View Item 

Show simple item record

Lineage‐specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales
dc.contributor.authorBrockington, Samuel F.en_US
dc.contributor.authorYang, Yaen_US
dc.contributor.authorGandia‐herrero, Fernandoen_US
dc.contributor.authorCovshoff, Sarahen_US
dc.contributor.authorHibberd, Julian M.en_US
dc.contributor.authorSage, Rowan F.en_US
dc.contributor.authorWong, Gane K. S.en_US
dc.contributor.authorMoore, Michael J.en_US
dc.contributor.authorSmith, Stephen A.en_US
dc.date.accessioned2015-08-05T16:46:38Z
dc.date.available2016-10-10T14:50:23Zen
dc.date.issued2015-09en_US
dc.identifier.citationBrockington, Samuel F.; Yang, Ya; Gandia‐herrero, Fernando ; Covshoff, Sarah; Hibberd, Julian M.; Sage, Rowan F.; Wong, Gane K. S.; Moore, Michael J.; Smith, Stephen A. (2015). "Lineageâ specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales." New Phytologist 207(4): 1170-1180.en_US
dc.identifier.issn0028-646Xen_US
dc.identifier.issn1469-8137en_US
dc.identifier.urihttps://hdl.handle.net/2027.42/112177
dc.publisherUniversity of Tubingenen_US
dc.publisherWiley Periodicals, Inc.en_US
dc.subject.othertaxonomically restricted genesen_US
dc.subject.otheranthocyaninen_US
dc.subject.otherCaryophyllalesen_US
dc.subject.otherlineage‐specific genesen_US
dc.subject.otherpigmentationen_US
dc.subject.otherbetalainsen_US
dc.titleLineage‐specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllalesen_US
dc.typeArticleen_US
dc.rights.robotsIndexNoFollowen_US
dc.subject.hlbsecondlevelNatural Resources and Environmenten_US
dc.subject.hlbtoplevelScienceen_US
dc.description.peerreviewedPeer Revieweden_US
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/112177/1/nph13441-sup-0001-FigS1-S4.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/112177/2/nph13441.pdf
dc.identifier.doi10.1111/nph.13441en_US
dc.identifier.sourceNew Phytologisten_US
dc.identifier.citedreferenceRognes T. 2011. Faster Smith‐Waterman database searches with inter‐sequence SIMD parallelisation. BMC Bioinformatics 12: 221.en_US
dc.identifier.citedreferenceKrajka‐Kuźniak V, Szaefer H, Ignatowicz E, Adamska T, Baer‐Dubowska W. 2012. Beetroot juice protects against N‐nitrosodiethylamine‐induced liver injury in rats. Food and Chemical Toxicology 50: 2027 – 2033.en_US
dc.identifier.citedreferenceLiu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, Linder CR. 2012. SATe‐II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Systematic Biology 61: 90 – 106.en_US
dc.identifier.citedreferenceLöytynoja A. 2014. Phylogeny‐aware alignment with PRANK. Methods in Molecular Biology 1079: 155 – 170.en_US
dc.identifier.citedreferenceLu X, Wang Y, Zhang Z. 2009. Radioprotective activity of betalains from red beets in mice exposed to gamma irradiation. European Journal of Pharmacology 615: 223 – 227.en_US
dc.identifier.citedreferenceMabry T. 1964. The betacyanins, a new class of red violet pigments, and their phylogenetic significance. New York, NY, USA: Roland Press.en_US
dc.identifier.citedreferenceMaddison WP, Maddison DR. 2015. Mesquite: a modular system for evolutionary analysis. version 3.03. URL http://mesquiteproject.org [accessed 15 March].en_US
dc.identifier.citedreferenceMatasci N, Hung L‐H, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M et al. 2014. Data access for the 1,000 Plants (1KP) project. GigaScience 3: 17.en_US
dc.identifier.citedreferenceMizutani M, Ohta D. 2010. Diversification of P450 genes during land plant evolution. Annual Review of Plant Biology 61: 291 – 315.en_US
dc.identifier.citedreferencePrice MN, Dehal PS, Arkin AP. 2010. FastTree 2‐approximately maximum‐likelihood trees for large alignments. PLoS One 5: e9490.en_US
