No description available.

Helicosporidia are single-celled obligate endoparasites of invertebrates. They have a unique morphology and infection strategy, which make them unlike any other eukaryote. Molecular data were produced to clarify their phylogenetic relationship and to examine the evolution of their cryptic plastid. Phylogenetic analyses of 69 ribosomal proteins identified from an expressed sequence tag (EST) library showed that Helicosporidia are derived green algae and more specifically, are related to the trebouxiophyte algae. An obligate parasitic lifestyle is rare among plant and algal groups, and because Helicosporidium possesses no pigments and no chloroplast-like structure has been identified, photosynthetic ability has presumably been lost in this organism. I sought to examine the role that a relict plastid might play in Helicosporidium. I identified ESTs of 20 putatively plastid-targeted enzymes that are involved in a wide variety of metabolic pathways. As expected, no components of photosynthesis were found, but components of other metabolic pathways including sulfur metabolism and fatty acid, isoprenoid and heme biosynthesis suggest that Helicosporidium retains its plastid for these functions. The complete plastid genome of this species of Helicosporidium was sequenced and revealed only four protein-coding genes not involved in transcription or translation, with two of these confirming the metabolic functions suggested by the nuclear-encoded, plastid-targeted genes identified from the ESTs. In addition, the Helicosporidium plastid genome is one of the smallest known (37.5 kb). Its reduced size results from loss of many genes commonly found in plastids of other plants and algae (including all proteins that function in photosynthesis), elimination of duplicated genes and redundant tRNA isoacceptors, and minimization of intergenic spaces. The Helicosporidium plastid genome is also highly structured, with each half of the circular genome containing nearly all genes on one strand. Both the structure and content of the plastid genome and the deduced function of the organelle show parallels with the relict plastid found in the malaria parasite, Plasmodium falciparum. These unrelated organisms each evolved from photosynthetic ancestors, and the convergence in form and function of their relict plastids suggest that common forces shape plastid evolution, following the switch from autotrophy to parasitism.

Helicosporidia are single-celled obligate endoparasites of invertebrates. They have a unique morphology and infection strategy, which make them unlike any other eukaryote. Molecular data were produced to clarify their phylogenetic relationship and to examine the evolution of their cryptic plastid. Phylogenetic analyses of 69 ribosomal proteins identified from an expressed sequence tag (EST) library showed that Helicosporidia are derived green algae and more specifically, are related to the trebouxiophyte algae. An obligate parasitic lifestyle is rare among plant and algal groups, and because Helicosporidium possesses no pigments and no chloroplast-like structure has been identified, photosynthetic ability has presumably been lost in this organism. I sought to examine the role that a relict plastid might play in Helicosporidium. I identified ESTs of 20 putatively plastid-targeted enzymes that are involved in a wide variety of metabolic pathways. As expected, no components of photosynthesis were found, but components of other metabolic pathways including sulfur metabolism and fatty acid, isoprenoid and heme biosynthesis suggest that Helicosporidium retains its plastid for these functions. The complete plastid genome of this species of Helicosporidium was sequenced and revealed only four protein-coding genes not involved in transcription or translation, with two of these confirming the metabolic functions suggested by the nuclear-encoded, plastid-targeted genes identified from the ESTs. In addition, the Helicosporidium plastid genome is one of the smallest known (37.5 kb). Its reduced size results from loss of many genes commonly found in plastids of other plants and algae (including all proteins that function in photosynthesis), elimination of duplicated genes and redundant tRNA isoacceptors, and minimization of intergenic spaces. The Helicosporidium plastid genome is also highly structured, with each half of the circular genome containing nearly all genes on one strand. Both the structure and content of the plastid genome and the deduced function of the organelle show parallels with the relict plastid found in the malaria parasite, Plasmodium falciparum. These unrelated organisms each evolved from photosynthetic ancestors, and the convergence in form and function of their relict plastids suggest that common forces shape plastid evolution, following the switch from autotrophy to parasitism.

