Computational protocol: SVP-like MADS Box Genes Control Dormancy and Budbreak in Apple

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Protocol publication

[…] The full-length apple ‘Royal Gala’ DAM-like (MdDAMb) and SVP-like (MdSVPa) transcripts were identified from the Plant & Food Research Malus EST database () by BLAST alignment (). The remaining DAM-like and SVP-like coding sequences were amplified using oligonucleotide primers designed from ‘Royal Gala’ partial sequences and previously reported apple DAM/SVP/JOINTLESS genes (Supplementary Table ). The predicted full length amino acid sequences were aligned with the full length of amino acid sequences of Arabidopsis SVP (AT2G22450) and AGL24 (AT4G24540), potato StMADS11 (AF008652), apple MdDAM1 (KT582786), MdDAM2 (KT582787), MdDAM4 (KT582789), MdJb (LC004730), apricot PmDAM6 (AB437345), leafy spurge EeDAM2 (EU339320), three pear DAM (PpyDAM1, PpyDAM2 and PpyDAM3) and one pear SVP (PpySVP) (), six peach DAM (PpeDAM1, PpeDAM2, PpeDAM3, PpeDAM4, PpeDAM5 and PpeDAM6) () and one peach SVP (PpeMADS57) (), trifoliate orange PtSVP (FJ373211), kiwifruit SVP genes (AcSVP1, AcSVP2, AcSVP3 and AcSVP4) (). The alignments were performed using Clustal W (opening = 10, extension = 0.2). Phylogenetic and molecular evolutionary analyses were conducted using MEGA version 7.0 (), minimum evolution phylogeny tested with 1000 bootstrap replicates and above 50% of the cut-off value for condensed tree. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Malus domestica