The FT/TFL1 gene family controls important aspects of plant development: MFT-like genes affect germination, TFL1-like genes act as floral inhibitors, and FT-like genes are floral activators. Gene duplications produced paralogs with modified functions required by the specific lifestyles of various angiosperm species. We constructed the transcriptome of the weedy annual plant Chenopodium rubrum and used it for the comprehensive search for the FT/TFL1 genes. We analyzed their phylogenetic relationships across Amaranthaceae and all angiosperms. We discovered a very ancient phylogenetic clade of FT genes represented by the CrFTL3 gene of C. rubrum Another paralog CrFTL2 showed an unusual structural rearrangement which might have contributed to the functional shift. We examined the transcription patterns of the FT/TFL1 genes during the vegetative growth and floral transition in C. rubrum to get clues about their possible functions. All the genes except for the constitutively expressed CrFTL2 gene, and the CrFTL3 gene, which was transcribed only in seeds, exhibited organ-specific expression influenced by the specific light regime. The CrFTL1 gene was confirmed as a single floral activator from the FT/TFL1 family in C. rubrum Its floral promoting activity may be counteracted by CrTFL1 C. rubrum emerges as an easily manipulated model for the study of floral induction in weedy fast-cycling plants lacking a juvenile phase.

Institute of Experimental Botany Academy of Sciences of the Czech Republic 165 02 Prague 6 Czech Republic

Institute of Experimental Botany Academy of Sciences of the Czech Republic 165 02 Prague 6 Czech Republic Department of Experimental Plant Biology Faculty of Natural Sciences Charles University 128 44 Prague 2 Czech Republic

Institute of Experimental Botany Academy of Sciences of the Czech Republic 165 02 Prague 6 Czech Republic Department of Genetics and Microbiology Faculty of Natural Sciences Charles University 128 44 Prague 2 Czech Republic

Zobrazit více v PubMed

Ahn J. H., Miller D., Winter V. J., Banfield M. J., Lee J. H., et al. , 2006.  A divergent external loop confers antagonistic activity on floral regulators PubMed PMC

Blackman B. K., Strasburg J. L., Raduski A. R., Michaels S. D., Rieseberg L. H., 2010.  The role of recently derived PubMed PMC

Bolger A. M., Lohse M., Usadel B., 2014.  Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114–2120. PubMed PMC

Cháb D., Kolář J., Olson M. S., Štorchová H., 2008.  Two PubMed

Coelho C. P., Minow M. A., Chalfun A., Colasanti J., 2014.  Putative sugarcane PubMed PMC

Conti L., Bradley D., 2007. PubMed PMC

Corbesier L., Vincent C., Jang S. H., Fornara F., Fan Q. Z., et al. , 2007.  FT protein movement contributes to long-distance signaling in floral induction of PubMed

Cumming B. G., 1967.  Early-flowering plants, pp. 277–299 in

D’Aloia M., Bonhomme D., Bouche F., Tamseddak K., Ormenese S., et al. , 2011.  Cytokinin promotes flowering of Arabidopsis via transcriptional activation of the PubMed

Dohm J. C., Minoche A. E., Holtgräwe D., Capella-Gutierrez S., Zakrzewski F., et al. , 2014.  The genome of the recently domesticated crop plant sugar beet ( PubMed

Drabešová J., Cháb D., Kolář J., Haškovcová K., Štorchová H., 2014.  A darklight transition triggers expression of the floral promoter PubMed PMC

Duarte J. M., Wall P. K., Edger P. P., Landherr L. L., Ma H., et al. , 2010.  Identification of shared single copy nuclear genes in PubMed PMC

Edgar R. C., 2004.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792–1797. PubMed PMC

Fuentes-Bazan S., Mansion G., Borsch T., 2012.  Towards a species level tree of the globally diverse genus Chenopodium (Chenopodiaceae). Mol. Phylogenet. Evol. 62: 359–374. PubMed

Goodstein D. M., Shu S., Howson R., Neupane R., Hayes R. D., et al. , 2012.  Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40: D1178–D1186. PubMed PMC

Grabherr M. G., Haas B. J., Yassour M., Levin J. Z., Thompson D. A., et al. , 2011.  Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29: 644–652. PubMed PMC

Hanano S., Goto K., 2011. PubMed PMC

Hanzawa Y., Money T., Bradley D., 2005.  A single amino acid converts a repressor to an activator of flowering. Proc. Natl. Acad. Sci. USA 102: 7748–7753. PubMed PMC

Harig L., Beinecke F. A., Oltmanns J., Muth J., Müller O., et al. , 2012.  Proteins from the PubMed

Hayama R., Agashe B., Luley E., King R., Coupland G., 2007.  A circadian rhythm set by dusk determines the expression of PubMed PMC

Hedman H., Källman T., Lagercrantz U., 2009.  Early evolution of the PubMed

Ho W. W. H., Weigel D., 2014.  Structural features determining flower-promoting activity of PubMed PMC

Huang N. C., Jane W. N., Chen J., Yu T. S., 2012. PubMed

Jaeger K. E., Wigge P. A., 2007.  FT protein acts as a long-range signal in Arabidopsis. Curr. Biol. 17: 1050–1054. PubMed

Kalgren A., Gyllestrand N., Källman T., Sundström J. F., Moore D., et al. , 2011.  Evolution of the PEBP gene family in plants: functional diversification in seed plant evolution. Plant Physiol. 156: 1967–1977. PubMed PMC

Kardailsky I., Shukla V., Ahn J. H., Dagenais N., Christensen S. K., et al. , 1999.  Activation tagging of the floral inducer PubMed

Kobayashi Y., Kaya H., Goto K., Iwabuchi M., Araki T., et al. , 1999.  A pair of related genes with antagonistic roles in mediating flowering signals. Science 286: 1960–1962. PubMed

Kolano B., Tomczak H., Molewska R., Jellen E. N., Maluszynska J., 2012.  Distribution of 5S and 35S rRNA gene sites in 34

Kozik, A., I. Kozik, H. Van Leeuwen, A. Van Deynze, and R. Michelmore, 2008 Eukaryotic ultra conserved orthologs and estimation of gene capture in EST libraries. Plant and Animal Genomes Conference XVI, San Diego.

