Pipeline publication

[…] was used to estimate the divergence times with the Jules Cantor substitution model, with a log normal relaxed clock and Yule model. The chain length of MCMC analysis was 10,000,000. TimeTree44 is a public database containing divergence time estimates from various publications along with their own estimation. These estimates, ignoring the outliers, were used for selecting the range of lower and upper uniform calibration priors. The lower and upper calibration values were chosen as 1.9–12.8, 15.6–41, 58.6–95.1, 93.3–128.3, 101.2–156.3 and 110–216 for the most common ancestor of the seven species belonging to Solanum, Solanaceae, Solanales, asterids, dicotyledons and all plants, respectively. FigTree ( http://tree.bio.ed.ac.uk/software/figtree) was used to view the phylogenetic trees. Synteny analysis of the 15 pseudo-chromosomes against the chromosomes of other species was performed using the MCScanX toolkit69 utilizing the following options: ‘-m 15 -e 1e-10 -k 50'. PAML's70 yn00 module was used to calculate the Ks values of the orthologous and paralogous gene pairs in the sytenic regions using Nei-Gojobori method. The assembled genome was compared against the genome of I. trifida (Supplementary Fig. 19)., All sequencing data used in this work are available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession numbers DRA001121, DRA002710, and DRA004158 for PacBio and Illumina sequencing, DRA002647 for RNA-seq, and DRA002758 for RAD-seq. The genomic assembly sequences are available from accession numbers BDFN01000001-BDFN01003416 (scaffolds), and two organelle DNA sequences are available from accession numbers AP017303-AP0173 […]

Pipeline specifications

Software tools FigTree, MCScanX, PAML
Organisms Ipomoea nil