Fig 1.
Chloroplast genome of Ipomoea batats.
The outer circle shows positions of genes in the large single copy (LSC), small single copy (SSC), and two inverted repeat (IR A and IR B) regions. The inner circle is a graph depicting GC content across the genome. Plastome maps were generated in OGDraw v1.2.
Table 1.
Functional genes encoded by the sweet potato cp genome (72 single-copy genes and 11 two-copy genes).
Table 2.
Codon usage of the sweet potato cp genome.
Fig 2.
Chloroplast genome alignment among species in Ipomoea genus.
The relative position of tRNA genes were determined and marked as short vertical line in black. The thickness of the vertical bar represented the relative length of the tRNA genes. The LSC, SSC and IRs regions of each chloroplast genome were shown in four different colors.
Fig 3.
Comparison of gene distribution in chloroplast genomes of sweet potato and other three inter- and intra-Ipomoea species.
The relative position of functional-protein encoding genes were determined and marked as short vertical line in black. The thickness of the vertical bar represented the relative length of the genes. The name and position of some differential genes between two genomes were marked. The LSC, SSC and IRs regions of each chloroplast genome were shown in four different colors (except for Medicago truncatula with incomplete genome).
Table 3.
Repeat sequences and their distribution in cp genome of sweet potato.
Fig 4.
Boundary gene-flow and IR region expansion/contraction events.
Comparison of the junction positions of IR boundaries among 11 basal angiosperms cp genome. ILa, ILb represented the positions between the two IRs and the LSC region, ISa and ISb represented the positions between the two IRs and the SSC region.
Fig 5.
Gene map and genome alignment of 13 basal important angiosperms species.
MAUVE multiple alignment implemented in Geneious. Colored outlined blocks surround regions of the genome sequence that aligned with part of another genome. The coloured bars inside the blocks are related to the level of sequence similarities. Lines link blocks with homology between two genomes.
Fig 6.
Phylogram based on sequence analysis of 77 chloroplast genes from 33 plant species.
Numbers above each node indicate the ML bootstrap support values. The current taxonomic classifications are indicated on the right.
Table 4.
Position of RNA editing sites in chloroplast transcripts of sweet potato.
Fig 7.
Differentially expressed transcripts (DETs) of cp genes in sweet potato.
(A) Numbers of DETs in leaves and stems of sweet potato. PS, CR, EM, MP, PG represented genes related to photosynthesis, chloro-respiration, expression machinery, metabolic pathway and pseudogenes. (B) Numbers of DETs among young leaves (YL), mature leaves (ML) and stems in sweet potato. The Up-(red) and down-regulated (black) statistics of DETs were calculated in edgeR.
Fig 8.
Expression levels of some DETs in young leaves (YL), mature leaves (ML) and stems.
(A) The expression of 9 DETs identified in digital gene expression profile. (B) Validation the expression of these DETs in relative real-time PCR-based quantification.