Angiosperm Phylogeny Based on 18S/26S rDNA Sequence Data: Constructing a Large Data Set Using Next-Generation Sequence Data

Vitor H. Maia, Matthew A. Gitzendanner, Pamela S. Soltis, Gane Ka-Shu Wong and Douglas E. Soltis
International Journal of Plant Sciences
Vol. 175, No. 6 (July/August 2014), pp. 613-650
DOI: 10.1086/676675
Stable URL:
Page Count: 38
  • Download PDF
  • Cite this Item

You are not currently logged in.

Access your personal account or get JSTOR access through your library or other institution:


Log in to your personal account or through your institution.

Angiosperm Phylogeny Based on 18S/26S rDNA Sequence Data: Constructing a Large Data Set Using Next-Generation Sequence Data
We're having trouble loading this content. Download PDF instead.


The utility of 18S and 26S in broad phylogenetic analyses has been much maligned due in large part to the low signal in both genes. However, few analyses have employed complete 26S rDNA sequences over a broad range of taxa, and most alignments of the two genes are done de novo, without taking into account the secondary structure of the two rRNA genes. Here we mine next-generation sequence data to compile large matrices (429 taxa) of complete 18S + 26S gene sequences, and we compare both de novo alignment methods with curated alignments done by eye that take into account secondary structure and hard-to-align regions (profile alignments). The combined 18S + 26S topology is overall very similar to recently published gene trees for the angiosperms based on three or more genes. Overall support for the backbone or framework of the combined tree is low (bootstrap support below 50%). Few major clades have bootstrap support above 50%. Most well-supported clades are tip clades (families and orders sensu APG III 2009). Importantly, the 18S + 26S rDNA topology is consistent with current estimates of relationships: the basalmost angiosperms are recovered (Amborellaceae, Nymphaeales, Austrobaileyales), as are most major clades, including Mesangiospermae, eudicots (Eudicotyledoneae sensu Cantino et al. 2007), core eudicots (Gunneridae sensu Cantino et al. 2007), rosids (Rosidae sensu Cantino et al. 2007), asterids (Asteridae sensu Cantino et al. 2007), and Caryophyllales. Most clades recognized at the ordinal level (sensu APG III 2009) are also recovered. However, there are also some unusual placements in the 18S + 26S topology, but none of these receives bootstrap support above 50%. The profile and de novo alignments gave very similar topologies. 18S + 26S trees remain useful sources of data in large combined analyses. This is the first time a large data set of complete 26S gene sequences has been employed at this scale; this gene in particular proved to be useful phylogenetically. Targeted sequencing of 18S/26S rDNA is not advocated here, but given that these regions provide useful phylogenetic information and are abundant in next-generation sequencing runs, we suggest that the data be used rather than discarded.

Notes and References

This item contains 42 references.

