Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

BMC Evolutionary Biology

Aaron Liston²  Richard Cronn¹  Matthew Parks² 

[1] Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR 97331, USA;Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-2902, USA

关键词: Chloroplast;    Pinus;    Plastome;    Phylogenetic noise;   

Others  :  1140964
DOI  :  10.1186/1471-2148-12-100

 received in 2012-01-19, accepted in 2012-06-14,  发布年份 2012

【 摘 要 】

Background

Through next-generation sequencing, the amount of sequence data potentially available for phylogenetic analyses has increased exponentially in recent years. Simultaneously, the risk of incorporating ‘noisy’ data with misleading phylogenetic signal has also increased, and may disproportionately influence the topology of weakly supported nodes and lineages featuring rapid radiations and/or elevated rates of evolution.

Results

We investigated the influence of phylogenetic noise in large data sets by applying two fundamental strategies, variable site removal and long-branch exclusion, to the phylogenetic analysis of a full plastome alignment of 107 species of Pinus and six Pinaceae outgroups. While high overall phylogenetic resolution resulted from inclusion of all data, three historically recalcitrant nodes remained conflicted with previous analyses. Close investigation of these nodes revealed dramatically different responses to data removal. Whereas topological resolution and bootstrap support for two clades peaked with removal of highly variable sites, the third clade resolved most strongly when all sites were included. Similar trends were observed using long-branch exclusion, but patterns were neither as strong nor as clear. When compared to previous phylogenetic analyses of nuclear loci and morphological data, the most highly supported topologies seen in Pinus plastome analysis are congruent for the two clades gaining support from variable site removal and long-branch exclusion, but in conflict for the clade with highest support from the full data set.

Conclusions

These results suggest that removal of misleading signal in phylogenomic datasets can result not only in increased resolution for poorly supported nodes, but may serve as a tool for identifying erroneous yet highly supported topologies. For Pinus chloroplast genomes, removal of variable sites appears to be more effective than long-branch exclusion for clarifying phylogenetic hypotheses.

