Fig 1.
Circular gene map of I. dabieshanensis chloroplast genome.
The gray arrowheads indicate gene directions. Genes inside and outside the circle represent transcribed clockwisely and counterclockwisely. Different functional genes are color coded. The innermost darker gray conforms to GC content, whereas the lighter gray conforms to AT content. LSC, large single copy region; SSC, small single copy region; IR, inverted repeat.
Table 1.
Summary of I. dabieshanensis chloroplast genome.
Table 2.
List of genes in the chloroplast genome of I. dabieshanensis.
Fig 2.
Distribution of SSR Types in I. dabieshanensis chloroplast genome.
A) Number of SSRs detected; B) Number of identified SSRs in different repeat class types; C) Number of identified SSRs in different genomic regions; and D) Number of identified SSRs in intergenic regions, introns, and coding regions.
Fig 3.
Analysis of identified long repeat sequences in I. dabieshanensis chloroplast genome.
A) Number of long repeats in four identified types; B) Number of palindromic repeats by length; and C) Number of forward repeats by length.
Table 3.
Codon usage in I. dabieshanensis.
Fig 4.
Chloroplast genome comparisons among four Ilex species by mVISTA.
The chloroplast genome of I. dabieshanensis was used as a reference. Gray arrows above the alignment represent gene orientation. Different genome regions are color-coded as exons (purple bars), rRNA or tRNA (sky-blue bars), and non-coding sequences (CNS, pink bars). The horizontal axis indicates the coordinates within the chloroplast genome and vertical scale indicates the percentage of identity ranging from 50 to 100%. Regions with sequence variation among the four Ilex species were marked with white peaks.
Fig 5.
Comparisions of the SSC/IRs and LSC/IRs junctions among four Ilex chloroplast genomes.
Colored boxes above the strip with scaled sequence length represent the denoted genes. Between boxed genes and boundaries are the gaps in base length (bp). JLB, JSB, JSA, and JLA indicate IRB/LSC, IRB/SSC, IRA/SSC, and IRA/LSC junctions, respectively.
Fig 6.
Phylogenetic tree for 19 Ilex species in the family Aquifoliaceae using Maximum Likelihood (ML) method, based on alignments of complete chloroplast genomes.
The genomes of Helwingia chinensis and H. himalaica were set as outgroups. Numbers next to the branches indicated bootstrap values from 1,000 replicates.