dc.identifier.citedreferenceSasaki N, Abe Y, Goda Y, Adachi T, Kasahara K, Ozeki Y. 2009. Detection of DOPA 4,5‐dioxygenase (DOD) activity using recombinant protein prepared from Escherichia coli cells harboring cDNA encoding DOD from Mirabilis jalapa. Plant and Cell Physiology 50: 1012 – 1016.en_US
dc.identifier.citedreferenceShimada S, Inoue Y, Sakuta M. 2005. Anthocyanidin synthase in non‐anthocyanin‐producing Caryophyllales species. Plant Journal 44: 950 – 959.en_US
dc.identifier.citedreferenceShimada S, Otsuki H, Sakuta M. 2007. Transcriptional control of anthocyanin biosynthetic genes in the Caryophyllales. Journal of Experimental Botany 58: 957 – 967.en_US
dc.identifier.citedreferenceShimada S, Takahashi K, Sato Y, Sakuta M. 2004. Dihydroflavonol 4‐reductase cDNA from non‐anthocyanin‐producing species in the Caryophyllales. Plant and Cell Physiology 45: 1290 – 1298.en_US
dc.identifier.citedreferenceSimola DF, Wissler L, Donahue G, Waterhouse RM, Helmkampf M, Roux J, Nygaard S, Glastad KM, Hagen DE, Viljakainen L et al. 2013. Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality. Genome Research 23: 1235 – 1247.en_US
dc.identifier.citedreferenceSmith SA, Dunn CW. 2008. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24: 715 – 716.en_US
dc.identifier.citedreferenceStafford HA. 1994. Anthocyanins and betalains: evolution of the mutually exclusive pathways. Plant Science 101: 91 – 98.en_US
dc.identifier.citedreferenceStamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post‐analysis of large phylogenies. Bioinformatics 30: 1312 – 1313.en_US
dc.identifier.citedreferenceSuzuki M, Miyahara T, Tokumoto H, Hakamatsuka T, Goda Y, Ozeki Y, Sasaki N. 2014. Transposon‐mediated mutation of CYP76AD3 affects betalain synthesis and produces variegated flowers in four o'clock ( Mirabilis jalapa ). Journal of plant physiology 171: 1586 – 1590.en_US
dc.identifier.citedreferenceTanaka Y, Sasaki N, Ohmiya A. 2008. Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids. Plant Journal 54: 733 – 749.en_US
dc.identifier.citedreferenceThe Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796 – 815.en_US
dc.identifier.citedreferenceTomato Genome Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635 – 641.en_US
dc.identifier.citedreferenceWickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA et al. 2014. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences, USA 111: E4859 – E4868.en_US
dc.identifier.citedreferenceWu L‐C, Hsu H‐W, Chen Y‐C, Chiu C‐C, Lin Y‐I, Ho J‐AA. 2006. Antioxidant and antiproliferative activities of red pitaya. Food Chemistry 95: 319 – 327.en_US
dc.identifier.citedreferenceYagi M, Kosugi S, Hirakawa H, Ohmiya A, Tanase K, Harada T, Kishimoto K, Nakayama M, Ichimura K, Onozaki T et al. 2014. Sequence analysis of the genome of carnation ( Dianthus caryophyllus L.). DNA Research 21: 231 – 241.en_US
dc.identifier.citedreferenceYang Y, Moore MJ, Brockington SF, Soltis DE, Wong GK‐S, Carpenter EJ, Zhang Y, Chen L, Yan Z‐X, Xie Y‐L et al. 2015. Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Molecular Biology and Evolution. doi: 10.1093/molbev/msv081.en_US
dc.identifier.citedreferenceYang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24: 1586 – 1591.en_US
dc.identifier.citedreferenceZwickl D. 2000. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion, PhD Thesis. University of Texas, Austin, USA.en_US
dc.identifier.citedreferenceBate‐Smith EC, Lerner NH. 1954. Leuco‐anthocyanins. 2. Systematic distribution of leuco‐anthocyanins in leaves. Biochemical Journal 58: 126 – 132.en_US
dc.identifier.citedreferenceBischoff H. 1876. Das Caryophyllinenroth. Inaugural dissertation, University of Tubingen, Tubingen, Germany.en_US
dc.identifier.citedreferenceBoycheva S, Daviet L, Wolfender J‐L, Fitzpatrick TB. 2014. The rise of operon‐like gene clusters in plants. Trends in Plant Science 19: 447 – 459.en_US