Plastid genomes of flowering plants are largely identical in gene order and content, but a few lineages have been identified with many gene and intron losses, genomic rearrangements, and accelerated rates of nucleotide substitutions. These aberrant lineages present an opportunity to understand the modes of selection acting on these genomes as well as their long-term stability. My research has focused on two areas within plastid genome evolution in Geraniaceae: first, an investigation of the diversity of unusual plastid genomes in a single genus, Erodium (Geraniaceae) for chapters one and three. Chapter two focuses on the evolution of subunits of the plastid-encoded RNA polymerase (PEP). The first chapter described the loss of plastid-encoded NADPH dehydrogenase (ndh) genes from a clade of 13 Erodium species. Divergence time estimates indicate this clade is less than 5 million years old. This recent loss of ndh genes in Erodium presents an opportunity to investigate changes in photosynthetic function through comparative biochemistry between Erodium species with and without plastid-encoded ndh genes. Second, I examined the evolution of the gene encoding the alpha subunit (rpoA) of PEP in three disparate angiosperm lineages—Pelargonium (Geraniaceae), Passiflora (Passifloraceae), and Annonaceae—in which this gene has diverged so greatly that it is barely recognizable. PEP is conserved in the plastid genomes of all photosynthetic angiosperms. I found multiple lines of evidence indicating that the genes remain functional despite retaining only ~30% sequence identity with rpoA genes from outgroups. The genomes containing these divergent rpoA genes have undergone significant rearrangement due to illegitimate recombination and gene conversion, and I hypothesized that these phenomena have also driven the divergence of rpoA. Third, I conducted a survey of plastid genome evolution in Erodium with the completion of 15 additional whole genomes. Except for Erodium and some legumes, all angiosperm plastid genomes share a quadripartite structure with large and small single copy regions (LSC, SSC) and two inverted repeats (IR). I discovered a species of Erodium that has re-formed a large inverted repeat. Demonstrating a precedent for loss and regain of the IR also impacts models of evolution for other highly rearranged plastid genomes. / text

Made available in DSpace on 2016-06-02T20:21:30Z (GMT). No. of bitstreams: 1 4533.pdf: 2866936 bytes, checksum: a3b1ef75c45a68a6305453e240c9d466 (MD5) Previous issue date: 2012-05-18 / Universidade Federal de Minas Gerais / PILOSOCEREUS AURISETUS is a taxonomic group composed by eight columnar cacti species occurring on rock outcrops in xeric environments. As other xerophitic species found outside the Caatinga domain, the species populations of P. AURISETUS group exhibit a disjunct distribution pattern within the Cerrado domain in central and eastern Brazil. Such a distribution pattern may have resulted from long-distance dispersal events or fragmentation of a more extensive distribution in the past. The main goal of this work was identify demographic events that possibly shaped the evolutionary history of the group and resulted in the current biogeographic pattern. In the present work, phylogenetic analyses and phylogeographical inferences were implemented using the nucleotide variation of plastid genomic sequences. The phylogenetic analyses showed the absence of reciprocal monophyly for great part of the species and the occurring of quite divergent species from the others of the group: P. jauruensis, P. aureispinus e P. bohlei. In addition, P. machrisii populations formed two distinct clades highly supported by the phylogeny which partly agree with the geographic distribution of the species (north and central-south). Population analyses and phylogeographical inferences allowed the identification of the diversification origin of the group and the possible expansion and fragmentation events which determined the evolutionary pathway of the populations. The genetic variability level and the genetic structure observed alongside the current distribution pattern of the populations and biological information about the species suggest that fragmentation events were the main responsible for the biogeographical pattern of the group, which should be related to the palioclimatic oscillations of the Quaternary. / PILOSOCEREUS AURISETUS é um grupo taxonômico composto por oito espécies de cactos colunares que ocorrem associadas a afloramentos rochosos em ambientes xéricos. Assim como outras espécies xerófitas encontradas fora do domínio da Caatinga, as populações das espécies do grupo P. AURISETUS exibem um padrão de distribuição descontínua dentro do domínio Cerrado no centro e leste do Brasil. Esse padrão de distribuição pode ser resultado de eventos de dispersão a longa distância ou de fragmentação de uma distribuição mais extensa no passado. O objetivo principal desse trabalho foi identificar eventos demográficos que possivelmente moldaram a história evolutiva do grupo e resultaram no padrão biogeográfico atual. No presente trabalho foram realizadas análises filogenéticas e inferências filogeográficas a partir da variação nucleotídica de sequências do genoma plastidial. As análises filogenéticas demonstraram que a maior parte das espécies do grupo não apresenta monofilia recíproca de seus haplótipos e que o grupo abrange três espécies bastante divergentes das demais: P. jauruensis, P. aureispinus e P. bohlei. Adicionalmente, as populações da espécie P. machrisii formaram dois clados distintos e bem suportados na filogenia, os quais concordam parcialmente com a distribuição geográfica da espécie (norte e centro-sul). As análises populacionais e as inferências filogeográficas permitiram inferir a origem da diversificação do grupo e os possíveis eventos de expansão e fragmentação que determinaram o caminho evolutivo das populações. Os níveis de variabilidade genética e estruturação observados, juntamente com o padrão atual de distribuição das populações e informações sobre a biologia das espécies, sugerem que eventos de fragmentação foram os principais responsáveis pelo padrão biogeográfico do grupo, os quais devem estar relacionados às oscilações palioclimáticas do Quaternário.