Literature Cited
  • ['APG (Angiosperm Phylogeny Group) III\u20022009\u2002An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc 161:105–121.']
  • ['Brockington SF, R Alexandre, J Ramdial, MJ Moore, S Crawley, A Dhingra, K Hilu, PS Soltis, DE Soltis\u20022009\u2002Phylogeny of the Caryophyllales sensu lato: revisiting hypotheses on pollination biology and perianth differentiation in the core Caryophyllales. Int J Plant Sci 170:627–643.']
  • ['Bult CJ, JA Sweere, EA Zimmer \u20021995\u2002Cryptic sequence simplicity, nucleotide composition bias, and molecular coevolution in the large subunit of ribosomal DNA in plants: implications for phylogenetic analyses. Ann Mo Bot Gard 82:235–246.']
  • ['Bult CJ, EA Zimmer\u20021993\u2002Nuclear ribosomal RNA sequences for inferring tribal relationships within Onagraceae. Syst Bot 18:48–63.']
  • ['Cantino P, JA Doyle, S Graham, W Judd, R Olmstead, DE Soltis, PS Soltis, MJ Donoghue\u20022007\u2002Towards a phylogenetic nomenclature of Tracheophyta. Taxon 56:822–846.']
  • ['Chanderbali AS, H van der Werff, SS Renner\u20022001\u2002Phylogeny and historical biogeography of Lauraceae: evidence from the chloroplast and nuclear genomes. Ann Mo Bot Gard 88:104–134. ']
  • ['Chase MW, MF Fay, D Devey, O Maurin, N Rønsted, J Davies,Y Pillon, et al\u20022006\u2002Multigene analyses of monocot relationships: a summary. Pages 63–75 in JT Columbus, EA Friar, JM Porter, LM Prince, MG Simpson, eds. Monocots: comparative biology and evolution, excluding poales. Rancho Santa Ana Botanical Garden, Claremont, CA.']
  • ['Fan C, QY Xiang\u20022001\u2002Phylogenetic relationships within Cornus (Cornaceae) based on 26S rDNA sequences. Am J Bot 88:1131–1138.']
  • ['———\u20022003\u2002Phylogenetic analyses of Cornales based on 26S rRNA and combined 26S rRNA-matK-rbcL sequence data. Am J Bot 90:1357–1372.']
  • ['Felsenstein J\u20021973\u2002Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst Zool 22:240–249. ']
  • ['Givnish TJ, M Ames, JR McNeal, MR McKain, PR Steele, CW dePamphilis, SW Graham, et al\u20022010\u2002Assembling the tree of the monocotyledons: plastome sequence phylogeny and evolution of Poales. Ann Mo Bot Gard 97:584–616.']
  • ['Hamby KR, EA Zimmer\u20021988\u2002Ribosomal RNA sequences for inferring phylogeny within the grass family (Poaceae). Plant Syst Evol 160:29–37.']
  • ['———\u20021992\u2002Ribosomal RNA as a phylogenetic tool in plant systematics. Pages 50–91 in P Soltis, D Soltis, J Doyle, eds. Molecular systematics of plants. Chapman & Hall, New York.']
  • ['Johnson MTJ, EJ Carpenter, Z Tian, R Bruskiewich, JN Burris, CT Carrigan, MW Chase, et al\u20022012\u2002Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS ONE 7:e50226. doi:10.1371/journal.pone.0050226.']
  • ['Katoh K, T Hiroyuki\u20022008\u2002Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9:286–298. doi:10.1093/bib/bbn013.']
  • ['Kent WJ\u20022002\u2002BLAT—the BLAST-like alignment tool. Genome Res 12:656–664.']
  • ['Kron K\u20021996\u2002Phylogenetic relationships of Empetraceae, Epacridaceae, and Ericaceae: evidence from nuclear ribosomal 18S sequence data. Ann Bot 77:293–303.']
  • ['Kuzoff RK, JA Sweere, DE Soltis, PS Soltis, EA Zimmer\u20021998\u2002The phylogenetic potential of entire 26S rDNA sequences in plants. Mol Biol Evol 15:251–263.']
  • ['Li R, H Zhu, J Ruan, W Qian, X Fang, Z Shi, Y Li, et al\u20022010\u2002De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265-272.']
  • ['Moore MJ, N Hassan, PS Soltis, MA Gitzendanner, DE Soltis\u20022011\u2002Inferring angiosperm phylogeny using complete inverted repeat sequence data. Int J Plant Sci 172:541–558.']
  • ['Moore MJ, PS Soltis, CD Bell, JG Burleigh, DE Soltis\u20022010\u2002Phylogenetic analysis of 83 plastid genes resolves relationships among major clades of eudicot angiosperms and reveals multiple rapid radiations. Proc Natl Acad Sci USA 107:4623–4628.']