dc.identifier.citedreferenceBremer B, Bremer K, Chase M, Fay M, Reveal J, Soltis D, Soltis P, Stevens P. 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society 161: 105 – 121.en_US
dc.identifier.citedreferenceBrockington SF, Alexandre R, Ramdial J, Moore M, Crawley S, Dhingra A, Hilu K, Soltis P, Soltis DE. 2009. Phylogeny of the Caryophyllales sensu lato: Revisiting hypotheses on pollination biology and perianth differentiation in the core Caryophyllales. International Journal of Plant Science 170: 627 – 643.en_US
dc.identifier.citedreferenceBrockington SF, Walker RH, Glover BJ, Soltis PS, Soltis DE. 2011. Complex pigment evolution in the Caryophyllales. New Phytologist 190: 854 – 864.en_US
dc.identifier.citedreferenceCai Y, Sun M, Corke H. 2003. Antioxidant activity of betalains from plants of the amaranthaceae. Journal of Agriculture and Food Chemistry 51: 2288 – 2294.en_US
dc.identifier.citedreferenceCampanella JJ, Smalley JV, Dempsey ME. 2014. A phylogenetic examination of the primary anthocyanin production pathway of the Plantae. Botanical Studies 55: 10.en_US
dc.identifier.citedreferenceChristenhusz MJM, Brockington SF, Christin P‐A, Sage RF. 2014. On the disintegration of Molluginaceae: a new genus and family ( Kewa, Kewaceae) segregated from Hypertelis, and placement of Macarthuria in Macarthuriaceae. Phytotaxa 181: 238 – 242.en_US
dc.identifier.citedreferenceChristinet L, Burdet FX, Zaiko M, Hinz U, Zrÿd J‐P. 2004. Characterization and functional identification of a novel plant 4,5‐extradiol dioxygenase involved in betalain pigment biosynthesis in Portulaca grandiflora. Plant Physiology 134: 265 – 274.en_US
dc.identifier.citedreferenceClement J, Mabry T. 1996. Pigment evolution in the Caryophyllales: a systematic overview. Botanica Acta 109: 360 – 367.en_US
dc.identifier.citedreferenceDohm JC, Lange C, Holtgräwe D, Sörensen TR, Borchardt D, Schulz B, Lehrach H, Weisshaar B, Himmelbauer H. 2012. Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene‐based physical and genetic mapping of the sugar beet genome ( Beta vulgaris ). Plant Journal 70: 528 – 540.en_US
dc.identifier.citedreferenceDohm JC, Minoche AE, Holtgräwe D, Capella‐Gutíerrez S, Zakrzewski F, Tafer H, Rupp O, Sörensen TR, Stracke R, Reinhardt R et al. 2014. The genome of the recently domesticated crop plant sugar beet ( Beta vulgaris ). Nature 505: 546 – 549.en_US
dc.identifier.citedreferenceEscribano J, Pedreño MA, García‐Carmona F, Muñoz R. 1998. Characterization of the antiradical activity of betalains from Beta vulgaris L. roots. Phytochemical Analysis 9: 124 – 127.en_US
dc.identifier.citedreferenceFinn RD, Miller BL, Clements J, Bateman A. 2014. iPfam: a database of protein family and domain interactions found in the Protein Data Bank. Nucleic acids research 42: D364 – D373.en_US
dc.identifier.citedreferenceFry BG, Roelants K, Winter K, Hodgson WC, Griesman L, Kwok HF, Scanlon D, Karas J, Shaw C, Wong L et al. 2010. Novel venom proteins produced by differential domain‐expression strategies in beaded lizards and gila monsters (genus Heloderma ). Molecular Biology and Evolution 27: 395 – 407.en_US
dc.identifier.citedreferenceGandía‐Herrero F, Cabanes J, Escribano J, García‐Carmona F, Jiménez‐Atiénzar M. 2013. Encapsulation of the most potent antioxidant betalains in edible matrixes as powders of different colors. Journal of Agriculture and Food Chemistry 61: 4294 – 4302.en_US
dc.identifier.citedreferenceGandía‐Herrero F, García‐Carmona F. 2012. Characterization of recombinant Beta vulgaris 4,5‐DOPA‐extradiol‐dioxygenase active in the biosynthesis of betalains. Planta 236: 91 – 100.en_US
