Assessment of a short phylogenetic marker based on comparisons of 3' end 16S rDNA and 5' end 16S-23S ITS nucleotide sequences on the genus Xanthomonas

Jean-Charles Côté,Sabarimatou Yakoubou

doi:10.4236/ns.2010.212167

Abstract

A short phylogenetic marker previously used in the reconstruction of the Class γ-proteobacteria was assessed here at a lower taxa level, species in the genus Xanthomonas. This maker is 224 nucleotides in length. It is a combination of a 157 nucleotide sequence at the 3' end of the 16S rRNA gene and a 67 nucleotide sequence at the 5' end of the 16S-23S ITS sequence. A total of 23 Xanthomonas species were analyzed. Species from the phylogenetically related genera Xylella and Stenotrophomonas were included for com- parison purposes. A bootstrapped neighbor- joining phylogenetic tree was inferred from comparative analyses of the 224 bp nucleotide sequence of all 30 bacterial strains under study. Four major Groups were revealed based on the topology of the neighbor-joining tree, Group I to IV. Group I and II contained the genera Steno-trophomonas and Xylella, respectively. Group III included five Xanthomonas species: X. theicola, X. sacchari, X. albineans, X. transluscens and X. hyacinthi. This group of Xanthomonas species is often referred to as the hyacinthi group. Group IV contained the other 18 Xanthomonas species. The overall topology of the neighbor-joining tree was in agreement with currently accepted phylogenetic. The short phylogenetic marker used here could resolve species from three dif-ferent Xanthomonadacea genera: Stenotro-phomonas, Xylella and Xanthomonas. At the level of the Xanthomonas genus, distant spe-cies could be distinguished, and whereas some closely-related species could be distinguished, others were undistinguishable. Pathovars could not be distinguished. We have met the resolving limit of this marker: pathovars and very closely related species from same genus.

Highlights

Other approaches based on different nucleotide sequences have been used to study the phylogeny of Xanthomonas: the 16S rRNA gene [13], a multilocus sequence typing (MLST), [14], the 16S-23S intergenic spacer [15], the repetitive palindromic-based
Our results are in agreement with the first identification of the hyacinthi group based on the homology of their 16S rRNA [13], 16S-23S internal transcribed spacer (ITS) [15] and gyrB nucleotide sequences [17] and multilocus sequence analysis (MLSA) [18]
The grouping of X. perforans, X. euvesicatoria and X. alfalfae is in agreement with the work of Young et al [18] based on MLSA

Summary

Introduction

Most Xanthomonas species are plant pathogens [3]. Up to the mid-90’s, the classification of Xanthomonas species and isolates was based on phenotypic data. Several methods were used in an attempt to classify Xanthomonas species and pathovars: restriction fragment-length polymorphism (RFLP) [7,8], protein profiles [9] and fatty acid methyl ester profiles [10,11]. Vauterin et al reorganized the classification of the genus Xanthomonas based on DNA-DNA hybridization [12]. They revealed 20 DNA homology groups which they considered genomic species. Other approaches based on different nucleotide sequences have been used to study the phylogeny of Xanthomonas: the 16S rRNA gene [13], a multilocus sequence typing (MLST), [14], the 16S-23S intergenic spacer [15], the repetitive palindromic-based

Methods

Results

Conclusion