AUTHOR=Sawana Amandeep , Adeolu Mobolaji , Gupta Radhey S. 

TITLE=Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species

JOURNAL=Frontiers in Genetics

VOLUME=5

YEAR=2014

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2014.00429

DOI=10.3389/fgene.2014.00429

ISSN=1664-8021

ABSTRACT=<p>The genus <italic>Burkholderia</italic> contains large number of diverse species which include many clinically important organisms, phytopathogens, as well as environmental species. However, currently, there is a paucity of biochemical or molecular characteristics which can reliably distinguish different groups of <italic>Burkholderia</italic> species. We report here the results of detailed phylogenetic and comparative genomic analyses of 45 sequenced species of the genus <italic>Burkholderia</italic>. In phylogenetic trees based upon concatenated sequences for 21 conserved proteins as well as 16S rRNA gene sequence based trees, members of the genus <italic>Burkholderia</italic> grouped into two major clades. Within these main clades a number of smaller clades including those corresponding to the clinically important <italic>Burkholderia cepacia</italic> complex (BCC) and the <italic>Burkholderia pseudomallei</italic> groups were also clearly distinguished. Our comparative analysis of protein sequences from <italic>Burkholderia</italic> spp. has identified 42 highly specific molecular markers in the form of conserved sequence indels (CSIs) that are uniquely found in a number of well-defined groups of <italic>Burkholderia</italic> spp. Six of these CSIs are specific for a group of <italic>Burkholderia</italic> spp. (referred to as Clade I in this work) which contains all clinically relevant members of the genus (viz. the BCC and the <italic>B. pseudomallei</italic> group) as well as the phytopathogenic <italic>Burkholderia</italic> spp. The second main clade (Clade II), which is composed of environmental <italic>Burkholderia</italic> species, is also distinguished by 2 identified CSIs that are specific for this group. Additionally, our work has also identified multiple CSIs that serve to clearly demarcate a number of smaller groups of <italic>Burkholderia</italic> spp. including 3 CSIs that are specific for the <italic>B. cepacia</italic> complex, 4 CSIs that are uniquely found in the <italic>B. pseudomallei</italic> group, 5 CSIs that are specific for the phytopathogenic <italic>Burkholderia</italic> spp. and 22 other CSI that distinguish two groups within Clade II. The described molecular markers provide highly specific means for the demarcation of different groups of <italic>Burkholderia</italic> spp. and they also offer novel and useful targets for the development of diagnostic assays for the clinically important members of the BCC or the <italic>pseudomallei</italic> groups. Based upon the results of phylogenetic analyses, the identified CSIs and the pathogenicity profile of <italic>Burkholderia</italic> species, we are proposing a division of the genus <italic>Burkholderia</italic> into two genera. In this new proposal, the emended genus <italic>Burkholderia</italic> will correspond to the Clade I and it will contain only the clinically relevant and phytopathogenic <italic>Burkholderia</italic> species. All other <italic>Burkholderia</italic> spp., which are primarily environmental, will be transferred to a new genus <italic>Paraburkholderia</italic> gen. nov.</p>