Table 1.
The gene content of the C. nucifera mt genome.
Fig 1.
Circular display of C. nucifera mt genome.
We display (from outside to inside): physical map scaled in kb; coding sequences transcribed in the clockwise and counterclockwise directions (nad in red; cob, matR and mttB in green; cox in blue; atp in purple; ccm in orange; rpl in yellow; rps in dark red; rRNA in dark green; tRNA in dark blue; orf in dark purple; and others in black); chloroplast-derived regions (green); repeats (forward repeats in green, palindrome repeats in red and tandem repeats in blue); RNA edit sites (synonymous in green and non-synonymous in red); gene conserve scores (black); proper HiSeq mate-pair (MP) reads percent with insert size 5kb and 8kb (blue); and the four regions (thick lines indicate IRs and thin lines indicate LSC and SSC). * indicates pseudogenes.
Fig 2.
Phylogenetic trees of 31 mt proteins from 19 plant species.
Shown in the left is a maximum parsimony tree and the right is a maximum likelihood tree based on MEGA 6.06. The C. nucifera mt proteins form a cluster with those of P. dactylifera and B. umbellatus among monocotyledons.
Table 2.
Codon usage and codon-anticodon recognition pattern in the C. nucifera mt genome.
Table 3.
Mt transcriptome profiles of the 8 coconut RNA-Seq datasets.
Table 4.
The mt read coverage of the 8 coconut RNA-Seq datasets.
Fig 3.
Circular display of C. nucifera mt transcriptomes.
We display (from outside to inside): physical map scaled in kb; coding sequences transcribed in the clockwise and counterclockwise directions (nad in red; cob, matR and mttB in green; cox in blue; atp in purple; ccm in orange; rpl in yellow; rps in dark red; rRNA in dark green; tRNA in dark blue; orf in dark purple; and others in black); histogram of transcriptome data (plus strand in red and minus strand in green, standing for normalized average coverage value per 100 bp ranging from 0 to 100) for sample Health_leaf1, CYD_leaf, Callus, RWDS_leaf, Endosperm, Embryo, Health_leaf2 and Leaf_fruit; coding sequences transcribed in the clockwise and counterclockwise directions; and the four regions (thick lines indicate IRs and thin lines indicate LSC and SSC). * indicates pseudogene.
Fig 4.
Expression patterns of mt genes among 8 RNA-Seq datasets.
The expression levels are normalized based on DEseq.