Plastid genomes of photosynthetic flowering plants are usually highly conserved in both structure and gene content. However, the plastomes of parasitic and mycoheterotrophic plants may be released from selective constraint due to the reduction or loss of photosynthetic ability. Here we present the greatly reduced and highly divergent, yet functional, plastome of the nonphotosynthetic holoparasite Hydnora visseri (Hydnoraceae, Piperales). The plastome is 27 kb in length, with 24 genes encoding ribosomal proteins, ribosomal RNAs, tRNAs and a few non-bioenergetic genes, but no genes related to photosynthesis. The inverted repeat and the small single copy region are only ~1.5 kb, and intergenic regions have been drastically reduced. Despite extreme reduction, gene order and orientation are highly similar to the plastome of Piper cenocladum, a related photosynthetic plant in Piperales. Gene sequences in Hydnora are highly divergent and several complementary approaches using the highest possible sensitivity were required for identification and annotation of this plastome. Active transcription is detected for all of the protein coding genes in the plastid genome, and one of two introns is appropriately spliced out of rps12 transcripts. The whole genome shotgun read depth is 1,400X coverage for the plastome, while the mitochondrial genome is covered at 40X and the nuclear genome at 2X. Despite the extreme reduction of the genome and high sequence divergence, the presence of syntenic, long transcriptionally-active open reading frames with distant similarity to other plastid genomes and a high plastome stoichiometry relative to the mitochondrial and nuclear genomes suggests that the plastome remains functional in Hydnora visseri. A four stage model of gene reduction, including the potential for complete plastome loss, is proposed to account for the range of plastid genomes in nonphotosynthetic plants.

Plastid genomes of photosynthetic flowering plants are usually highly conserved in both structure and gene content. However, the plastomes of parasitic and mycoheterotrophic plants may be released from selective constraint due to the reduction or loss of photosynthetic ability. Here we present the greatly reduced and highly divergent, yet functional, plastome of the nonphotosynthetic holoparasite Hydnora visseri (Hydnoraceae, Piperales). The plastome is 27 kb in length, with 24 genes encoding ribosomal proteins, ribosomal RNAs, tRNAs and a few non-bioenergetic genes, but no genes related to photosynthesis. The inverted repeat and the small single copy region are only ~1.5 kb, and intergenic regions have been drastically reduced. Despite extreme reduction, gene order and orientation are highly similar to the plastome of Piper cenocladum, a related photosynthetic plant in Piperales. Gene sequences in Hydnora are highly divergent and several complementary approaches using the highest possible sensitivity were required for identification and annotation of this plastome. Active transcription is detected for all of the protein coding genes in the plastid genome, and one of two introns is appropriately spliced out of rps12 transcripts. The whole genome shotgun read depth is 1,400X coverage for the plastome, while the mitochondrial genome is covered at 40X and the nuclear genome at 2X. Despite the extreme reduction of the genome and high sequence divergence, the presence of syntenic, long transcriptionally-active open reading frames with distant similarity to other plastid genomes and a high plastome stoichiometry relative to the mitochondrial and nuclear genomes suggests that the plastome remains functional in Hydnora visseri. A four stage model of gene reduction, including the potential for complete plastome loss, is proposed to account for the range of plastid genomes in nonphotosynthetic plants.

No description available.