AR (2008) Cyanidin 3-rutinoside and cyanidin 3-xylosylrutinoside as primary phenolic antioxidants in black raspberry. J Agric Food Chem 56:1880–1888
VanBuren R, Bryant D, Bushakra JM, Vining KJ, Edger PP, Rowley ER, Priest HD, Michael TP, Lyons E, Filichkin SA (2016) The genome of black raspberry (Rubus occidentalis). Plant J
Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagne D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouze P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel C-E, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R (2010) The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet 42:833–839
Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F, Zuccolo A, Rossini L, Jenkins J, Vendramin E, Meisel LA, Decroocq V, Sosinski B, Prochnik S, Mitros T, Policriti A, Cipriani G, Dondini L, Ficklin S, Goodstein DM, Xuan P, Fabbro CD, Aramini V, Copetti D, Gonzalez S, Horner DS, Falchi R, Lucas S, Mica E, Maldonado J, Lazzari B, Bielenberg D, Pirona R, Miculan M, Barakat A, Testolin R, Stella A, Tartarini S, Tonutti P, Arus P, Orellana A, Wells C, Main D, Vizzotto G, Silva H, Salamini F, Schmutz J, Morgante M, Rokhsar DS (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487–494
Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, Barry K, Lucas S, Harmon-Smith M, Lail K (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768
Wang S, Shi C, Gao L (2013) Plastid genome sequence of a wild woody oil species, prinsepia utilis, provides insights into evolutionary and mutational patterns of rosaceae chloroplast genomes. PLoS One 8
Wang SY, Lin H-S (2000) Antioxidant activity in fruits and leaves of blackberry, raspberry, and strawberry varies with cultivar and developmental stage. J Agric Food Chem 48:140–146
Weber CA (2003) Genetic diversity in black raspberry detected by RAPD markers. HortScience 38:269–272
Woodhead M, Weir A, Smith K, McCallum S, MacKenzie K, Graham J (2010) Functional markers for red raspberry. J Am Soc Hortic Sci 135:418–427
Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, Wang H (2013a) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23:396–408
Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, Wang H, Chen NJ, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, Deng C, Gou C, Zhou W, Yin H, Qin G, Sha Y, Tao Y, Chen H, Yang Y, Song Y, Zhan D, Wang J, Li L, Dai M, Gu C, Wang Y, Shi D, Wang X, Zhang H, Zeng L, Zheng D, Wang C, Chen M, Wang G, Xie L, Sovero V, Sha S, Huang W, Zhang S, Zhang M, Sun J, Xu L, Li Y, Liu X, Li Q, Shen J, Wang J, Paull RE, Bennetzen JL, Wang J, Zhang S (2013b) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23:396–408
Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E (2008) A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319:1527–1530
Yan M, Dai T, Deak JC, Kyriakis JM, Zon LI, Woodgett JR, Templeton DJ (1994) Activation of stress-activated protein kinase by MEKK1 phosphorylation of its activator SEK1. Nature 372:798–800
Zhang Q, Chen W, Sun L, Zhao F, Huang B, Yang W, Tao Y, Wang J, Yuan Z, Fan G, Xing Z, Han C, Pan H, Zhong X, Shi W, Liang X, Du D, Sun F, Xu Z, Hao R, Lv T, Lv Y, Zheng Z, Sun M, Luo L, Cai M, Gao Y, Wang J, Yin Y, Xu X, Cheng T, Wang J (2012) The genome of Prunus mume. Nat Commun 3:8
Zhang Z, Knobloch TJ, Seamon LG, Stoner GD, Cohn DE, Paskett ED, Fowler JM, Weghorst CM (2011) A black raspberry extract inhibits proliferation and regulates apoptosis in cervical cancer cells. Gynecol Oncol 123:401–406
Zikri NN, Riedl KM, Wang L-S, Lechner J, Schwartz SJ, Stoner GD (2009) Black raspberry components inhibit proliferation, induce apoptosis, and modulate gene expression in rat esophageal epithelial cells. Nutr Cancer 61:816–826
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG, part of Springer Nature
About this chapter
Cite this chapter
VanBuren, R. et al. (2018). Sequence and Analysis of the Black Raspberry (Rubus occidentalis) Genome. In: Hytönen, T., Graham, J., Harrison, R. (eds) The Genomes of Rosaceous Berries and Their Wild Relatives. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-76020-9_13
Download citation
DOI: https://doi.org/10.1007/978-3-319-76020-9_13
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-76019-3
Online ISBN: 978-3-319-76020-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)