An improved and general streamlined phylogenetic protocol applied to the fatty acid desaturase family

Matthew Wilding*, Matthias Nachtschatt, Robert Speight, Colin Scott

*Corresponding author for this work

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Numerous tools to generate phylogenetic estimates are available, but there is no single protocol that will produce an accurate phylogenetic tree for any dataset. Here, we investigated some of those tools, paying particular attention to different alignment algorithms, in order to produce a phylogeny for the integral membrane fatty acid desaturase (FAD) family. Herein, we report a novel streamlined protocol which utilises peptide pattern recognition (PPR). This protocol can theoretically be applied universally to generate accurate multiple sequence alignments and improve downstream phylogenetic analyses. Applied to the desaturases, the protocol generated the first detailed phylogenetic estimates for the family since 2003, which suggested they may have evolved from three functionally distinct desaturases and further, that desaturases evolved first in cyanobacteria. In addition to the phylogenetic outputs, we mapped PPR sequence motifs onto an X-ray protein structure to provide insights into biochemical function and demonstrate the complementarity of PPR and phylogenetics.

Original languageEnglish
Pages (from-to)50-57
Number of pages8
JournalMolecular Phylogenetics and Evolution
Volume115
DOIs
Publication statusPublished - Oct 2017
Externally publishedYes

Keywords

  • phylogenetics
  • desaturase
  • peptide pattern recognition
  • multiple sequence alignment

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