Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life

BACKGROUND: Completed genome sequences are rapidly increasing for Rickettsia, obligate intracellular alpha-proteobacteria responsible for various human diseases, including epidemic typhus and Rocky Mountain spotted fever. In light of phylogeny, the establishment of orthologous groups (OGs) of open reading frames (ORFs) will distinguish the core rickettsial genes and other group specific genes (class 1 OGs or C1OGs) from those distributed indiscriminately throughout the rickettsial tree (class 2 OG or C2OGs). METHODOLOGY/PRINCIPAL FINDINGS: We present 1823 representative (no gene duplications) and 259 non-representative (at least one gene duplication) rickettsial OGs. While the highly reductive (approximately 1.2 MB) Rickettsia genomes range in predicted ORFs from 872 to 1512, a core of 752 OGs was identified, depicting the essential Rickettsia genes. Unsurprisingly, this core lacks many metabolic genes, reflecting the dependence on host resources for growth and survival. Additionally, we bolster our recent reclassification of Rickettsia by identifying OGs that define the AG (ancestral group), TG (typhus group), TRG (transitional group), and SFG (spotted fever group) rickettsiae. OGs for insect-associated species, tick-associated species and species that harbor plasmids were also predicted. Through superimposition of all OGs over robust phylogeny estimation, we discern between C1OGs and C2OGs, the latter depicting genes either decaying from the conserved C1OGs or acquired laterally. Finally, scrutiny of non-representative OGs revealed high levels of split genes versus gene duplications, with both phenomena confounding gene orthology assignment. Interestingly, non-representative OGs, as well as OGs comprised of several gene families typically involved in microbial pathogenicity and/or the acquisition of virulence factors, fall predominantly within C2OG distributions. CONCLUSION/SIGNIFICANCE: Collectively, we determined the relative conservation and distribution of 14354 predicted ORFs from 10 rickettsial genomes across robust phylogeny estimation. The data, available at PATRIC (PathoSystems Resource Integration Center), provide novel information for unwinding the intricacies associated with Rickettsia pathogenesis, expanding the range of potential diagnostic, vaccine and therapeutic targets

Comportamento epidemiológico da malária no Estado de Mato Grosso, 1980-2003 Epidemiological trends of malaria in the State of Mato Grosso, from 1980 to 2003

Descreveu-se a evolução temporal e espacial de malária em Mato Grosso, discriminadas em períodos de 1980-1985; 1986-1991; 1992-1997 e 1998-2003, distribuídas por microrregião homogênea. O índice parasitário anual do estado cresceu até 1992, reduzindo para 1,9 casos/mil habitantes em 2003; o coeficiente de mortalidade e a taxa de letalidade foram maiores nos anos de 1980 a 1989. Das 22 microrregiões, 13 apresentaram IPA inferior a 10 casos/1.000 habitantes em todos os períodos, ocorrendo concentração de casos nas microrregiões de Colíder, Alta Floresta, Aripuanã e Alto Guaporé. Em 2003, apenas a microrregião de Aripuanã persistia com IPA superior a 50 casos/1.000 habitantes. As microrregiões de Colíder, em 1983, 1985 a 1988 e 1990 e Alta Floresta, em 1991, apresentaram óbitos acima de 50/100.000 habitantes, sendo a maioria do sexo masculino, na faixa etária de 20 a 49 anos. A distribuição da doença por microrregiões evidenciou que a malária é predominantemente focal.<br>The temporal and spatial evolution of malaria in Mato Grosso was determined in periods from 1980-1985, 1986-1991, 1992-1997 and 1998-2003 and distributed by homogeneous microregion. The annual parasitic index of the state rose until 1992 and then diminished to 1.9 cases/1,000 inhabitants in 2003, the ratio of mortality and the lethality rate were greater in the 1980s. Of the 22 microregions, 13 presented an API inferior to 10 cases/1,000 inhabitants in all periods. Cases were concentrated in the microregions of Colíder, Alta Floresta, Aripuanã and Alto Guaporé. In 2003, only the microregion of Aripuanã continued to present an API superior to 50 cases/1,000 inhabitants. The microregions of Colíder, in 1983, 1985 to 1988 and 1990 and Alta Floresta, in 1991 presented deaths over 50/100,000 inhabitants, mainly in males aged 20-49 years. The distribution of the disease in microregions showed that malaria is predominantly found in concentrated sites

