Abstract
Fragaria L. and Rubus L. are two Rosaceae genera with strikingly different levels of taxonomic diversity (20 vs. ~500 species, respectively), yet with similar processes likely at play in their evolution—polyploidisation, hybridisation and apomixis. Each genus contains important soft fruit crops—garden strawberry in Fragaria, red raspberry and blackberries in Rubus. Furthermore, congeneric wild species have been used as a source of agronomically beneficial alleles. Both Rubus and Fragaria display well-supported monophyly, but resolution below the subgenus level in Rubus and beyond the two main clades in Fragaria is limited. More comprehensive sampling of plant genomes at a population level combined with more sophisticated models of phylogenetic inference is required for complete detangling of the reticulate genealogies in Fragaria and Rubus.
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References
Alice LA, Campbell CS (1999) Phylogeny of Rubus (Rosaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences. Am J Bot 86:81–97
Alice LA, Dodson TM, Sutherland BL (2008) Diversity and relationships of Bhutanese Rubus (Rosaceae). Acta Hortic 777:63–69. https://doi.org/10.17660/ActaHortic.2008.777.5
Alice LA, Eriksson T, Eriksen B et al (2001) Hybridization and gene flow between distantly related species of Rubus (Rosaceae): evidence from nuclear ribosomal DNA internal transcribed spacer region sequences. Syst Bot 26:769–778
Amsellem L, Noyer J-L, Hossaert-McKey M (2001) Evidence for a switch in the reproductive biology of Rubus alceifolius (Rosaceae) towards apomixis, between its native range and its area of introduction. Am J Bot 88:2243–2251
Bors RH, Sullivan JA (2005a) Interspecific hybridization of Fragaria moschata with two diploid species, F. nubicola and F. viridis. Euphytica 143:201–207
Bors RH, Sullivan JA (2005b) Interspecific hybridization of Fragaria vesca subspecies with F. nilgerrensis, F. nubicola, F. pentaphylla, and F. viridis. J Am Soc Hortic Sci 130:418–423
Briggs JB, Danek J, Lyth M et al (1982) Resistance to the raspberry beetle, Byturus tomentosus, in Rubus species and their hybrid derivatives with R. idaeus. J Hort Sci 57:73–78
Bringhurst RS (1990) Cytogenetics and evolution in American Fragaria. HortScience 25:879–881
Bringhurst RS, Gill T (1970) Origin of Fragaria polyploids. II. Unreduced and doubled-unreduced gametes. Am J Bot 57:969–976
Bringhurst RS, Khan DA (1963) Natural pentaploid Fragaria chiloensis-F. vesca hybrids in coastal California and their significance in polyploid Fragaria evolution. Am J Bot 50:658–661
Caplan JS, Yeakley JA (2010) Water relations advantages for invasive Rubus armeniacus over two native ruderal congeners. Plant Ecol 210:169–179
Clark LV, Jasieniuk M (2012) Spontaneous hybrids between native and exotic Rubus in the Western United States produce offspring both by apomixis and by sexual recombination. Heredity 109:320–328
Clark JR, Stafne ET, Hall HK et al (2011) Blackberry breeding and genetics. Fruit Veg Cereal Sci Biotechnol 5:27–43
Clark LV, Evans KJ, Jasieniuk M (2013) Origins and distribution of invasive Rubus fruticosus L. agg. (Rosaceae) clones in the Western United States. Biol Invasions 15:1331–1342
Degnan JH, Rosenberg NA (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol 24:332–340
DeVore ML, Pigg KB (2007) A brief review of the fossil history of the family Rosaceae with a focus on the Eocene Okanogan Highlands of eastern Washington State, USA, and British Columbia, Canada. Plant Syst Evol 266:45–57
Dickinson TA, Lo E, Talent N (2007) Polyploidy, reproductive biology, and Rosaceae: understanding evolution and making classifications. Plant Syst Evol 266:59–78
DiMeglio LM, Staudt G, Yu H et al (2014) A phylogenetic analysis of the genus Fragaria (strawberry) using intron-containing sequence from the ADH-1 gene. PLoS ONE 9:e102237
Eriksson T, Donoghue MJ, Hibbs MS (1998) Phylogenetic analysis of Potentilla using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS), and implications for the classification of Rosoideae (Rosaceae). Plant Syst Evol 211:155–179
Evans KJ, Symon DE, Whalen MA et al (2007) Systematics of the Rubus fruticosus aggregate (Rosaceae) and other exotic Rubus taxa in Australia. Aust Syst Bot 20:187–251
Focke WO (1914) Species Ruborum. Monographiae Generis Rubi Prodromus part I. Schweizerbart, Stuttgart
Folta KM, Davis TM (2006) Strawberry genes and genomics. Crit Rev Plant Sci 25:399–415
Govindarajulu R, Parks M, Tennessen JA et al (2015) Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species. Am J Bot 102:544–554
