The root of angiosperm phylogeny inferred from duplicate phytochrome genes

Science

Volumn 286, Issue 5441, 1999, Pages 947-950

  Mathews, Sarah ^a   Donoghue, Michael J ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

PHYTOCHROME;

ANGIOSPERM; ARTICLE; BIODIVERSITY; EVOLUTION; GENE EXPRESSION; GENETIC ANALYSIS; NONHUMAN; PHYLOGENY; PLANT ROOT; PRIORITY JOURNAL;

ANGIOSPERMS; APOPROTEINS; ARABIDOPSIS PROTEINS; GENE DUPLICATION; GENES, PLANT; PHYLOGENY; PHYTOCHROME; PHYTOCHROME A; PLANT PROTEINS;

EID: 0033615479     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.286.5441.947     Document Type: Article

References (48)

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4. Analyses of morphological characters consistently suggest that Gnetales are the closest living relatives of angiosperms, but analyses of molecular data often unite Gnetales with conifers and support a dade of all extant seed plants except angiosperms [J. A. Doyle, Int. J. Plant Sci. 157, S3 (1996); K.-U. Winter et al., Proc. Natl. Acad. Sci. U.S.A. 96, 7342 (1999); A. Hansen, S. Hansmann, T. Samigullin, A. Antonov, W. Martin, Mol. Biol. Evol. 16, 1006 (1999)].
5. Analyses of morphological characters consistently suggest that Gnetales are the closest living relatives of angiosperms, but analyses of molecular data often unite Gnetales with conifers and support a dade of all extant seed plants except angiosperms [J. A. Doyle, Int. J. Plant Sci. 157, S3 (1996); K.-U. Winter et al., Proc. Natl. Acad. Sci. U.S.A. 96, 7342 (1999); A. Hansen, S. Hansmann, T. Samigullin, A. Antonov, W. Martin, Mol. Biol. Evol. 16, 1006 (1999)].
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17. Analyses of complete coding sequences from land plants place PHY from angiosperms in four independent gene lineages, each comprising homologs of Arabidopsis PHYA, PHYB/D, PHYC, or PHYE [all supported by bootstrap values of 100% (10)], and PHY from conifers in two gene lineages, one that diverges before divergence of PHYB/D from PHYE, and another that diverges before divergence of PHYA from PHYC [supported by bootstrap values of 100% and 74%, respectively (Z)]. Phylogenies that include partial sequences from conifers, ginkgo, cycads, and Gnetales also resolve just two gene lineages in nonangiosperms, but the PHYA/PHYC-related lineage is equivocally resolved. Some analyses place it on the branch to PHYA, others on the branch to PHYC, but neither position is supported [H. A. W. Schneider-Poetsch, Ü. Kolukisaoglu, D. H. Clapham, J. Hughes, T. Lamparter, Physiol. Plant. 102, 612 (1998); S. Mathews, unpublished data]. Thus, divergence of PHYA from PHYC before the origin of any nonangiosperm group is not supported. PHYC may have been lost from some eudicot lineages (32) [G. T. Howe et al., Mol. Biol. Evol. 15, 160 (1998)] and PHYA has diversified in others (10, 32). Diversification or loss of PHYA or PHYC (or both) has not been detected in early-diverging angiosperms except for Ceratophyllum (10), which is excluded from these analyses.
18. Analyses of complete coding sequences from land plants place PHY from angiosperms in four independent gene lineages, each comprising homologs of Arabidopsis PHYA, PHYB/D, PHYC, or PHYE [all supported by bootstrap values of 100% (10)], and PHY from conifers in two gene lineages, one that diverges before divergence of PHYB/D from PHYE, and another that diverges before divergence of PHYA from PHYC [supported by bootstrap values of 100% and 74%, respectively (Z)]. Phylogenies that include partial sequences from conifers, ginkgo, cycads, and Gnetales also resolve just two gene lineages in nonangiosperms, but the PHYA/PHYC- related lineage is equivocally resolved. Some analyses place it on the branch to PHYA, others on the branch to PHYC, but neither position is supported [H. A. W. Schneider-Poetsch, Ü. Kolukisaoglu, D. H. Clapham, J. Hughes, T. Lamparter, Physiol. Plant. 102, 612 (1998); S. Mathews, unpublished data]. Thus, divergence of PHYA from PHYC before the origin of any nonangiosperm group is not supported. PHYC may have been lost from some eudicot lineages (32) [G. T. Howe et al., Mol. Biol. Evol. 15, 160 (1998)] and PHYA has diversified in others (10, 32). Diversification or loss of PHYA or PHYC (or both) has not been detected in early-diverging angiosperms except for Ceratophyllum (10), which is excluded from these analyses.
