Acquisition of cyanobacterial genes in green/red plant genomes http://mbe.oxfordjournals.org/cgi/content/abstract/25/4/748?etoc Genes of Cyanobacterial Origin in Plant Nuclear Genomes Point to a Heterocyst-Forming Plastid Ancestor * Oliver Deusch^* , Giddy Landan^{dagger} , Mayo Roettger^* , Nicole Gruenheit^* , Klaus V. Kowallik^* , John F. Allen^{ddagger} , William Martin^* and Tal Dagan^* * Plastids are descended from a cyanobacterial symbiosis which^ occurred over 1.2 billion years ago. During the course of endosymbiosis,^ most genes were lost from the cyanobacterium's genome and many^ were relocated to the host nucleus through endosymbiotic gene^ transfer (EGT). The issue of how many genes were acquired through^ EGT in different plant lineages is unresolved. Here, we report^ *the genome-wide frequency of gene acquisitions from cyanobacteria^ in 4 photosynthetic eukaryotes---/Arabidopsis/, rice, /Chlamydomonas/,^ and the red alga /Cyanidioschyzon/*---by comparision of the^ 83,138 proteins encoded in their genomes with 851,607 proteins^ encoded in 9 sequenced cyanobacterial genomes, 215 other reference^ prokaryotic genomes, and 13 reference eukaryotic genomes. The^ analyses entail *11,569 phylogenies *inferred with both maximum^ likelihood and Neighbor-Joining approaches. Because each phylogenetic^ result is dependent not only upon the reconstruction method^ but also upon the site patterns in the underlying alignment,^ we investigated how the reliability of site pattern generation^ via alignment affects our results: if the site patterns in an^ alignment differ depending upon the order in which amino acids^ are introduced into multiple sequence alignment---N- to^ C-terminal versus C- to N-terminal---then the phylogenetic^ result is likely to be artifactual. Excluding unreliable alignments^ by this means, we obtain a conservative estimate, wherein *about^ 14% of the proteins examined in each plant genome indicate a^ cyanobacterial origin *for the corresponding nuclear gene, with^ higher proportions (17--25%) observed among the more reliable^ alignments. The identification of cyanobacterial genes in plant^ genomes affords access to an important question: From which^ type of cyanobacterium did the ancestor of plastids arise? *Among^ the 9 cyanobacterial genomes sampled, /Nostoc/ sp. PCC7120 and^ /Anabaena variabilis/ ATCC29143 were found to harbor collections^ of genes which are---in terms of presence/absence and sequence^ similarity---more like those possessed by the plastid ancestor^ *than those of the other 7 cyanobacterial genomes sampled here.^ This suggests that the ancestor of plastids might have been^ an organism more similar to filamentous, heterocyst-forming^ (nitrogen-fixing) representatives of section IV recognized in^ Stanier's cyanobacterial classification. Members of section^ IV are very common partners in contemporary symbiotic associations^ involving endosymbiotic cyanobacteria, which generally provide^ nitrogen to their host, consistent with suggestions that fixed^ nitrogen supplied by the endosymbiont might have played an important^ role during the origin of plastids.^ *Key Words:* endosymbiosis . phylogenomics . multiple sequence alignment . plastid origin . nitrogen