【 授权许可】

   
2012 Parks et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

• [1]Fitch WM: Cautionary remarks on using gene expression events in parsimony procedures. Systematic Zool 1979, 28:375-379.
• [2]Fitch WM: Cladistic and other methods: problems, pitfalls, and potentials. In Cladistics: Perspectives on the Reconstruction of Evolutionary History. Edited by Duncan T, Stuessy TF. New York: Columbia University Press; 1984:221-252.
• [3]Felsenstein J: Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 1978, 27:401-410.
• [4]Hendy MD, Penny D: A framework for the quantitative study of evolutionary trees. Syst Biol 1989, 38:297-309.
• [5]Huelsenbeck JP: Tree-length distribution skewness: an indicator of phylogenetic information. Syst Biol 1991, 40:257-270.
• [6]Hillis DM, Huelsenbeck JP: Signal, noise, and reliability in molecular phylogenetic analyses. J Hered 1992, 83:189-195.
• [7]Farris JS, Källersjö M, Kluge AG, Bult C: Constructing a significance test for incongruence. Syst Biol 1995, 44:570-572.
• [8]Dowton M, Austin AD: Increased congruence does not necessarily indicate increased phylogenetic accuracy - the behavior of the incongruence length difference test in mixed-model analyses. Syst Biol 2002, 51:19-31.
• [9]Hipp AL, Hall JC, Sytsma KJ: Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test. Syst Biol 2004, 53:81-89.
• [10]Strimmer K, von Haeseler A: Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc Nat Acad Sci USA 1997, 94:6815-6819.
• [11]Pollock DD, Zwickl DJ, McGuire JA, Hillis DM: Increased taxon sampling is advantageous for phylogenetic inference. Syst Biol 2002, 51:664-671.
• [12]Soltis DE, Albert VA, Savolainen V, Hilu K, Qiu Y-L, Chase MW, Farris JS, Stefanovic S, Rice DW, Palmer JD, Soltis PS: Genome-scale data, Angiosperm relationships, and ‘ending incongruence’: a cautionary tale in phylogenetics. Trends Plant Sci 2004, 9:477-483.
• [13]Townsend JP, Leuenberger C: Taxon sampling and the optimal rates of evolution for phylogenetic inference. Syst Biol 2011, 60:358-365.
• [14]Townsend JP: Profiling phylogenetic informativeness. Syst Biol 2007, 56:222-231.
• [15]Klopfstein S, Kropf C, Quicke DLJ: An evaluation of phylogenetic informativeness profiles and the molecular phylogeny of Diplazontinae (Hymenoptera, Ichneumonidae). Syst Biol 2010, 59:226-241.
• [16]Bergsten J: A review of long-branch attraction. Cladistics 2005, 21:163-193.
• [17]Delsuc F, Brinkmann H, Philippe H: Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 2005, 6:361-375.
• [18]Jeffroy O, Brinkmann H, Delsuc F, Philippe H: Phylogenomics: the beginning of incongruence? Trends Genet 2006, 22:225-231.
• [19]Philippe H, Delsuc F, Brinkmann H, Lartillot N: Phylogenomics. Ecol, Evol and Syst 2005, 36:541-562.
• [20]Degnan JH, Rosenberg NA: Discordance of species trees with their most likely gene trees. PLoS Genet 2006, 2:762-768.
• [21]Kubatko LS, Degnan JH: Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol 2007, 56:17-24.
• [22]Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M, Wörheide G, Baurain D: Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biology 2011, 9:e1000602.
• [23]Stefanovic S, Rice D, Palmer J: Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots? BMC Evol Biol 2004, 4:35.
• [24]Phillips MJ, Delsuc F, Penny D: Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol 2004, 21:1455-1458.
• [25]Brinkmann H, van der Giezen M, Zhou Y, de Raucourt GP, Philippe H: An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Syst Biol 2005, 54:743-757.
• [26]Rokas A, Carroll SB: Bushes in the tree of life. PLoS Biology 2006, 4:e352.
• [27]Cai Z, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson JE, dePamphilis CW, Boore JL, Jansen RK: Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of Magnoliids. BMC Evol Biol 2006, 6:77.
• [28]Jansen RK, Cai Z, Raubeson LA, Daniell H, dePamphilis CW, Leebens-Mack J, Muller KF, Guisinger-Bellian M, Haberle RC, Hansen AK: Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci USA 2007, 104:19369.
• [29]Jansen RK, Kaittanis C, Saski C, Lee SB, Tomkins J, Alverson AJ, Daniell H: Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol 2006, 6:32.
