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Proceedings X-Meeting 2015 Editor: AB3C December 4, 2015 ii Conference Program 1 Organizing Committee 1 2 Introduction 3 3 Abstracts 5 Poster Session 7 Education and Training 7 7 Meeting the Global Thirst for Bioinformatics Training Global Organisation of Bioinformatics Learning, Education and Training 8 Standardizing sequence analysis methods on the web: working on the Bioinformatics Platform at the Fiocruz-BA Alisson Fonseca, Artur Lopo, Luciano Silva Genes and Genomics 9 9 Comparative genomics of three species of the genus Echinococcus Lucas Luciano Maldonado, Juliana Assis, Flávio Marcos Gomes-Aráujo, Izinara Rosse, Natalia Macchiaroli, Marcela Cucher, Mara Rosenzvit, Guilherme Oliveira, Laura Kamenetzky 10 BIOMARKERS STUDY OF NEPHROTOXICITY CAUSED BY GENTAMICIN THROUGH GENE EXPRES- SION Marina Grossi Stellamaris Soares, Sarah Silva, Mariana Nunes, Leonardo Almeida, Anete Valente, Carlos Tagliati 11 Identification of small deletions within human exons in Asian and European genomes using trancriptome data. Gabriel Wajnberg, Nicole de Miranda Scherer, Carlos Gil Ferreira, Fabio Passetti 12 Characterization of pathogenicity islands of 15 genome of Corynebacterium pseudotuberculosis biovar equi Yan Patrick de Moraes Pantoja, Adonney Allan Oliveira Veras, Pablo Henrique Caracciolo Gomes de Sá, Vasco Azevedo, Adriana Ribeiro, Artur Silva, Rommel Ramos 13 Analysis of HPV regulatory elements by k-mer index approach Taina Raiol, Lucas Akayama, Luciana Montera 14 Maximum entropy: an effective strategy to discriminate anomalous regions in bacterial genomes Gesiele Barros-Carvalho, Marie-Anne Van Sluys, Fabrício Lopes 15 The complete mitochondrial genome of a brazilian carnivorous plant Utricularia reniformis (Lentibulariaceae): Insights into the evolution of an organellar genome of a specialized plant. Yani C A Diaz, Saura R Silva, Cristine G Menezes, Vitor F O Miranda, Todd P Michael, Alessandro M. Varani 16 OBO-RO Editor: Supporting development and integration of ontologies in the biomedical domain Ricardo Cacheta Waldemarin, Cléver Ricardo Guareis de Farias 17 THE DRAFT GENOME OF Fonsecaea multimorphosa CBS 980.96 Aniele C Ribas Leao, Vinicius Almir Weiss, Emanuel Maltempi de Souza, Vania A Vicente ACR Leao1, VA Weiss1, RR Gomes3, VA Vicente3, RT Raittz1, MZ Tadra-Sfeir, E Balsanelli, V Baura, MBR Steffens, EM Souza 18 COMPARISON OF BINNING SOFTWARES IN METAGENOMIC SEQUENCES FROM HUMAN GUT MI- CROBIAL José Pilan, Agnes Takeda, José Rybarczyk-Filho 19 SEQUENCING AND ANALYSIS OF Derxia lacustris HL12 Sheyla Trefflich, Vinícius Almir Weiss, Arnaldo Glogauer, Dieval Guizelini, Roberto Tadeu Raittz, Shih-Yi Sheu, Wei-Cheng Huang, Wen-Ming Chen, Michelle Zibetti Tadra-Sfeir, Helisson Faoro, Valter Baura, Emanuel Mal- tempi Souza 20 Challenges associated to the search of specific targets for drug development against Leishmania major Larissa Catharina Costa, Carlyle Lima, Ana Carolina Ramos Guimarães, Nicolas Carels iii 21 Assembly, Annotation and Comparative Analysis of Mitochondrial Genome of two Asian Cattle breeds: Guzerá and Gir Juliana Assis Geraldo, Izinara Rosse Maria Raquel Carvalho, Francislon Oliveira, Flávio Araújo, Marcos Viní- cius Silva, Guilherme Oliveira 22 The utility of whole-exome sequencing for genetic diagnosis of heterogeneous background disorders: an epilepsy and delayed psychomotor development case report Maíra Cristina Freire, Michele Pereira, Giovana Torrezan, Mariano Zalis, Elvis Mateo, Alessandro Ferreira 23 OPTICAL MAPPING TO DETECT MISASSEMBLIES IN GENOME OF CORYNEBACTERIUM PSEUDO- TUBERCULOSIS STRAIN 1002 Thiago Jesus Sousa, Diego Cesar Batista Mariano, Flavia Figueira Aburjaile, Flávia Souza Rocha, Felipe Luiz Pereira, Henrique Cesar Pereira Figueiredo, Artur Silva, Rommel Thiago Jucá Ramos, Vasco Azevedo 24 EVOLUTIONARY AND FUNCTIONAL GENOMICS OF PSEUDOGENES IN TRYPANOSOMATIDS Marcio silva, Marcos Catanho, Fernando Valín, Antonio Basilio Miranda 25 Identification of Non-homologous Isofunctional Enzymes (NISE) between Solanum lycopersicum and the phy- topathogens Botritys cinerea and Fusarium Oxyosporum Rangeline Silva, Leandro Pereira, Antonio Miranda 26 Comparative genomics of probiotic yeasts: Saccharomyces cerevisiae var. boulardii and S. cerevisiae UFMG A-905. 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Carazzolle 31 Bacterial community profiling of human rectal cancers Andrew Maltez Thomas, Eliane Camargo de Jeses, Ademar Lopes, Samuel Aguiar Junior, Ariana Ferrari João Carlos Setubal, Diana Noronha Nunes, Emmanuel Dias-Neto 32 Identification and classification of microexon genes in a collection of genome annotations Bruno Souza, Murilo Amaral, João Carlos Setubal, Sergio Verjovski-Almeida 33 Missense mutations in candidate genes for reproductive disorders in a Gir bull identified through whole-genome sequencing Ana Emília de Paiva, Pablo Augusto de Souza Fonseca, Fernanda Caroline dos Santos, Izinara Rosse da Cruz, Guilherme Silva Moura 34 Using the Mean Shift clustering algorithm to predict Genomic Islands in bacteria Daniel Miranda de Brito, Thaís De Almeida Ratis Ramos, Vinicius Maracaja-Coutinho, Sávio Torres de Farias, Leonardo Vidal Batista, Thaís Gaudencio do Rêgo 35 Analysis of fecal bacterial diversity in howler monkeys (Alouatta) through metagenomics Raquel Franco, Arthur Berselli, Layla Martins, Andrew Thomaz, João Batista, Julio de Oliveira, Aline Silva, João Setubal iv 36 Computational methods for metagenomic data processing in the Metazoo Project Gianluca Major, Felipe Lima, Andrew Thomas, Leandro Lemos, Deyvid Amgarten, Deibs Barbosa, Calos Morais, Luciana Antunes, Aline Silva, João Setubal 37 Metagenomic Analysis of Rumen from Cattle Fed With Different Levels of Mate Extract (Ilex Paraguariensis A.St.-Hil.) 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    Reclassification of Beijerinckia Fluminensis CIP 106281T and Beijerinckia

