Sequencing of Bothrops jararaca genome to characterize toxins gene structure and their regulatory elements

• Grant number: 13/07974-0
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: November 01, 2013
• End date: August 31, 2016
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Inácio de Loiola Meirelles Junqueira de Azevedo
• Grantee: Diego Dantas Almeida
• Host Institution: Instituto Butantan. Secretaria da Saúde (São Paulo - Estado). São Paulo , SP, Brazil
• Associated research grant: 13/07467-1 - CeTICS - Center of Toxins, Immune-Response and Cell Signaling, AP.CEPID

Abstract

Most studies involving snake venoms were based on traditional approaches like Biochemistry and Molecular Biology, contributing to many fields of biological sciences. The global characterization techniques, such as transcriptomics and proteomics, enriched this knowledge by indicating the complex gene organization of toxin families and the presence of important molecular evolutionary processes, such as accelerated evolution, exon shuffling, functional convergence, retrotransposition, etc. Surprisingly, despite all acquired knowledge, the molecular basis of snake genomes is poorly known. Even in the Era of Next Generation Sequencing (NGS), no genome of poisonous snake, Brazilian or not, has been resolved. Furthermore, the "Squamata" (snakes and lizards) group remains unexplored particularly when compared to many vertebrate groups.In this project, we propose to achieve a high coverage of the genome sequence of Bothrops jararaca - the major medically important species in Brazil. To do so, we will build shotgun and mate-pair libraries to perform Next Generation Sequencing (NGS) using Illumina technology. The mate-pair libraries will be constructed using fragments of different sizes to provide a better mapping, as it was shown to achieve better results for the resolution of other vertebrates genomes. Longer sequences (>400bp) will be obtained by the 454 technology with the Roche-GSFLX equipment. BAC libraries will also be constructed and sequenced in 454-GSJunior equipment in order to obtain continuous and longer segments of the genome. These BACs could be randomly selected or screened with probes consisted of cDNAs from toxins of interest. All generated sequences will be assembled in contigs and scaffolds of the genome. These will allow us to obtain a large collection of genome segments that may be selected in silico. Therefore, we hope to identify and characterize genes of toxins, genes involved in venom production and secretion, retrotransposable elements and other elements with relevance in the evolution of the venom system. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

ALMEIDA, DIEGO DANTAS; KITAJIMA, JOAO PAULO; NISHIYAMA, JR., MILTON YUTAKA; CONDOMITTI, GEORGE WILLIAN; DE OLIVEIRA, URSULA CASTRO; SETUBAL, JOAO CARLOS; JUNQUEIRA-DE-AZEVEDO, INACIO L. M.. The complete mitochondrial genome of Bothrops jararaca (Reptilia, Serpentes, Viperidae). MITOCHONDRIAL DNA PART B-RESOURCES, v. 1, p. 907-908, 2016. (13/07467-1, 13/07974-0, 12/00177-5)

ALMEIDA, DIEGO DANTAS; KITAJIMA, JOAO PAULO; NISHIYAMA, MILTON YUTAKA, JR.; CONDOMITTI, GEORGE WILLIAN; DE OLIVEIRA, URSULA CASTRO; SETUBAL, JOAO CARLOS; JUNQUEIRA-DE-AZEVEDO, INACIO L. M.. The complete mitochondrial genome of Bothrops jararaca (Reptilia, Serpentes, Viperidae). MITOCHONDRIAL DNA PART B-RESOURCES, v. 1, n. 1, p. 2-pg., 2016-01-01. (13/07467-1, 13/07974-0, 12/00177-5)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

ALMEIDA, Diego Dantas. Genome sequencing of Bothrops jararaca snake for toxin gene structure characterization.. 2016. Doctoral Thesis - Universidade de São Paulo (USP). Instituto de Ciências Biomédicas (ICB/SDI) São Paulo.