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A Bioinformatics Protocol for Quickly Creating Large-Scale Phylogenetic Trees

  • Hugo López-Fernández
  • Pedro Duque
  • Sílvia Henriques
  • Noé Vázquez
  • Florentino Fdez-Riverola
  • Cristina P. Vieira
  • Miguel Reboiro-Jato
  • Jorge Vieira
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 803)

Abstract

The large scale genome datasets that are now available can provide unprecedented insight into the evolution of genes and gene families. Nevertheless, handling and transforming such datasets into the desired format for downstream analyses is often a difficult and time-consuming task for researchers without a background in informatics. Here, we present a simple and fast protocol for data preparation and high quality phylogenetic tree inferences using simple to install cross-platform software applications with rich graphical interfaces. To illustrate its potential, this protocol was used to provide insight into the evolution of GULO gene in animals, a gene that encodes the enzyme responsible for the last step of vitamin C synthesis in this group of organisms. We find that GULO is always a single copy gene in all animal groups with the exception of Echinodermata. Surprisingly, we find potentially functional GULO genes in several Prostotomian groups such as Molluscs, Priapulida and Arachnida. To our knowledge, this is the first time a putative functional GULO gene is reported in Protostomians. All previously reported GULO gene losses were easily identified using the presented protocol.

Keywords

Large scale analyses GULO Animals 

Notes

Acknowledgements

This article is a result of the project Norte-01-0145-FEDER-000008 - Porto Neurosciences and Neurologic Disease Research Initiative at I3S, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER). Financial support from the Xunta de Galicia (Centro singular de investigación de Galicia accreditation 2016-2019) and the European Union (European Regional Development Fund - ERDF), is gratefully acknowledged. H. López-Fernández is supported by a post-doctoral fellowship from Xunta de Galicia (ED481B 2016/068-0).

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Hugo López-Fernández
    • 1
    • 2
    • 3
    • 4
    • 5
  • Pedro Duque
    • 4
    • 5
    • 6
  • Sílvia Henriques
    • 4
    • 5
  • Noé Vázquez
    • 1
    • 2
  • Florentino Fdez-Riverola
    • 1
    • 2
    • 3
  • Cristina P. Vieira
    • 4
    • 5
  • Miguel Reboiro-Jato
    • 1
    • 2
    • 3
  • Jorge Vieira
    • 4
    • 5
  1. 1.ESEI - Escuela Superior de Ingeniería Informática, Edificio PolitécnicoUniversidad de VigoOurenseSpain
  2. 2.Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia)VigoSpain
  3. 3.SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur). SERGAS-UVIGOVigoSpain
  4. 4.Instituto de Investigação e Inovação em Saúde (I3S)Universidade do PortoPortoPortugal
  5. 5.Instituto de Biologia Molecular e Celular (IBMC)PortoPortugal
  6. 6.Faculdade de CiênciasUniversidade do PortoPortoPortugal

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