Abstracts (first author)

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Making the best of your 454 dataset using the 4Pipe4 analysis pipeline – from an unknown genome to a detailed SNPs analysis: A case study with a Quercus suber dataset

Author(s): Pina-Martins F, Vieira BM, Seabra SG, Batista D, Paulo OS

Summary:

The widespread use of Next Generation Sequencing (NGS) techniques and its application to non model organisms provided biologists with large amounts of genetic data and the ability to address problems which were untreatable just a few years ago. However, the frequent lack of reference genomes on non-model organisms usually creates difficulties to researchers when trying to answer specific genetic questions, such as finding candidate genes or looking for intra and inter-population variation. For instance, mining SNPs in NGS datasets of anonymous pooled individuals that cannot be compared to a reference is still not a simple task. Here is described 4Pipe4, a NGS data analysis pipeline, optimized for SNP mining in the aforementioned datasets, particularly on Roche 454 data. In order to assess its efficiency, a dataset of anonymous pooled individuals of Quercus suber (Cork Oak), which does not have a reference genome available, was analysed with 4Pipe4, and a subset of tenths of SNPs detected by the pipeline was randomly selected and sequenced in an array for validation. The results of the genotyping array were explored to: a) provide insights on population structure and gene flow patterns and b) make an association study with environmental factors such as temperature, precipitation or drought periods. This combined approach of 454/genotyping array with the 4Pipe4 pipeline proved to be a very efficient and cost effective way to obtain validated and mapped SNPs from orthologous regions, for population genomics studies.


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Abstracts (coauthor)

Experimental and genomic approaches in the study of the balanced colour-polymorphism of the meadow spittlebug (Philaenus spumarius)

Author(s): Seabra, SG, Rodrigues AS, Silva SE, Silva J, Marabuto E, Pina-Martins F, Gharbi K, Blaxter M, Borges PAV, Jiggins C, Quartau JA, Paulo OS

Summary:

Philaenus spumarius (Insecta, Hemiptera, Aphrophoridae) has for long been a subject of interest of evolutionary biologists due to its heritable colour polymorphism that shows evidence of balancing selection and of clinal variation in the colour mophs frequencies. We are studying the adaptive significance of this polymorphism, particularly to understand if the melanic morphs (e.g. “marginellus” morph) have any advantage/disadvantage in terms of survival and reproductive success, efficiency of egg maturation and resistance to desiccation compared to non-melanic morphs (“typicus” and “trilineatus”). Results so far indicate a higher survival, higher number of eggs clutches and higher number of eggs laid by the “trilineatus” females than “typicus” or “marginellus” females. We are also taking a genomic approach for a) the identification of genetic basis of the colour polymorphism and b) for detecting signatures of balancing and directional selection in the genome of P. spumarius. For this purpose we are applying RAD sequencing in a) a set of samples from the three different morphs referred above, using a high frequency cutter enzyme (PstI) and in b) another set of samples from 8 populations across the distribution range of the species representing the main mitochondrial haplogroups, using a lower frequency cutter enzyme (SbfI). We are also assembling a draft of the genome that will aid in the identification of homologous regions to available references, although the very large genome size of this insect constitutes an extra challenge.

Identifying signatures of natural selection in cork oak (Quercus suber L.) genes

Author(s): Modesto, IS, Miguel C, Pina-Martins F, Glushkova M, Veloso M, Batista D, Paulo OS

Summary:

Cork oak (Quercus suber L.) is an evergreen tree species holding a great economical and social relevance within its distribution range, the western Mediterranean Basin, associated with cork production. This tree is exploited mainly in orchards known as montado, which comprise great biodiversity. Despite its importance, cork oak stands have been facing a significant decline and climate changes expected to occur during this century may aggravate this decay. In this scenario, the assessment of adaptive genetic variation is essential to understand how cork oak may cope with these threats and to delineate management strategies of its genetic resources. In this work, we started by validating single nucleotide polymorphisms (SNPs) detected through the analysis of cork oak pyrosequenced transcriptome, for a set of putative functional genes. Six fragments were then selected to be analysed with the purpose of finding signatures of natural selection. Samples from populations representing the species’ entire distribution range were sequenced and several neutrality tests were performed as well as environmental association tests. Two gene fragments showed signals of balancing selection: the Arabidopsis thaliana orthologs non-expresser of pathogenesis related 1 (NPR1), involved in plant defence response against pathogens, and auxin response factor 16 (ARF16), a gene previously identified as a candidate gene for drought resistance. Additionally, in a class I heat shock protein (HSP), one amino acid position was detected as possibly being under positive selection and associated with several precipitation variables, revealing its potential relevance in adaptation to local climatic conditions. In this study the first steps were taken to start unveiling important information on cork oak adaptation to biotic and abiotic environmental conditions. Funded by Fundação para a Ciência e Tecnologia (FCT): projects PTDC/AGR-GPL/104966/2008 and EST/036/2009.

Contacts

Chairman: Octávio S. Paulo
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Address

XIV Congress of the European Society for Evolutionary Biology

Organization Team
Department of Animal Biology (DBA)
Faculty of Sciences of the University of Lisbon
P-1749-016 Lisbon
Portugal

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Computational Biology & Population Genomics Group 
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