PMC

We used 40 house-keeping (conserved over diverse plant lineages) genes for hierarchical clustering (Manhattan distance method). Red and green indicate high and low levels of gene expression, respectively.

We constructed an ML tree using PHYML (version 3.0) (Chara vulgaris as outgroup, see for details). Nodes receive over 90% bootstrap replicates are indicated. P. dactylifera mt genome rooted at the basal position of monocots (red).

We analyzed long repeats (repeat unit >50 bp) using REPuter and tandem repeats based on Tandem Repeat Finder (see for details). The genus names are used to represent the sequenced mitochondrial genomes and arranged according to their relative phylogenetic positions in .

Native tRNA genes in mitochondrial and chloroplast genomes are shown in open square and circles, respectively. Solid squares indicate cp-derived tRNAs found in mt genome and ψ stands for pseudogene. There are ten tRNAs (their anticodons are highlighted in bold) that are gradually lost in genome evolution and four tRNAs (their anticodons are underlined) that are gradually replaced by their cp-derived counterparts. These eight mt genomes are listed according to their relative phylogenetic positions in .

We display (starting from outside to inside): physical map scaled in kb, coding sequences transcribed in the clockwise (red) and counterclockwise directions (blue), chloroplast-derived regions (green boxes), sequence repeats (black), histogram of transcriptome data (green bar, standing for average RPKM value per 200 bp, transformed using natural logs and ranging from 0 to 10), GC content variations (brown bar in a 500 bp sliding window and 500 bp increments), and SOLiD mate-pair (MP) read validation (sliding window 2 kb, MP insertion size 5–6 kb, Step size 15 kb). This figure was generated by using the Circos program . Ψ indicates pseudogene.