  • ['Neyland R\u20022001\u2002A phylogeny inferred from large ribosomal subunit (26S) rDNA sequences suggests that Cuscuta is a derived member of Convolvulaceae. Brittonia 53:108–115.']
  • ['Nickrent DL, A Blarer, YL Qiu, DE Soltis, PS Soltis, M Zanis\u20022002\u2002Molecular data place Hydnoraceae with Aristolochiaceae. Am J Bot 89:1809–1817.']
  • ['Nickrent DL, CR Franchina\u20021990\u2002Phylogenetic relationships of the Santalales and relatives. J Mol Evol 31:294–301.']
  • ['Nickrent DL, DE Soltis\u20021995\u2002A comparison of angiosperm phylogenies from nuclear 18S rDNA and rbcL sequences. Ann Mo Bot Gard 82:208–234.']
  • ['Nickrent DL, EM Starr\u20021994\u2002High rates of nucleotide substitution in nuclear small-subunit (18S) rDNA from holoparasitic flowering plants. J Mol Evol 39:62–70.']
  • ['Posada D, KA Crandall\u20021998\u2002MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818.']
  • ['Qiu YL, L Li, B Wang, JY Xue, TA Hendry, RQ Li, JW Brown, et al\u20022010\u2002Angiosperm phylogeny inferred from sequences of four mitochondrial genes. J Syst Evol 48:391–425.']
  • ['Schäferhoff B, A Fleischmann, E Fischer, DC Albach, T Borsch, G Heubl, KF Müller\u20022010\u2002Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences. BMC Evol Biol 10:352.']
  • ['Simmons MP, V Savolainen, CC Clevinger, RH Archer, JI Davis\u20022001\u2002Phylogeny of the Celastraceae inferred from 26S nuclear ribosomal DNA, phytochrome B, rbcL, atpB, and morphology. Mol Phylogenet Evol 19:353–366.']
  • ['Soltis DE, PS Soltis, MW Chase, ME Mort, DC Albach, MJ Zanis, V Savolainen, et al\u20022000\u2002Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Bot J Linn Soc 133:381–461.']
  • ['Soltis DE, PS Soltis, PK Endress, MW Chase\u20022005\u2002Phylogeny and evolution of the angiosperms. Sinauer, Sunderland, MA.']
  • ['Soltis DE, PS Soltis, DR Morgan, SM Swensen, BC Mullin, JM Dowd, PG Martin\u20021995\u2002Chloroplast gene sequence data suggest a single origin of symbiotic nitrogen fixation in angiosperms. Proc Natl Acad Sci USA 92:2647–2651.']
  • ['Soltis DE, PS Soltis, ME Mort, MW Chase, V Savolainen, SB Hoot, CM Morton\u20021998\u2002Inferring complex phylogenies using parsimony: an empirical approach using three large DNA data sets for angiosperms. Syst Biol 47:32–42.']
  • ['Soltis DE, PS Soltis, DL Nickrent, LA Johnson, WJ Hahn, SB Hoot, JA Sweere, et al\u20021997\u2002Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Ann Mo Bot Gard 84:1–49.']
  • ['Soltis DE, PS Soltis, A Senters, S Kim, JD Thompson, PS Soltis, MJ Zanis, L Ronse de Craene, PK Endress\u20022003\u2002Gunnerales are sister to other core eudicots, and exhibit floral features of early-diverging eudicots. Am J Bot 90:461–470.']
  • ['Soltis PS, DE Soltis\u20021998\u2002Molecular evolution of 18S rDNA in angiosperms: implications for character weighting in phylogenetic analysis. Pages 188–210 in DE Soltis, PS Soltis, J Doyle, eds. Molecular systematics of plants II. Kluwer, Boston.']
  • ['Soltis PS, DE Soltis, PG Wolf, DL Nickrent, S-M Chaw, RL Chapman\u20021999\u2002The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal? Mol Biol Evol 16:1774–1784.']
  • ['Stefanovic S, M Jager, J Deutsch, J Broutin, M Masselot\u20021998\u2002Phylogenetic relationships of conifers inferred from partial 28S rRNA gene sequences. Am J Bot 85:688–697.']
  • ['Tank DC, MJ Donoghue\u20022010\u2002Phylogeny and phylogenetic nomenclature of the Campanulidae based on an expanded sample of genes and taxa. Syst Bot 35:425–441.']
  • ['Zanis MJ, DE Soltis, PS Soltis, S Mathews, MJ Donoghue\u20022002\u2002The root of the angiosperms revisited. Proc Natl Acad Sci USA 99:6848–6853.']
  • ['Zerbino DR, E Birney\u20022008\u2002Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829.']