Polymorphic microsatellites of analysis in cultivars of taro Análise polimórfica por microssatélites em cultivares de taro

Taro (Colocasia esculenta) is a tuberous plant belonging to the Araceae family whose tuber is the 14th most consumed food crop in the world. Characterized as an unconventional vegetable, taro is grown in Brazil as a subsistence crop, but in recent years began to gain commercial importance, especially in the states of Espirito Santo, Minas Gerais and Rio de Janeiro. To avoid loss of genetic diversity of the local varieties traditionally grown in Brazil a core collection for taro germplasm has been developed by the Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural do estado do Espirito Santo (Incaper). The aim of this study was to perform a molecular characterization of the seven regional core collections. Genetic diversity of the cultivars was investigated by using SSR (Simple Sequence Repeats) polymorphisms, in seven loci (Xuqtem55, Xuqtem73, Xuqtem84, Xuqtem88, Xuqtem91, Xuqtem97 and Xuqtem110). Genetic diversity of the cultivars, based on the seven microsatellite alleles, was evaluated by using the software GelCompar II, showed that the loci Xuqtem73, Xuqtem88 and Xuqtem110 were the most informative, featuring 7, 10 and 8 alleles, respectively, a percentage of cultivars with polymorphic alleles of 85, 57 and 100% and identical PIC of 0.91. Based on Xuqtem110 locus analysis, the seven cultivars were grouped in two clusters. Chinês Regional Incaper cultivar was originated from Chinês cultivar which originated the São Bento cultivar, corroborating previous results. Macaquinho and Chinês cultivars were shown to be the primitive ones originating the allelic collections found in the states of Mato Grosso do Sul and Espirito Santo.<br>O taro (Colocasia esculenta) é uma hortaliça da família Araceae cujo rizoma é o décimo quarto alimento vegetal mais consumido no mundo. Caracterizado como uma hortaliça não convencional, o taro é cultivado no Brasil como uma cultura de subsistência, mas nos últimos anos começou a ser cultivado comercialmente, sobretudo nos estados de Espirito Santo, Minas Gerais e Rio de Janeiro. Para evitar a perda da diversidade genética das variedades locais tradicionalmente cultivadas no Brasil é necessária a manutenção das cultivares em bancos de germoplasma. O objetivo do trabalho foi caracterizar geneticamente as cultivares do taro provenientes do banco de germoplasma do Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural do estado do Espirito Santo (Incaper). Foi extraído o DNA dos tecidos desidratados das amostras de taro e a diversidade genética de sete cultivares foi investigada por PCR utilizando sete pares de iniciadores que detectam polimorfismos do tipo SSR (simple sequence repeats), em sete loci (Xuqtem55, Xuqtem73, Xuqtem84, Xuqtem88, Xuqtem91, Xuqtem97 e Xuqtem110). A diversidade genética das cultivares, com base nos alelos destes microssatélites foi avaliada com o software GelCompar II. Os loci Xuqtem73, Xuqtem88 e Xuqtem110 foram os mais informativos, apresentando 7, 10 e 8 alelos, respectivamente, com 85, 57 e 100% de cultivares com alelos polimórficos e PIC idênticos de 0,91. A análise do polimorfismo do locus Xuqtem110 permitiu o agrupamento das 7 cultivares em dois clusters com características fenotípicas semelhante e permitiu afimar que o clone Chinês originou o clone Chinês Regional Incaper, que por sua vez deu origem à variedade São Bento, corroborando dados da literatura. As cultivares Macaquinho e Chinês podem ser consideradas enraizadoras dos loci analisados, indicando que estas cultivares podem ter originado as cultivares das regiões dos estados de Mato Grosso do Sul e do Espirito Santo