Antonie van Leeuwenhoek

, Volume 101, Issue 1, pp 105–124

Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades

Original Paper

DOI: 10.1007/s10482-011-9628-4

Cite this article as:
Naushad, H.S. & Gupta, R.S. Antonie van Leeuwenhoek (2012) 101: 105. doi:10.1007/s10482-011-9628-4

Abstract

The members of the order Pasteurellales are currently distinguished primarily on the basis of their branching in the rRNA trees and no convincing biochemical or molecular markers are known that distinguish them from all other bacteria. The genome sequences for 20 Pasteurellaceae species/strains are now publicly available. We report here detailed analyses of protein sequences from these genomes to identify conserved signature indels (CSIs) that are specific for either all Pasteurellales or its major clades. We describe more than 23 CSIs in widely distributed genes/proteins that are uniquely shared by all sequenced Pasteurellaceae species/strains but are not found in any other bacteria. Twenty-one additional CSIs are also specific for the Pasteurellales except in some of these cases homologues were not detected in a few species or the CSI was also present in an isolated non-Pasteurellaceae species. The sequenced Pasteurellaceae species formed two distinct clades in a phylogenetic tree based upon concatenated sequences for 10 conserved proteins. The first of these clades consisting of Aggregatibacter,Pasteurella,Actinobacillus succinogenes, Mannheimia succiniciproducens, Haemophilus influenzae and Haemophilus somnus was also independently supported by 13 uniquely shared CSIs that are not present in other Pasteurellaceae species or other bacteria. Another clade consisting of the remaining Pasteurellaceae species (viz. Actinobacillus pleuropneumoniae, Actinobacillus minor,Haemophilus ducryi, Mannheimia haemolytica and Haemophilus parasuis) was also strongly and independently supported by nine CSIs that are uniquely present in these bacteria. The order Pasteurellales is presently made up of a single family, Pasteurellaceae, that encompasses all of its genera. In this context, our identification of two distinct clades within the Pasteurellales, which are supported by both phylogenetic analyses and by multiple highly specific molecular markers, strongly argues for and provides potential means for the division of various genera from this order into a minimum of two families. The genetic changes responsible for these CSIs were likely introduced in the common ancestors of either all Pasteurellales or of these two specific clades. These CSIs provide novel means for the identification and circumscription of these groups of Pasteurellales in molecular terms.

Keywords

Conserved indelsPasteurellales taxonomy and systematicsPasteurellales cladesPhylogenetic analysesPasteurellaceae genomesComparative genomicsMolecular markers for PasteurellalesLateral gene transfers

Supplementary material

10482_2011_9628_MOESM1_ESM.pdf (1.7 mb)
Supplementary material 1 (PDF 1705 kb)

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.Department of Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonCanada