Computational protocol: Leaf-Like Sepals Induced by Ectopic Expression of a SHORT VEGETATIVE PHASE (SVP)-Like MADS-Box Gene from the Basal Eudicot Epimedium sagittatum

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Protocol publication

[…] The fragment of EsSVP cDNA of E. sagittatum was obtained by 454 GS-FLX pyrosequencing technology (). Cloning of the full-length EsSVP gene was accomplished by using a 3′/5′-RACE (rapid amplification of cDNA ends) strategy as previously reported (), using GSP5-3 and GSP3-5 to amplify the 3′ and 5′ terminal regions of SVP-orthologous gene, respectively. Universal 3′ and 5′ PCR primers were supplied by the SMARTTM cDNA Library Construction Kit (Clontech, Palo Alto, CA, USA). For vector construction, the complete cDNA sequence of EsSVP was obtained by primer pairs EsSVP-V-F and EsSVP-V-R (Supplementary Table ; Supplementary Figure ). The sequences of selected species were downloaded from the NCBI GenBank Multiple alignment of predicted amino acid sequences were generated using Clustal W 1.83 () with a gap open penalty of 10.00 and a gap extension penalty of 0.05. Neighbor-joining (NJ) bootstrap analysis (1,000 replications) with the maximum composite likelihood model for the DNAs and the Poisson correction for the amino-acids were performed by MEGA 4 (). During the analyses, Arabidopsis SOC1 was used as an out-group. Sequence data from this article can be found in the GenBank/EMBL databases under the following accession numbers: SVP (NM_127820), AGL24 (NM_118587) and SOC1 (NM_130128) in Arabidopsis, potato StMADS11 (AF008652), StMADS16 (AY643736), rice OsMADS22 (AB107957), OsMADS47 (AY345221), OsMADS55 (AY345223), barley HvBM1 (AJ249142), HvBM10 (EF043040), AfSVP.1 (HQ173338) and AfSVP.2 (HQ173339) in Aquilegia formosa, MpMADS1 (AB050643) in Magnolia praecocissima and DlSVP (KM657947) in Dimocarpus longan. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics