Figure 1.
Gene map of the Monomorphina aenigmatica (UTEX 1284) plastid genome.
Genes (filled boxes) located inside/outside the map are transcribed clockwise/counterclockwise. Introns are denoted by open boxes whereas intronic ORFs are illustrated as half-height boxes within the open boxes. tRNA genes are indicated by the one-letter amino acid code followed by the anticodon in parentheses. ORFs smaller than 150 amino acids are not shown. A+T/G+C content are shown in the inner circle in light and dark grey, respectively. Conserved gene clusters between M. aenigmatica and E. gracilis are denoted by brackets: rpoB to Y(gua), M1(cau) to L(caa), rrs to rrl, and S(gcu) to H(gug).
Table 1.
Main features of euglenid plastid DNAs and their closest known relative.
Table 2.
Intron insertion sites in M. aenigmatica that are shared with other euglenid plastid DNAs.
Table 3.
Intron insertion sites unique to M. aenigmatica.
Figure 2.
Euglena gracilis twintron insertion sites found in M. aenigmatica.
Internal introns not found in M. aenigmatica are indicated by dashed lines. The total length of each insertion site is indicated on the right. Group II (GII) and group III (GIII) introns are indicated below the corresponding introns. Maen, Monomorphina aenigmatica; Egra, Euglena gracilis. The number after the period corresponds to the insertion site on the gene. In psbC.Egra.2, the fragmented ORF spliced together after excision of the internal introns is marked by asterisks.
Figure 3.
Phylogenetic mapping of intron insertion sites among euglenid chloroplast genomes.
At the top is a matrix showing the number of insertion sites shared between pairwise taxa (shared twintron insertions sites are indicated between brackets). At the bottom is a cladogram showing the distribution of shared intron insertion sites across the euglenids. The total number of insertion sites for each species is indicated between parentheses below its name. Insertions across the phylogenetic tree are denoted by triangles. For this analysis, the ambiguous rpoB intron insertion sites were considered distinct. The no-longer-photosynthetic E. longa was not included in this figure due to its many gene losses. The phylogenetic relationships described here are schematized from Kim et al. [21].