Gu Y, Wang C, Zhao C et al (1995) Evaluation of Rubus genetic resources. J Plant Resour Environ 5:6–13
Harrison RE, Luby JJ, Furnier GR (1997) Chloroplast DNA restriction fragment variation among strawberry (Fragaria spp.) taxa. J Am Soc Hortic Sci 122:63–68
Hokanson KE, Smith MJ, Connor AM et al (2006) Relationships among subspecies of New World octoploid strawberry species, Fragaria virginiana and Fragaria chiloensis, based on simple sequence repeat marker analysis. Can J Bot 84:1829–1841
Howarth DG, Gardner DE, Morden CW (1997) Phylogeny of Rubus subgenus Idaeobatus (Rosaceae) and its implications toward colonization of the Hawaiian Islands. Syst Bot 22:433–441
Hummer KE (2012) A new species of Fragaria (Rosaceae) from Oregon. J Bot Res Inst Texas 6:9–15
Hummer KE, Nathewet P, Yanagi T (2009) Decaploidy in Fragaria iturupensis (Rosaceae). Am J Bot 96:713–716
Hummer KE, Bassil N, Njuguna W (2011) Genomic and breeding resources. In: Kole C (ed) Wild crop relatives. Springer, Berlin, pp 17–44
Illa E, Sargent DJ, Girona EL et al (2011) Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family. BMC Evol Biol 11:9
Jennings DL (1988) Raspberries and blackberries: their breeding, diseases and growth. Academic Press, London
Kalkman C (2004) Flowering plants—dicotyledons. The families and genera of vascular plants, vol 6. Springer, Berlin, pp 343–386
Kamneva OK, Syring J, Liston A et al (2017) Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing. BMC Evol Biol 17:180
Keep E, Knight VH, Parker JH (1977) Rubus coreanus as donor of resistance to cane diseases and mildew in red raspberry breeding. Euphytica 26:505–510
Korpelainen H, Antonius-Klemola K, Werlemark G (1999) Clonal structure of Rubus chamaemorus populations: comparison of different molecular methods. Plant Ecol 143:123–128
Kraft T, Nybom H, Werlemark G (1995) Rubus vestervicensis (Rosaceae)—its hybrid origin revealed by DNA fingerprinting. Nord J Bot 15:237–242
Lin J, Davis TM (2000) S1 analysis of long PCR heteroduplexes: detection of chloroplast indel polymorphisms in Fragaria. Theor Appl Genet 101:415–420
Liston A, Cronn R, Ashman TL (2014) Fragaria: a genus with deep historical roots and ripe for evolutionary and ecological insights. Am J Bot 101:1686–1699
Lu LD (1983) A study on the genus Rubus of China. J Syst Evol 21:13–25
Lu LD, Boufford DE (2003) Rosaceae. In: Wu ZY, Raven PH (eds) Flora of China, vol 9. Missouri Botanical Garden Press, St. Louis, pp 195–285
Lundberg M, Töpel M, Eriksen B et al (2009) Allopolyploidy in Fragariinae (Rosaceae): comparing four DNA sequence regions, with comments on classification. Mol Phylogenet Evol 51:269–280
Mahoney LL, Quimby ML, Shields ME et al (2009) Mitochondrial DNA transmission, ancestry, and sequences in Fragaria. Acta Hort 859:301–308
Meng R, Finn C (2002) Determining ploidy level and nuclear DNA content in Rubus by flow cytometry. J Am Soc Hort Sci 127:767–775
Mimura M, Mishima M, Lascoux M et al (2014) Range shift and introgression of the rear and leading populations in two ecologically distinct Rubus species. BMC Evol Biol 14:1
Miyashita T, Kunitake H, Yotsukura N et al (2015) Assessment of genetic relationships among cultivated and wild Rubus accessions using AFLP markers. Sci Hort 193:165–173
Morden CW, Gardner DE, Weniger DA (2003) Phylogeny and biogeography of Pacific Rubus subgenus Idaeobatus (Rosaceae) species: investigating the origin of the endemic Hawaiian raspberry R. macraei. Pacific Sci 57:181–197
Morgan R (1994) Systematic and evolutionary implications of rbcl sequence variation in Rosaceae. Am J Bot 81:890–903
Morrison DA (2014) Is the tree of life the best metaphor, model, or heuristic for phylogenetics? Syst Biol 63:628–638
Naruhashi N, Iwatsubo Y, Peng C-I (2002) Chromosome numbers in Rubus (Rosaceae) of Taiwan. Bot Bull Acad Sin 43:193–201
Njuguna W, Liston A, Cronn R et al (2013) Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing. Mol Phylogenet Evol 66:17–29
Noguchi Y, Mochizuki T, Sone K (2002) Breeding of a new aromatic strawberry by interspecific hybridization Fragaria × ananassa × F. nilgerrensis. J Jpn Soc Hortic Sci 71:208–213
Nybom H, Schaal BA (1990) DNA‘ fingerprints’ reveal genotypic distributions in natural populations of blackberries and raspberries (Rubus, Rosaceae). Am J Bot 77:883–888
Potter D, Luby JJ, Harrison RE (2000) Phylogenetic relationships among species of Fragaria (Rosaceae) inferred from non-coding nuclear and chloroplast DNA sequences. Syst Bot 25:337
