Table 1.
Species used for comparative genomic analysis.
Figure 1.
Pipeline of chloroplast genome assembly.
Details are described under Methods.
Table 2.
De novo assembly statistics for the three sequenced species.
Figure 2.
Coverage of Lemnoideae chloroplast genome by SOLiD system reads.
Depth of coverage was plotted along the genome coordinates. Blue peaks show the coverage.
Figure 3.
Alignment of Lemnoideae chloroplast genomes.
The sequence of L. minor chloroplast genome was compared to those of S. polyrhiza (top), W. lingulata (middle), W. australiana (bottom). Sequences were aligned in mVISTA and the annotation shown above the alignment corresponds to the L. minor genome. Grey arrows above the alignment indicate genes and their orientation. Thick black lines show the position of the IRs. The grey peaks determine the percent identity between two sequences of L. minor as the reference and our sequenced genomes.
Figure 4.
Complete chloroplast genome phylogeny of Lemnoideae.
The phylogram was drawn by Maximum Parsimony with 1000 replicates of bootstrap test. The tree was rooted by Phoenix dactylifera as an outgroup. Support from bootstrap value was shown at the nodes. The GenBank accessions used for the analyses are JN160603 (S. polyrhiza), DQ400350 (L. minor), JN160604 (W. lingulata), JN160605 (W. australiana) and GU811709 (P. dactylifera). The whole genome sequences were aligned by Multi-LAGAN and MEGA 5 was used to draw the tree.
Table 3.
Pairwise sequence divergence of the whole genome and protein coding regions in the subfamily Lemnoideae compared with those of the subfamily Pooideae (wheat, barley and Brachypodium).