    1 Reclassification of Beijerinckia fluminensis CIP 106281T and Beijerinckia 2 fluminensis UQM 1685T as Rhizobium radiobacter strains, and proposal of 3 Beijerinckia fluminensis LMG 2819 as Beijerinckia doebereinerae sp. nov. 4 5 Monike Oggerin1, David R. Arahal2, Víctor Rubio3, Irma Marín1* 6 7 1Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Cantoblanco, 8 28049 Madrid, Spain 9 2Spanish Type Culture Collection (CECT) and Department of Microbiology and Ecology, 10 University of Valencia, Campus de Burjassot, 46100 Valencia, Spain 11 3Instituto de Ciencias Agrarias, Centro de Ciencias Medio Ambientales, CSIC, 28006 Madrid, 12 Spain 13 14 15 Running title: Beijerinckia doebereinerae sp. nov. 16 17 Correspondence: Irma Marín 18 e-mail: [email protected]. Phone: +34 914978078. Fax: +34 914978300 19 20 ……………………………………………………………………………………………………… 21 Footnote: The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of 22 strain LMG 2819T, UQM 1685 and CIP 106281 are EU401905, EU401907 and EU401908 23 respectively. 24 Transmission electron micrographs of strains LMG 2819T and UQM 1685 are available as a 25 supplementary figure in IJSEM Online. 26 26 During the course of a research project with free-living nitrogen fixing bacteria we 27 determined the 16S rRNA gene sequence of strains Beijerinckia fluminensis UQM 1685T 28 and B. fluminensis CIP 106281T and discovered that they were only 90.6-91.2 % similar to 29 the sequences of other Beijerinckia species and subspecies. Moreover, the highest 30 similarity to these sequences (99.7 %) corresponded to Rhizobium radiobacter (including 31 Agrobacterium tumefaciens). Other diagnostic features confirmed that both strains have 32 the same origin but do not descend from the nomenclatural type.
  • Outline Release 7 7C

    Outline Release 7 7C

    Taxonomic Outline of Bacteria and Archaea, Release 7.7 Taxonomic Outline of the Bacteria and Archaea, Release 7.7 March 6, 2007. Part 4 – The Bacteria: Phylum “Proteobacteria”, Class Betaproteobacteria George M. Garrity, Timothy G. Lilburn, James R. Cole, Scott H. Harrison, Jean Euzéby, and Brian J. Tindall Class Betaproteobacteria VP Garrity et al 2006. N4Lid DOI: 10.1601/nm.16162 Order Burkholderiales VP Garrity et al 2006. N4Lid DOI: 10.1601/nm.1617 Family Burkholderiaceae VP Garrity et al 2006. N4Lid DOI: 10.1601/nm.1618 Genus Burkholderia VP Yabuuchi et al. 1993. GOLD ID: Gi01836. GCAT ID: 001596_GCAT. Sequenced strain: SRMrh-20 is from a non-type strain. Genome sequencing is incomplete. Number of genomes of this species sequenced 2 (GOLD) 1 (NCBI). N4Lid DOI: 10.1601/nm.1619 Burkholderia cepacia VP (Palleroni and Holmes 1981) Yabuuchi et al. 1993. <== Pseudomonas cepacia (basonym). Synonym links through N4Lid: 10.1601/ex.2584. Source of type material recommended for DOE sponsored genome sequencing by the JGI: ATCC 25416. High-quality 16S rRNA sequence S000438917 (RDP), U96927 (Genbank). GOLD ID: Gc00309. GCAT ID: 000301_GCAT. Entrez genome id: 10695. Sequenced strain: ATCC 17760, LMG 6991, NCIMB9086 is from a non-type strain. Genome sequencing is completed. Number of genomes of this species sequenced 1 (GOLD) 1 (NCBI). N4Lid DOI: 10.1601/nm.1620 Pseudomonas cepacia VP (ex Burkholder 1950) Palleroni and Holmes 1981. ==> Burkholderia cepacia (new combination). Synonym links through N4Lid: 10.1601/ex.2584. Source of type material recommended for DOE sponsored genome sequencing by the JGI: ATCC 25416. High- quality 16S rRNA sequence S000438917 (RDP), U96927 (Genbank).