Genomic Resources

IMG-20151214-WA0000The “Genomic Resources” research group led by Dr. Andone Estonba has been designated a “Consolidated Research Group” by the Department of Education, Universities and Research of the Basque Government (2010-2015), and is part of the Faculty of Science and Technology at the University of the Basque Country/Euskal Herriko Unibertsitatea (UPV / EHU). Made up of a total of 12 people including three professors, four post-doctoral researchers and five PhD students, our research group has specialized in the analysis of genomic variability in animal species, including the human species, for over 15 years, acquiring a high level of both human and technological capacity. We have led more than 16 national and international research projects and contracts in the last five years. Currently, we are partners of the BEEHOPE Project from ERANET BIODIVERSA call funded by MINECO (PCIN-2014-090) and SMARTBEES Project funded by the European Union Seventh Framework Programme (FP7-KBBE-2013), both of them aimed to the conservation of local populations of honeybee. Recently, The Department of Economic Development and Competitiveness of the Basque Government, has awarded us with a grant for a new study on metagenomics  (Metagenómica del Txakoli: hacia una vitivinicultura personalizada, GVCV16/18).

Our main expertise is the application of DNA variability analyses to a diverse range of fields within the Bioscience area with, among others, the following aims:

  • improving the management of farms, semi-wild species and hunting species.
  • improving the management of the marine environment, especially of fisheries and mariculture species.
  • identifying genes associated with susceptibility to diseases and economically interesting traits, in both human and animal species, and
  • understanding the role of microbiota in the environment.

 

Since 2009, and without neglecting other research interests, we have specialized in the application of Next Generation Sequencing (NGS) technologies (mainly Illumina Hiseq and Miseq platforms). Currently, we are applying these technologies in our main research interests: (1) SNP discovery from the transcriptome (RNA-seq) and genome for population genomics purposes on Atlantic bluefin tuna (Thunnus thynnus), European anchovy (Engraulis encrasicolus), Atlantic mackerel (Scomber scombrus), and and sardine (Sardine pilchardus), (2) differential gene expression by RNAseq and functional annotation for the study of growth in clams (Ruditapes philippinarum), (3) identification of genomic selection signatures in sheep (Ovis aries), honeybee (Apis mellifera) and European anchovy , and (4) metagenomic studies of anthropologically impacted ecosystems such as vineyards and stuary waters. Using these technologies, together with other classical methods such as Sanger sequencing, we have generated a set of genomic resources, and multiple publications in international scientific journals. Specialization on NGS technologies has led us, also, to expand our knowledge on Bioinformatics, either by the initial collaboration with Dr. Darrell Conklin (Ikerbasque Research Professor at the Computer Science and Artificial Intelligence Department of the UPV/EHU) either by the incorporation in the group of qualified staff.

Dr. Andone Estonba is, in addition, the scientist in charge of the Sequencing and Genotyping Unit of the General Research Facilities of the UPV/EHU (SGIker). Together with her research team, she was a key player in the establishment of this Unit in 2004. The Unit’s mission is to provide knowledge and equipment needed for the analysis of DNA variation. It is aimed at the Basque Network of Science, Technology and Innovation, as well as any other public or private, national or international institution devoted to Biosciences. Since its creation, our “Genomic Resources” group has maintained close links with the Unit, thereby assuring that the group research projects are carried out in collaboration with highly qualified personnel, and with the most advanced techniques and equipment (Illumina Miseq, TaqMan Open Array and the BioMark platforms, among others).

Multidisciplinarity, internationalization and technology transference are the cornerstones of our work philosophy. All our research projects are developed in collaboration with other national and international research groups from universities, business agents or health services, as well as with Provincial Councils and breeding associations.

The Genomic Resources group is also fully involved in the training of new researchers, the welcoming of students who wish to enter the world of research, and the supervision of a wide range of academic studies ranging from undergraduate to post-graduate levels. Hence, within the Erasmus Mundus Msc in Marine Environment and Resources (MER) program, the group organizes and teaches annually the course entitled “Marine genomic resources”. The course covers mainly two aspects: marine population genomics in non-model organisms and metagenomics. In addition, we also organize an international postgraduate course for 2016-2017. This University Master, entitled Bioinformatics & “Omics”, will be taught jointly with the University of Bordeaux. The degree is aimed for students and professionals from Bioscience background (Biology and Biochemistry) who want to specialize in the management and analysis of NGS data to be able to develop bioinformatic-based technical solutions in academia or companies.