Integrated Mobilome in Coffea and it most devastating pest: the coffee Berry Borer

• Grant number: 13/15070-4
• Support Opportunities: Regular Research Grants
• Start date: October 01, 2013
• End date: September 30, 2015
• Field of knowledge: Biological Sciences - Biology
• Principal Investigator: Claudia Marcia Aparecida Carareto
• Grantee: Claudia Marcia Aparecida Carareto
• Host Institution: Instituto de Biociências, Letras e Ciências Exatas (IBILCE). Universidade Estadual Paulista (UNESP). Campus de São José do Rio Preto. São José do Rio Preto , SP, Brazil

Abstract

Transposable Elements (TEs) are DNA fragments which mean features are both moving and insert virtually elsewhere in genome and for this reason they constitute valuable molecular tools. Since TEs are distributed throughout genome and in several copies, are powerful instruments in order to analyze genetic diversity, both intra-population field until inside of varieties orclones. Using molecular tools is turning available in Coffea genus with development of large molecular databases, with both genomic andtranscriptomic sequencing which we have access through our international partnerships; however, using molecular tools in order to study coffee berry borer actually are not at the same level than it host species. Given the importance of coffee berry borer, National Coffee Research Center of Colombia (CENICAFE) sequenced the genome of this coleopteran and obtainedgene expression data through using Sanger, FLX-454 and RNA-Seq sequencing technologies. With the aim to develop and go in depth the knowledge in this species, we established a partnership with CENICAFE's researchers in order to make the beetle's genome annotation of TEs. In this work, genome and transcriptome TEs in both genus Coffea and coffee berry borer, his most important pest, will be annotated, classifies and characterized asregarding their abundance, frequency, distribution, structural variability and derivative sequences. Identifying insertion patterns of active TEs will contribute with theidentification of elements that can be use like as genetic markers in order to apply in coffee breeding programs as traceability and resolution of interesting genotypes or applied in genetic population control of insect pest, as well as for environmental stress response markers. Additionally, using retrotransposons as molecular markers can allow a clear identification of tetraploid hybrid parents in C. arabica in terms of parental species and diversity groups allowing better strategies in order to monitor the genetic heritage in descendents of plant crosses(traceability) and management and conservation of coffee genetic resources, which become important because climate change and forest fast destruction. (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)

SCHIETGAT, LEANDER; VENS, CELINE; CERRI, RICARDO; FISCHER, CARLOS N.; COSTA, EDUARDO; RAMON, JAN; CARARETO, CLAUDIA M. A.; BLOCKEEL, HENDRIK. A machine learning based framework to identify and classify long terminal repeat retrotransposons. PLOS COMPUTATIONAL BIOLOGY, v. 14, n. 4, APR 2018. (15/14300-1, 13/15070-4, 12/24774-2)

DIAS, ELAINE SILVA; HATT, CLEMENCE; HAMON, SERGE; HAMON, PERLA; RIGOREAU, MICHEL; CROUZILLAT, DOMINIQUE; CARARETO, CLAUDIA MARCIA APARECIDA; DE KOCHKO, ALEXANDRE; GUYOT, ROMAIN. Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families. Plant Molecular Biology, v. 89, n. 1-2, p. 83-97, SEP 2015. (11/18226-0, 13/15070-4)

HERNANDEZ-HERNANDEZ, ERIC M.; DANIELA FERNANDEZ-MEDINA, RITA; NAVARRO-ESCALANTE, LUCIO; NUNEZ, JONATHAN; BENAVIDES-MACHADO, PABLO; CARARETO, CLAUDIA M. A.. Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families. Molecular Genetics and Genomics, v. 292, n. 3, p. 565-583, JUN 2017. (12/24813-8, 13/15070-4)