19. Locus-specific (PHYA upstream: 5′-CCYTAYGARGRNC-CYATGACWGC-3′, 5′-GACTTTGARCCNGTBAAGCCT-TAYG-3′; PHYC upstream: 5′-GAYTTRGARCCWGT-DAAYC-3′; PHYA downstream: 5′-GDATDGCRTCCA-TYTCRTAGTC-3′, 5′-GTYTCMATBARDCKRACCATYTC-3′; PHYC downstream: 5′-GRATKGCATCCATYTCMAY-RTC-3′) or degenerate oligonucleotides [upstream: 5′-TCWGGNAARCCNTTYTAYGC-3′, 5′-CCITTYTAYGSIA-THYTICAYMG-3′; downstream: 5′-GTMACATCTTGRS-CMACAAARCAYAC-3′, 5′-GCWGTRTGNGAYCTRAAC-CA-3′ (I, inosine; R, Y, M, K, S, W, H, B, D, and N correspond to the IUPAC-IUB ambiguity set); see also S. Mathews, M. Lavin, R. A. Sharrock, Ann. Missouri Bot. Gard. 82, 296 (1995)] primed synthesis of 1- to 1.2-kb fragments of exon I using stepdown protocols [K. H. Hecker and K. H. Roux, Biotechniques 20, 478 (1996)]. Fragments were cloned into pGEM-T Easy (Promega). No PHYA clones were obtained from Lemna or Houttuynia; a 330-base pair PHYA done was obtained from Hedycarya. The data matrix of 1104 nucleotide sites comprised sequences of 24 PHYA and 26 PHYC clones. Cabombaceae is represented by Brasenia (PHYA) or Cabomba (PHYC). We obtained a 1.2-kb done of just one of the PHYA copies in Ceratophyllum (11); its homology with other PHYA in our analyses could not be assessed without the second copy, so we excluded it from analyses. Available sequences from Arabidopsis and Sorghum are highly diverged from those analyzed here and were excluded from final analyses; their inclusion did not alter tree topologies but decreased bootstrap support for several branches, including eudicots and monocots. When they were included in analyses of fewer species, gene subtrees were rooted at Sorghum (2), a topology likely resulting from long branch attraction. GenBank accession numbers of sequences analyzed here are AF190060 to AF190109. Data matrices analyzed in this study are available from the first author and from TreeBASE (http://phylogeny.harvard.edu/ treebase, SN295).
20. Locus-specific (PHYA upstream: 5′-CCYTAYGARGRNC- CYATGACWGC-3′, 5′-GACTTTGARCCNGTBAAGCCT- TAYG-3′; PHYC upstream: 5′-GAYTTRGARCCWGT- DAAYC-3′; PHYA downstream: 5′-GDATDGCRTCCA- TYTCRTAGTC-3′, 5′-GTYTCMATBARDCKRACCATYTC- 3′; PHYC downstream: 5′-GRATKGCATCCATYTCMAY- RTC-3′) or degenerate oligonucleotides [upstream: 5′- TCWGGNAARCCNTTYTAYGC-3′, 5′-CCITTYTAYGSIA- THYTICAYMG-3′; downstream: 5′-GTMACATCTTGRS- CMACAAARCAYAC-3′, 5′-GCWGTRTGNGAYCTRAAC- CA-3′ (I, inosine; R, Y, M, K, S, W, H, B, D, and N correspond to the IUPAC-IUB ambiguity set); see also S. Mathews, M. Lavin, R. A. Sharrock, Ann. Missouri Bot. Gard. 82, 296 (1995)] primed synthesis of 1- to 1.2-kb fragments of exon I using stepdown protocols [K. H. Hecker and K. H. Roux, Biotechniques 20, 478 (1996)]. Fragments were cloned into pGEM-T Easy (Promega). No PHYA clones were obtained from Lemna or Houttuynia; a 330-base pair PHYA done was obtained from Hedycarya. The data matrix of 1104 nucleotide sites comprised sequences of 24 PHYA and 26 PHYC clones. Cabombaceae is represented by Brasenia (PHYA) or Cabomba (PHYC). We obtained a 1.2-kb done of just one of the PHYA copies in Ceratophyllum (11); its homology with other PHYA in our analyses could not be assessed without the second copy, so we excluded it from analyses. Available sequences from Arabidopsis and Sorghum are highly diverged from those analyzed here and were excluded from final analyses; their inclusion did not alter tree topologies but decreased bootstrap support for several branches, including eudicots and monocots. When they were included in analyses of fewer species, gene subtrees were rooted at Sorghum (2), a topology likely resulting from long branch attraction. GenBank accession numbers of sequences analyzed here are AF190060 to AF190109. Data matrices analyzed in this study are available from the first author and from TreeBASE (http://phylogeny.harvard.edu/ treebase, SN295).
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48. We thank J. Doyle, P. Endress, L. Thein, P. Soltis, S. Graham, Y.-L. Qiu, J. Palmer, and C. dePamphilis for helpful discussions and for sharing unpublished data, and C. Soohoo and C. Davis for technical support Financial support was provided by NSF grant DEB-9806937.