Potter D, Gao F, Bortiri EP et al (2002) Phylogenetic relationships in Rosaceae inferred from chloroplast matK and trnL-trnF nucleotide sequence data. Plant Syst Evol 231:77–89
Potter D, Eriksson T, Evans RC et al (2007) Phylogeny and classification of Rosaceae. Plant Syst Evol 266:5–43
Qiao Q, Xue Li, Wang Q et al (2016) Comparative transcriptomics of strawberries (Fragaria spp.) provides insights into evolutionary patterns. Front Plant Sci 7:1–10
Rousseau-Gueutin M, Lerceteau-Köhler E, Barrot L et al (2008) Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of colinearity between their genomes and the essentially disomic behavior of the cultivated octoploid strawberry. Genetics 179:2045–2060
Rousseau-Gueutin M, Gaston A, Aïnouche A et al (2009) Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): new insights from phylogenetic analyses of low-copy nuclear genes. Mol Phylogenet Evol 51:515–530
Sargent DJ (2005) A genetic investigation of diploid Fragaria. University of Reading
Sargent DJ, Geibel M, Hawkins JA et al (2004) Quantitative and qualitative differences in morphological traits revealed between diploid Fragaria species. Ann Bot 94:787–796
Sargent DJ, Yang Y, Šurbanovski N et al (2015) HaploSNP affinities and linkage map positions illuminate subgenome composition in the octoploid, cultivated strawberry (Fragaria × ananassa). Plant Sci 242:140–150
Šarhanová P, Sharbel TF, Sochor M et al (2017) Hybridization drives evolution of apomicts in Rubus subgenus Rubus: evidence from microsatellite markers. Ann Bot 120:317–328
Schulze-Menz GK (1964) Rosaceae. Gebru der Borntraeger, Stuttgart
Sochor M, Vašut RJ, Sharbel TF et al (2015) How just a few makes a lot: Speciation via reticulation and apomixis on example of European brambles (Rubus subgen. Rubus, Rosaceae). Mol Phylogenet Evol 89:13–27
Staudt G (2008) Strawberry biogeography, genetics and systematics. Acta Hort 842:71–84
Staudt G, Dickoré WB (2001) Notes on Asiatic Fragaria species: Fragaria pentaphylla Losinsk. and Fragaria tibetica spec. nov. Bot Jahrbücher 123:341–354
Staudt G, Olbricht K (2008) Notes on Asiatic Fragaria species V: F. nipponica and F. iturupensis. Bot Jahrbücher 127:317–341
Tennessen JA, Govindarajulu R, Ashman T-L et al (2014) Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps. Genome Biol Evol 6:3295–3313
Thompson MM (1995) Chromosome numbers of Rubus species at the national clonal germplasm repository. HortScience 30:1447–1452
Thompson MM (1997) Survey of chromosome numbers in Rubus (Rosaceae: Rosoideae). Ann Missouri Bot Gard 84:128–164
Vamosi JC, Dickinson TA (2006) Polyploidy and diversification: a phylogenetic investigation in Rosaceae. Int J Plant Sci 167:349–358
Wang X-R, Tang H-R, Duan J et al (2008) A comparative study on karyotypes of 28 taxa in Rubus sect. Idaeobatus and sect. Malachobatus (Rosaceae) from China. J Syst Evol 46:505–515
Wang X, Liu Y, Zhong B et al (2010) Cytological and RAPD data revealed genetic relationships among nine selected populations of the wild bramble species, Rubus parvifolius and R. coreanus (Rosaceae). Genet Resour Crop Evol 57:431–441
Wang Y, Wang X, Chen Q et al (2015) Phylogenetic insight into subgenera Idaeobatus and Malachobatus (Rubus, Rosaceae) inferring from ISH analysis. Mol Cytogenet 8:11
Wang Y, Chen Q, Chen T et al (2016) Phylogenetic insights into Chinese Rubus (Rosaceae) from multiple chloroplast and nuclear DNAs. Front Plant Sci 7:1–13
Weber HE (1996) Former and modern taxonomic treatment of the apomictic Rubus complex. Folia Geobot 31:373–380
Wei N, Tennessen JA, Liston A et al (2017) Present-day sympatry belies the evolutionary origin of a high-order polyploid. New Phytol 216:279–290
Xiang Y, Huang C-H, Hu Y et al (2017) Evolution of Rosaceae fruit types based on nuclear phylogeny in the context of geological times and genome duplication. Mol Biol Evol 34:262–281
Yang Y, Davis TM (2017) A new perspective on polyploid Fragaria (strawberry) genome composition based on large-scale, multi-locus phylogenetic analysis. Genome Biol Evol
Yang JY, Pak J-H (2006) Phylogeny of Korean Rubus (Rosaceae) based on ITS (nrDNA) and trnL/F intergenic region (cpDNA). J Plant Biol 49:44–54
Yü DJ, Lu LD, Gu CZ et al (1985) Rosaceae. In: Flora Republicae Popularis Sinicae, vol 38. Science Press, pp 10–218
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Sobczyk, M.K. (2018). Phylogenetics of Fragaria, Rubus and Related Taxa. 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_2
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