• [30]Moore MJ, Bell CD, Soltis PS, Soltis DE: Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proc Natl Acad Sci USA 2007, 104:19363-19368.
• [31]Parks M, Cronn R, Liston A: Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol 2009, 7:84.
• [32]Goremykin VV, Holland B, Hirsch-Ernst KI, Hellwig FH: Analysis of Acorus calamus chloroplast genome and its phylogenetic implications. Mol Biol Evol 2005, 22:1813-1822.
• [33]Leebens-Mack J, Raubeson LA, Cui L, Kuehl JV, Fourcade MH, Chumley TW, Boore JL, Jansen RK, dePamphilis CW: Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Mol Biol Evol 2005, 22:1948-1963.
• [34]Lin C-P, Huang J-P, Wu C-S, Hsu C-Y, Chaw S-M: Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies. Gen Biol and Evol 2010, 2:504-517.
• [35]Goremykin V, Nikiforova S, Bininda-Emonds O: Automated removal of noisy data in phylogenomic analyses. J Mol Evol 2010, 71:319-331.
• [36]Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL: The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 2005, 92:142-166.
• [37]Shaw J, Lickey EB, Schilling EE, Small RL: Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot 2007, 94:275.
• [38]Millar CI: Early evolution of pines. In Ecology and biogeography of Pinus. Edited by Richardson DM. Cambridge: Cambridge University Press; 2000:69-91.
• [39]Klymiuk AA, Stockey RA, Rothwell GW: The first organismal concept for an extinct species of Pinaceae. Int J Plant Sci 2011, 172:294-313.
• [40]Willyard A, Syring J, Gernandt DS, Liston A, Cronn R: Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus. Mol Biol Evol 2007, 24:90-101.
• [41]Little EL, Critchfield WB: Subdivision of the Genus Pinus (Pines). Washington, D.C: USDA; 1969.
• [42]Gernandt DS, Lopez G, Garcia SO, Liston A: Phylogeny and classification of Pinus. Taxon 2005, 54:29-42.
• [43]Ortiz Garcia S: Evolucion y fiogenia en pinos y sus hongos endofitos: aspectos sistematicos de la coespeciacion PhD thesis. Universidad Nacional Autonoma de Mexico, Instituto de Ecologia; 1999.
• [44]Gernandt DS, Magallon S, Geada Lopez G, Zeron Flores O, Willyard A, Liston A: Use of simultaneous analyses to guide fossil-based calibrations of Pinaceae phylogeny. Int J Plant Sci 2008, 169:1086-1099.
• [45]Frankis MP: Morphology and affinities of Pinus brutia. In International Symposium on Pinus brutia Ten: 18-23 October 1993. Marmaris, Turkey: Ministry of Forestry; 1993:11-18.
• [46]Critchfield WB: Crossability and relationships of the closed-cone pines. Silvae Genetica 1966, 16:89-97.
• [47]Critchfield WB: Interspecific hybridization inPinus: a summary review. In Symposium on Interspecific and Interprovenance Hybridization in Forest Trees: 28-30 August 1975; Fredericton, New Brunswick. Edited by Fowler DP, Yeatman CY. Ottawa: Canadian Forestry Service; 1975:99-105.
• [48]Critchfield WB: Hybridization and classification of the white pines (Pinus section Strobus). Taxon 1986, 35:647-656.
• [49]Krupkin AB, Liston A, Strauss SH: Phylogenetic analysis of the hard pines (Pinus subgenus Pinus, Pinaceae) from chloroplast DNA restriction site analysis. Am J Bot 1996, 83:489-498.
• [50]Strauss SH, Doerksen AH: Restriction fragment analysis of pine phylogeny. Evolution 1990, 44:1081-1096.
• [51]Liston A, Gernandt DS, Vining TF, Campbell CS, Pinero D: Molecular phylogeny of Pinaceae and Pinus. Acta Hort (ISHS) 2003, 615:107-114.
• [52]Liston A, Robinson WA, Piñero D, Alvarez-Buylla ER: Phylogenetics of Pinus (Pinaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences. Mol Phylogenet Evol 1999, 11:95-109.
• [53]Syring J, Willyard A, Cronn R, Liston A: Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci. Am J Bot 2005, 92:2086-2100.
• [54]Palmé AE, Pyhäjärvi T, Wachowiak W, Savolainen O: Selection on nuclear genes in a Pinus phylogeny. Mol Biol Evol 2009, 26:893-905.
• [55]Geada Lopez G, Kamiya K, Harada K: Phylogenetic relationships of diploxylon pines (subgenus Pinus) based on plastid sequence data. Int J Plant Sci 2002, 163:737-747.
• [56]Wang XR, Szmidt AE, Nguyên HN: The phylogenetic position of the endemic flat-needle pine Pinus krempfii (Pinaceae) from Vietnam, based on PCR-RFLP analysis of chloroplast DNA. Plant Syst Evol 2000, 220:21-36.
