Genomic sequencing of Brazilian snakes focused on the study of toxins

• Grant number: 15/03509-7
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: December 01, 2015
• End date: June 30, 2020
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Inácio de Loiola Meirelles Junqueira de Azevedo
• Grantee: Vincent Louis Viala
• Host Institution: Instituto Butantan. São Paulo , SP, Brazil
• Associated research grant: 13/07467-1 - CeTICS - Center of Toxins, Immune-Response and Cell Signaling, AP.CEPID
• Associated scholarship(s): 16/26151-3 - Characterization of snake venom metalloproteinase toxin genes from Bothrops jararaca, BE.EP.PD

Abstract

Decades of investigation on snake venoms made major contributions to several fields of biomedical and biological sciences, such as pharmacology, immunology and evolutionary biology. However, in the present era of genomics and even in a time of New Generation Sequencing (NGS) few studies addressed the deep sequencing of snake genomes. Actually, the whole Squamate clade of reptiles (snakes and lizards) remains particularly underexplored when compared to the number of mammalian, bird and fish genomes available. The absence of snake genomic data impairs the use of the most recent cutting edge technologies, since genome of reference is a current requirement. For example: proteomic discovery and characterization of new toxins; investigation of expression of regulatory genes in venomous glands; analyses of exon shuffling and transposition movements; microRNA targeting prediction, etc. Thus, sequencing of snake genomes is a timely strategic initiative.General aim - Generate high coverage sequencing of snake genomes, aiming primarily at the discovery and identification of toxin genes and other relevant elements in studies of evolution of venomous systems and snake biology.Methodology and experimental outline - a) Preparation of genomic DNA samples of Brazilian species; b) Deep sequencing of genomes in NGS equipment (Illumina and PacBio Genomic Sequencers); shotgun and pair-end libraries will be used; c) Construction, organization and sequencing large fragment genomic libraries in BAC vectors; d) Assembly of all sequences (Illumina, PacBio and BACs) aiming the production of a large set of genomic scaffolds; e) In silico screening of scaffolds and contigs looking for interesting genes; f) Mapping of available and new ESTs to the genome contigs to identify expressed elements; g) Annotation of the remaining genomic elements for a comparative analysis of snake genomes.Expected results: We expect to supply the demand of sequenced snake genomes with enough quality to obtain sets of contigs and scaffolds, allowing us to retrieve the structure of important toxin genes, including their introns and flanking regions. We will be able to investigate the conservation between promoters of different families of toxins and the relationship of orthologous, paralogous and edited forms of toxin gene products found in venoms. The correlation with our previously generated data on snake transcriptomes will allow the identification of expressed elements and to check putative roles of retrotransposons on the venom system. In addition, the establishment of lab facilities and expertise in NGS genomics will have an enormous impact on the Center research and other areas of the I. Butantan. (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; VIALA, VINCENT LOUIS; NACHTIGALL, PEDRO GABRIEL; BROE, MICHAEL; GIBBS, H. LISLE; SERRANO, SOLANGE MARIA DE TOLEDO; MOURA-DA-SILVA, ANA MARIA; HO, PAULO LEE; NISHIYAMA-JR, MILTON YUTAKA; JUNQUEIRA-DE-AZEVEDO, INACIO L. M.. Tracking the recruitment and evolution of snake toxins using the evolutionary context provided by the Bothrops jararaca genome. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, v. 118, n. 20, MAY 18 2021. (16/50127-5, 13/07467-1, 15/03509-7, 12/00177-5, 18/26520-4)