Table 1.
Isolates utilized in this study.
Table 2.
Quantification of features in three Halamphora species, including % non-coding sequence, % GC, the number of ORFs (the number of ORFs shared by > 1 Halamphora genome), and gene density.
Fig 1.
Plastid genome map of Halamphora calidilacuna.
Genes on the outside are transcribed clockwise and those on the inside counterclockwise. The inner ring displays GC content in grey.
Fig 2.
Maximum likelihood phylogram inferred from twenty chloroplast encoded markers (see Materials and methods).
Node support is given as maximum likelihood bootstrap values (1000 bootstrap replicates). Asterisks indicate 100% support. Letters indicate morphological groups of diatoms as follows: (A) ‘radial’ centric; (B) ‘polar’ centric; (C) araphid; and (D) biraphid pennate diatoms.
Fig 3.
Gene order comparison of plastid genomes of eight biraphid pennate diatoms (three Halamphora spp. are from this study) with one copy of the inverted repeat removed prior to analysis.
Alignment and resulting locally collinear blocks (LCBs) were generated using MAUVE. Relationships between taxa displayed as a cladogram to the left of the diagram are based on Fig 2.
Fig 4.
Gene order comparison of plastid genomes of six thalassiosiroid diatoms with one copy of the inverted repeat removed prior to analysis.
Alignment and resulting locally collinear blocks (LCBs) were generated using MAUVE. Relationships between taxa displayed as a cladogram to the left of the diagram are based on Fig 2.
Fig 5.
Plot describing the relationship between rearrangement distance and Jukes-Cantor genetic distance.
Blue circles represent biraphid diatoms. Red triangles represent thalassiosiroid diatoms. Regression coefficient for the biraphid diatoms is significant (p = 0.04, R2 = 0.136), whereas for the thalassiosiroid diatoms it is not (p = 0.34, R2 = 0.069).