Lachowiec J., Shen X., Queitsch C., Carlgorg Ö., 2015.  A genome-wide association analysis reveals epistatic cancellation of additive genetic variance for root length in PubMed PMC

Langmead B., Trapnell C., Pop M., Salzberg S. L., 2009.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25. PubMed PMC

Li B., Dewey C. N., 2011.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12: 323. PubMed PMC

Li B., Fillmore N., Bai Y., Collins M., Thomson J. A., et al. , 2014.  Evaluation of PubMed PMC

Li W., Godzik A., 2006.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658–1659. PubMed

Librado P., Rozas J., 2009.  DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451–1452. PubMed

Libus J., Štorchová H., 2006.  Quantification of cDNA generated by reverse transcription of total RNA provides a simple alternative tool for quantitative RT-PCR normalization. Biotechniques 41: 156–164. PubMed

Lifschitz E., Ayre B. G., Eshed Y., 2014.  Florigen and anti-florigen – a systemic mechanism for coordinating growth and termination in flowering plants. Front. Plant Sci. 5: 465. PubMed PMC

Loeve A., Loeve D., 1982.  IOPB chromosome number reports LXXIV. Taxon 31: 120–126.

Martin J. A., Wang Z., 2011.  Next-generation transcriptome assembly. Nat. Rev. Genet. 13: 671–682. PubMed

Nakamura Y., Andres F., Kanehara K., Liu Y. C., Doermann P., et al. , 2014. PubMed PMC

Nakasugi K., Crowhurst R., Bally J., Waterhouse P., 2014.  Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant PubMed PMC

Navarro C. J. A., Abelenda E., Cruz-Oró C. A., Cuéllar S., Tamaki S., et al. , 2011.  Control of flowering and storage organ formation in potato by PubMed

O’Neil S. T., Dzurisin J. D. K., Carmichael R. D., Lobo N. F., Emrich S. J., et al. , 2010.  Population-level transcriptome sequencing of nonmodel organisms PubMed PMC

Pin P. A., Benlloch R., Bonnet D., Wremerth-Weich E., Kraft T., et al. , 2010.  An antagonistic pair of PubMed

Robertson G., Schein J., Chiu R., Corbett R., Field M., et al. , 2010. PubMed

Ryu J. Y., Park C. M., Seo P. J., 2011.  The floral repressor PubMed PMC

Schulz M. H., Zerbino D. R., Vingron M., Birney E., 2012.  Oases: robust PubMed PMC

Seidlová F., Krekule J., 1973.  The negative response of photoperiodic floral induction in

Simon R., Igeno M. I., Coupland G., 1996.  Activation of floral meristem identity genes in Arabidopsis. Nature 384: 59–62. PubMed

Stamatakis A., 2014.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313. PubMed PMC

Trapnell C., Williams B. A., Pertea G., Mortazavi A., Kwan G., et al. , 2010.  Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nat. Biotechnol. 28: 511–515. PubMed PMC

Vaňková R., Petrášek J., Zažímalová E., Kamínek M., Motyka V., et al. , 2014.  Auxins and cytokinins in plant development ... and interactions with other phytohormones 2014. J. Plant Growth Regul. 33: 709–714.

Veit J., Wagner E., Albrechtova J. T. P., 2004.  Isolation of a PubMed

Veit J., Wagner E., Albrechtova J. T. P., 2006.  Floral dip transformation of

Wada K. C., Yamada M., Shiraya T., Takeno K., 2010.  Salicylic acid and the flowering gene PubMed

Wang Z., Zhou Z. K., Liu Y. F., Liu T. F., Li Q., et al. , 2015.  Functional evolution of phosphatidylethanolamine binding proteins in soybean and arabidopsis. Plant Cell 27: 323–336. PubMed PMC

Webb B., Sali A., 2014.  Protein structure modeling with MODELLER. Methods Mol. Biol. 1137: 1–15. PubMed

Wickland D. P., Hanzawa Y., 2015.  The PubMed

Xi W., Liu C., Hou X., Yu H., 2010. PubMed PMC

Xie Y., Wu G., Tang J., Luo R., Patterson J., et al. , 2014.  SOAPdenovo-Trans, PubMed

Yang Y., Smith S. A., 2013.  Optimizing PubMed PMC

Zhang J., Ruhlman T. A., Mower J. P., Jansen R. K., 2013.  Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing. BMC Plant Biol. 13: 228. PubMed PMC

A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in Chenopodium

The FLOWERING LOCUS T LIKE 2-1 gene of Chenopodium triggers precocious flowering in Arabidopsis seedlings

Chenopodium ficifolium flowers under long days without upregulation of FLOWERING LOCUS T (FT) homologs