• [57]Wang XR, Tsumura Y, Yoshimaru H, Nagasaka K, Szmidt AE: Phylogenetic relationships of Eurasian pines (Pinus, Pinaceae) based on chloroplast rbcL, matK, rpl20-rps18 spacer, and trnV intron sequences. Am J Bot 1999, 86:1742-1753.
• [58]Zhang ZY, Li DZ: Molecular phylogeny of section Parrya of Pinus (Pinaceae) based on chloroplast matK gene sequence data. Acta Bot Sin 2004, 46:171-179.
• [59]Eckert AJ, Hall BD: Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae): phylogenetic tests of fossil-based hypotheses. Mol Phylogenet Evol 2006, 40:166-182.
• [60]Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T: Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 2008, 36:e122.
• [61]Parks M, Liston A, Cronn R: Newly developed primers for complete ycf1 amplification in Pinus (Pinaceae) chloroplasts with possible family-wide utility. Am J Bot 2011, 98(7):e185-e188.
• [62]Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, Sugiura M: Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Acad Sci USA 1994, 91:9794-9798.
• [63]Pan X, Urban AE, Palejev D, Schulz V, Grubert F, Hu Y, Snyder M, Weissman SM: A procedure for highly specific, sensitive, and unbiased whole-genome amplification. Proc Natl Acad Sci USA 2008, 105:15499-15504.
• [64]Solexa, Inc: Protocol for whole genome sequencing using Solexa technology. Biotechniques Protocol Guide 2007, 29.
• [65]Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C: Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotech 2009, 27:182-189.
• [66]Kent WJ: BLAT - the BLAST-like alignment tool. Genome Res 2002, 4:656-664.
• [67]Straub SC, Fishbein M, Livshultz T, Foster Z, Parks M, Weitemier K, Cronn RC, Liston A: Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing. BMC Genomics 2011, 12:211.
• [68]Ratan A: Assembly algorithms for next-generation sequence data.PhD Thesis. The Pennsylvania State University, Computer Science Department; 2009.
• [69]Harris RS: Improved pairwise alignment of genomic DNA.PhD Thesis. The Pennsylvania State University, Computer Science Department; 2007.
• [70]Kurtz S, Phyllippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL: Versatile and open software for comparing large genomes. Genome Biol 2004, 5:R12.
• [71]Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999, 41:95-98.
• [72]Katoh K, Kuma K, Toh H, Miyata T: MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 2005, 33:511-518.
• [73]Stamatakis A: A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 2008, 57:758-771.
• [74]Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
• [75]Swofford DL: PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sunderland, Massachusetts: Sinauer Associates; 2000.
• [76]Kumar S, Skjaeveland A, Orr R, Enger P, Ruden T, Mevik B-H, Burki F, Botnen A, Shalchian-Tabrizi K: AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses. BMC Bioinforma 2009, 10:357.
• [77]Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 1997, 13:555-556.
• [78]Yang Z: PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 2007, 24:1586-1591.
• [79]Kuhner MK, Felsenstein J: A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol 1994, 11:459-468.
• [80]Robinson DF, Foulds LR: Comparison of phylogenetic trees. Math Biosci 1981, 53:131-147.
• [81]Felsenstein J: PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author Department of Genome Sciences, University of Washington ; 2005.
• [82]Goremykin V, Viola R, Hellwig F: Removal of noisy characters from chloroplast genome-scale data suggests revision of phylogenetic placements of Amborella and Ceratophyllum. J Mol Evol 2009, 68:197-204.
• [83]Tamura K, Dudley J, Nei M, Kumar S: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007, 24:1596-1599.
• [84]Rodríguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF, Philippe H: Detecting and overcoming systematic errors in genome-scale phylogenies. Syst Biol 2007, 56:389-399.
• [85]Philippe H, Sörhannus U, Baroin A, Perasso R, Gasse F, Adoutte A: Comparison of molecular and paleontological data in diatoms suggests a major gap in the fossil record. J Evol Biol 1994, 7:247-265.
• [86]Zhong B, Deusch O, Goremykin VV, Penny D, Biggs PJ, Atherton RA, Nikiforova SV, Lockhart PJ: Systematic error in seed plant phylogenomics. Genome Biol Evol 2011, 1340-1348.
