title: Colponemids represent multiple ancient alveolate lineages.
abstract: The alveolates comprise three well-studied protist lineages of significant environmental, medical, and economical importance: apicomplexans (e.g., Plasmodium), dinoflagellates (e.g., Symbiodinium), and ciliates (e.g., Tetrahymena). These major lineages have evolved distinct and unusual characteristics, the origins of which have proved to be difficult evolutionary puzzles. Mitochondrial genomes are a prime example: all three groups depart from canonical form and content, but in different ways. Reconstructing such ancient transitions is difficult without deep-branching lineages that retain ancestral characteristics. Here we describe two such lineages and how they illuminate the ancestral state of alveolate mitochondrial genomes. We established five clonal cultures of colponemids, predatory alveolates without cultured representatives and molecular data. Colponemids represent at least two independent lineages at the phylum level in multilocus phylogenetic analysis; one sister to apicomplexans and dinoflagellates, and the other at a deeper position. A genome survey from one strain showed that ancestral state of the mitochondrial genomes in the three major alveolate lineages consisted of an unusual linear chromosome with telomeres and a substantially larger gene set than known alveolates. Colponemid sequences also identified several environmental lineages as colponemids, altogether suggesting an untapped potential for understanding the origin and evolution of apicomplexans, dinoflagellates, and ciliates.
authors: Botany Department, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. Electronic address: janjan.cz@gmail.com.
authors: Jan
authors: J
authors: Janouškovec
authors: Botany Department, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Province 152742, Russian Federation.
authors: Denis V
authors: DV
authors: Tikhonenkov
authors: Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation; A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russian Federation.
authors: Kirill V
authors: KV
authors: Mikhailov
authors: Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation.
authors: Timur G
authors: TG
authors: Simdyanov
authors: Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation; A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russian Federation.
authors: Vladimir V
authors: VV
authors: Aleoshin
authors: Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Province 152742, Russian Federation.
authors: Alexander P
authors: AP
authors: Mylnikov
authors: Botany Department, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. Electronic address: pkeeling@mail.ubc.ca.
authors: Patrick J
authors: PJ
authors: Keeling
mesh_terms: D056893:Alveolata / Q000145:classification* / Q000235:genetics; D001483:Base Sequence; D044822:Biodiversity; D054629:Genome, Mitochondrial; D008969:Molecular Sequence Data; D010802:Phylogeny