Fig. 3.

Phylogenetic tree constructed from amino acid sequences of predicted LHC proteins from two diatoms (P. tricornutum and T. pseudonana; black branches), two Ostreococcus species (O. tauri and O. lucimarinus; green branches), and A. anophagefferens (red branches). The tree constructed in MEGA4 (SI Appendix, Fig. S1) is displayed here after manipulation of the original branch lengths in Hypertree (http://kinase.com/tools/HyperTree.html) to aid visualization of major features of the tree. None of the Aureococcus LHCs were closely related to green plastid lineage LHCs, although four belonged to a group found in both the green and red plastid lineages (group I). None of the Aureococcus LHCs clustered with the major fucoxanthin-chlorophyll binding proteins (FCP) of diatoms and other heterokonts (major FCP group). However, many Aureococcus LHCs did group with similar sequences from P. tricornutum and T. pseudonana (as well as LHCs from other red-lineage algae not included in this tree; groups A–K). There were also five groups of A. anophagefferens LHCs that were not closely related to any other LHCs (Aur1 to Aur5). Group G includes 16 LHCs from A. anophagefferens and 2 LHCs from T. pseudonana, and it shares a unique PHYMKG motif near the end of helix two, with 10 additional A. anophagefferens LHCs plus 5 more from the diatoms. Cyanobacteria such as Synechococcus do not possess LHC proteins.