High scale genomic analysis of repetitive elements focusing on B chromosomes of Astatotilapia latifasciata cichlid

• Grant number: 14/16763-6
• Support Opportunities: Scholarships in Brazil - Master
• Start date: December 01, 2014
• End date: July 31, 2016
• Field of knowledge: Biological Sciences - Morphology - Cytology and Cell Biology
• Agreement: Coordination of Improvement of Higher Education Personnel (CAPES)
• Principal Investigator: César Martins
• Grantee: Rafael Luiz Buogo Coan
• Host Institution: Instituto de Biociências (IBB). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil

Abstract

B chromosomes (B) are supernumerary elements, non-homologous to the normal (A) set of chromosomes, found in many taxonomic groups. B chromosomes have been recognized as parasitic elements, but recent studies propose new models to their origin, evolution and function inside the cell. Bs heterochromatic constitution is caused by massive presence of repetitive elements. Previous genomic analysis and next generation sequencing were performed in Astatotilapia latifasciata cichlid and revealed high proportion of repetitive elements in their B chromosomes. Repetitive elements in next generation sequencing data can now be analyzed in a novel approach, without a reference genome, using a graph-base sequence clustering algorithm. Implementation of graph-base clustering and analysis of repetitive sequences is made through RepeatExplorer pipeline. Using a computer model, Real Time PCR (qPCR) and Fluorescence In Situ Hybridization (FISH), this project focus in the identification and characterization of repetitive elements using A. latifasciata as a model, trying to explain the role of these repeats in the constitution and evolution of B chromosomes. (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)

COAN, RAFAEL L. B.; MARTINS, CESAR. Landscape of Transposable Elements Focusing on the B Chromosome of the Cichlid Fish Astatotilapia latifasciata. GENES, v. 9, n. 6, JUN 2018. (14/16763-6, 15/16661-1, 13/04533-3)

Academic Publications

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

COAN, Rafael Luiz Buogo. High scale genomic analysis of repetitive elements focusing on B chromosomes of the cichlid fish Astatotilapia latifasciata. 2016. Master's Dissertation - Universidade Estadual Paulista (Unesp). Instituto de Biociências. Botucatu Botucatu.