Jmp 5.0.1a

JMP 5.01a (SAS Institute, Cary, NC) was used to analyze lifespan and stress survival data (log-rank tests) and negative geotaxis across age (two-way ANOVA). The severity of black ommatidia (categorical data) was analyzed with nonparametric Mann–Whitney tests or Kruskal–Wallis ANOVA followed by Dunn's multiple comparison using Prism 4.03 (GraphPad Software, San Diego, CA). Data for Ppt1 mRNA, PPT1 enzyme activity and negative geotaxis at a single age were analyzed with parametric t tests or one-way ANOVAs followed by Bonferroni multiple comparison tests using Prism 4.03. The number and percentage of GeneMania interactors from randomly seeded networks were compared to the CISD2/PPT1/CLN3 network by two-sided one-sample t tests. Statistical analyses on human CNVs were performed with the hypothesis that rare CNVs encompassing genes of interest would be enriched in cases compared to controls and thus one-tailed Fisher's exact tests were used.

BLAST and tBLASTx were used to compare sequences of candidate sweetpotato contigs/genes of GA biosynthesis and signaling, lignin biosynthesis, and upstream regulators, class I knotted 1-like and starch metabolism, derived from our published database (Firon et al., 2013 (link)) with Arabidopsis² and NCBI³ databases. For NAC-domain-containing sequences, in order to identify potential up-regulators of lignin and xylem development, homology against PlantTFDB database⁴ was performed. Selected sweetpotato NAC genes were further investigated by motif search⁵, and phylogenetic (using MEGA with neighbor-joining method and 1000 bootstrap replicates) analyses for their similarly to Arabidopsis genes, in order to identify potential orthologues of NAC075, VND, and SND genes (Supplementary Figure S2).
Data statistical analyses were performed using student’s t-test at P ≤ 0.05, using JMP 5.0.1a statistical software (SAS Institute Inc., NC, United States).