dc.identifier.citedreferenceGoldman IL, Austin D. 2000. Linkage among the R, Y and Bl loci in table beet. Theoretical Applied Genetics 100: 337 – 343.en_US
dc.identifier.citedreferenceGoodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N et al. 2012. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research 40: D1178 – D1186.en_US
dc.identifier.citedreferenceGotoh O. 1992. Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences. Journal of Biological Chemistry 267: 83 – 90.en_US
dc.identifier.citedreferenceGrabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q et al. 2011. Full‐length transcriptome assembly from RNA‐Seq data without a reference genome. Nature Biotechnology 29: 644 – 652.en_US
dc.identifier.citedreferenceHaas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M et al. 2013. De novo transcript sequence reconstruction from RNA‐Seq: reference generation and analysis with Trinity. Nature Protocols 8: doi: 10.1038/nprot.2013.084.en_US
dc.identifier.citedreferenceHarris NN, Javellana J, Davies KM, Lewis DH, Jameson PE, Deroles SC, Calcott KE, Gould KS, Schwinn KE. 2012. Betalain production is possible in anthocyanin‐producing plant species given the presence of DOPA‐dioxygenase and L‐DOPA. BMC Plant Biology 12: 34.en_US
dc.identifier.citedreferenceHatlestad GJ, Akhavan NA, Sunnadeniya RM, Elam L, Cargile S, Hembd A, Gonzalez A, McGrath JM, Lloyd AM. 2014. The beet Y locus encodes an anthocyanin MYB‐like protein that activates the betalain red pigment pathway. Nature Genetics 47: 92 – 96.en_US
dc.identifier.citedreferenceHatlestad GJ, Sunnadeniya RM, Akhavan NA, Gonzalez A, Goldman IL, McGrath JM, Lloyd AM. 2012. The beet R locus encodes a new cytochrome P450 required for red betalain production. Nature Genetics 44: 816 – 820.en_US
dc.identifier.citedreferenceHuang S, Ding J, Deng D, Tang W, Sun H, Liu D, Zhang L, Niu X, Zhang X, Meng M et al. 2013. Draft genome of the kiwifruit Actinidia chinensis. Nature Communications 4: 2640.en_US
dc.identifier.citedreferenceIbarra‐Laclette E, Lyons E, Hernández‐Guzmán G, Pérez‐Torres CA, Carretero‐Paulet L, Chang T‐H, Lan T, Welch AJ, Juárez MJA, Simpson J et al. 2013. Architecture and evolution of a minute plant genome. Nature 498: 94 – 98.en_US
dc.identifier.citedreferenceKatoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30: 772 – 780.en_US
dc.identifier.citedreferenceKeller W. 1936. Inheritance of some major color types in beets. Journal of Agricultural Research 52: 27 – 38.en_US
dc.identifier.citedreferenceKhalturin K, Anton‐Erxleben F, Sassmann S, Wittlieb J, Hemmrich G, Bosch TCG. 2008. A novel gene family controls species‐specific morphological traits in hydra. PLoS Biology 6: e278.en_US
dc.identifier.citedreferenceKhalturin K, Hemmrich G, Fraune S, Augustin R, Bosch TCG. 2009. More than just orphans: are taxonomically‐restricted genes important in evolution? Trends in Genetics 25: 404 – 413.en_US
dc.identifier.citedreferenceYang Z, Nielsen R. 2002. Codon‐substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular Biology and Evolution 19: 908 – 911.en_US
dc.identifier.citedreferenceKhan MI, Sri Harsha PSC, Giridhar P, Ravishankar GA. 2012. Pigment identification, nutritional composition, bioactivity, and in vitro cancer cell cytotoxicity of Rivina humilis L. berries, potential source of betalains. LWT – Food Science and Technology 47: 315 – 323.en_US
dc.owningcollnameInterdisciplinary and Peer-Reviewed


Files in this item

Name:
nph13441-sup-0001-FigS1-S4.pdf
Size:
1.257MB
Format:
PDF
View/Open
Name:
nph13441.pdf
Size:
784.8KB
Format:
PDF
View/Open

Show simple item record

Remediation of Harmful Language

The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.

Accessibility

If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.