• [87]Zwickl DJ, Hillis DM: Increased taxon sampling greatly reduces phylogenetic error. Syst Biol 2002, 51:588-598.
• [88]Kälersjö M, Albert VA, Farris JS: Homoplasy Increases Phylogenetic Structure. Cladistics 1999, 15:91-93.
• [89]Cummins CA, McInerney JO: A Method for Inferring the Rate of Evolution of Homologous Characters that Can Potentially Improve Phylogenetic Inference, Resolve Deep Divergence and Correct Systematic Biases. Syst Biol 2011, 60:833-844.
• [90]Chevalier A: Notes sur les coniferes de l'Indochine. Revue de Botanique Appliquee et d'Agriculture Tropicale 1944, 24:7-34.
• [91]Gaussen H: Les gymnospermes actuelles et fossiles. Fassicule VI Les Coniferales Chapter 11 Generalites, Genre Pinus Travaux du Toulous Universite Laboratoire Forestier. Volume Tome 2, Sect. 1, Vol. 1 1960, 1-272.
• [92]De Ferre Y: Division du genre Pinus en quatre sous-genres. Academie des Sciences Compte Rendu 1953, 236:226-228.
• [93]Farjon A: Pines: drawings and descriptions of the genus. Leiden: W. Backhuys; 1984.
• [94]Ickert-Bond S: Reexamination of wood anatomical features in Pinus krempfii (Pinaceae). IAWA J 2001, 22:355-365.
• [95]Van der Berg J: Holzer der niederrheinischen braunkohlenformation 2. Holzer der braunkohlengruben "Maria Theresia" zu Herzogenrath, "Zukunft West" zu Eschweiler und "Victor" Zulpich mitte zu Zulpich. Nebst einer systematisch-anatomischen bearbeitung der gattung Pinus L. Rev Palaeobot Palynol 1973, 15:73-275.
• [96]Ickert-Bond S: Cuticle Micromorphology of Pinus krempfii Lecomte (Pinaceae) and Additional Species from Southeast Asia. Int J Plant Sci 2000, 161:301-317.
• [97]Szmidt A, Wang XR, Changtragoon S: Contrasting patterns of genetic diversity in two tropical pines: Pinus kesiya (Royle ex Gordon) and P. merkusii (Jungh et De Vriese). TAG Theor Appl Genet 1996, 92:436-441.
• [98]Gernandt DS, Hernández-León S, Salgado-Hernández E, Rosa JAPdl: Phylogenetic relationships of Pinus subsection Ponderosae inferred from rapidly evolving cpDNA regions. Syst Bot 2009, 34:481-491.
• [99]Critchfield WB: Hybridization of the southern pines in California. Southern Forest Tree Improvement Committee Publications 1963, 22:40-48.
• [100]Saylor LC, Koenig RL: The slash x sand pine hybrid. Silvae Genetica 1967, 16:134-138.
• [101]Miller CN: Preserved cones of Pinus from the Neogene of Idaho and Oregon. Int J Plant Sci 1992, 153:147-154.
• [102]McKown AD, Stockey RA, Scheger CE: A new species of Pinus subgenus Pinus subsection Contortae from Pliocene sediments of Ch'ijee's Bluff, Yukon Territory, Canada. Int J Plant Sci 2002, 163:687-697.
• [103]Liston A, Parker-Defeniks M, Syring JV, Willyard A, Cronn R: Interspecific phylogenetic analysis enhances intraspecific phylogeographical inference: a case study in Pinus lambertiana. Mol Ecol 2007, 16:3926-3937.
• [104]Alkan C, Coe BP, Eichler EE: Genome structural variation discovery and genotyping. Nature Rev Genet 2011, 12:363-376.
• [105]Neale DB, Kremer A: Forest tree genomics: growing resources and applications. Nat Rev Genet 2011, 12:111-122.
• [106]Mardis ER: Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008, 9:387-402.
• [107]Shendure J, Ji H: Next-generation DNA sequencing. Nature Biotech 2008, 26:1135-1145.
• [108]Schweiger M, Kerick M, Timmermann B, Isau M: The power of NGS technologies to delineate the genome organization in cancer: from mutations to structural variations and epigenetic alterations. Cancer Metastasis Rev 2011, 30:199-210.
• [109]Metzker ML: Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46.
• [110]Mardis ER: A decade's perspective on DNA sequencing technology. Nature 2011, 470:198-203.
• [111]Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ: Target-enrichment strategies for next-generation sequencing. Nat Meth 2010, 7:111-118.
• [112]Seeb JE, Carvalho G, Hauser L, Naish K, Roberts S, Seeb LW: Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Mol Ecol Resour 2011, 11:1-8.
• [113]Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA: Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS One 2011, 6:e18561.
• [114]Cronn R, Knaus B, Liston A, Maughan J, Parks M, Syring J, Udall J: Targeted Enrichment Strategies for Next-Generation Plant Biology. Am J Bot 2012, 99:291-311.