A Comparative Genomics Approach to the Evolution of Eukaryotes and their Mitochondria1

Abstract

The Organelle Genome Megasequencing Program (OGMP) investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP. Some of the most interesting protists include the jakobid flagellates Reclinomonas americana, Malawimonas jakobiformis, and Jakoba libera, which share ultrastructural similarities with amitochondriate retortamonads, and harbor mitochondrial genes not seen before in mtDNAs of other organisms. In R. americana and J. libera, gene clusters are found that resemble, to an unprecedented degree, the contiguous ribosomal protein operons str, S10, spc, and alpha of eubacteria. In addition, their mtDNAs code for an RNase P RNA that displays all the elements of a bacterial minimum consensus structure. This structure has been instrumental in detecting the rnpB gene in additional protists. Gene repertoire and gene order comparisons as well as multiple-gene phylogenies support the view of a single endosymbiotic origin of mitochondria, whose closest extant relatives are Rickettsia-type alpha-Proteobacteria.

DNA Fingerprinting Analysis of the GenusPhytophthorain Korea

“…brown) algae, has been well established using molecular phylogenies that are based on ribosomal RNA (rRNA) sequences (Kumar and Rzhetsky, 1996;Paquin et al, 1997;van de Peer and de Wachter, 1997). Recently, these findings were supported by results of analyses of mitochondrial proteins (Lang et al, 1999) and four protein-encoding chromosomal genes (Baldauf et al, 2000). From these analyses, it became evident that oomycetes have the ability to infect plants independent of other eukaryotic plant pathogens and are likely to have unique mechanisms for doing so.…”

Molecular Genetics of Pathogenic Oomycetes

“…Similar phylogenetic affinity to fungal sequences was also observed for exo-1,3-␤-glucanases and an endo-1,3-␤-glucanase from P. infestans (61). The phylogenies of these enzymes are unexpected and contrast with phylogenies obtained using ribosomal sequences or compiled protein sequences from mitochondrial and housekeeping chromosomal genes (2,51,72,102). These exceptional phylogenies could reflect convergent evolution through which phylogenetically distinct enzymes evolved to share significant similarity, perhaps by targeting similar substrates.…”

Wolbachiagenome integrated in an insect chromosome: Evolution and fate of laterally transferred endosymbiont genes

“…These organelles are evolutionarily of bacterial endosymbiont origins (Margulis 1981), acquired by ancestral eukaryotes very anciently (Hedges et al 2004); most of their original gene repertoire has been lost in the evolutionary course, leading to drastically reduced organellar genomes (Lang et al 1999;Simpson and Stern 2002), and some of the genes are transferred to the nuclear genome where such genes are transcribed, translated, and transported to the organelles for functioning (Leister 2003;Brown 2003). Aside from the ancient endosymbiotic gene transfers, a large number of organellar genomic DNA fragments of much more recent origins are present in the nuclear genomes of diverse eukaryotes, indicating that endosymbiotic gene transfer is a ubiquitous and currently ongoing process that pervades nuclear DNA dynamics (Bensasson et al 2001;Timmis et al 2004).…”