ABSTRACT
Phylogenetic 16S rRNA gene analysis was used to assign the bacterial leaf-nodulating endosymbionts of two tropical African Psychotria species to the genus Burkholderia. The microsymbionts of the different Psychotria hosts were recognized as distinct and novel species of Burkholderia on the basis of relatively low intersequence similarities and sufficiently large evolutionary distances when compared with each other and their closest validly named neighbours. The obligate endosymbiotic nature of the bacteria prevented their in vitro cultivation and the deposition of type strains to culture collections. Therefore, the provisional status Candidatus is assigned to the bacterial partners of Psychotria calva and Psychotria nigropunctata, with the proposal of the names 'Candidatus Burkholderia calva' and 'Candidatus Burkholderia nigropunctata', respectively.
Subject(s)
Burkholderia/classification , Burkholderia/isolation & purification , Psychotria/microbiology , Symbiosis , Burkholderia/physiology , Burkholderia/ultrastructure , DNA, Bacterial/chemistry , DNA, Bacterial/isolation & purification , DNA, Ribosomal/chemistry , DNA, Ribosomal/isolation & purification , Genes, rRNA , Microscopy, Electron, Scanning , Molecular Sequence Data , Phylogeny , Plant Leaves/microbiology , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNAABSTRACT
SUMMARY: RnaViz has been developed to easily create nice, publication quality drawings of RNA secondary structure. RnaViz 2 supports CT, DCSE, and RNAML input formats and improves on many aspects of the first version, notably portability and structure annotation. RnaViz is written using a hybrid programming approach combining pieces written in C and in the scripting language Tcl/Tk, making the program very portable and extensible. AVAILABILITY: Source code, binaries for Linux and MS Windows, and additional documentation are available athttp://rrna.uia.ac.be/rnaviz/
Subject(s)
Database Management Systems , Nucleic Acid Conformation , RNA/chemistry , Software , User-Computer Interface , Base Sequence , Databases, Nucleic Acid , Documentation , Imaging, Three-Dimensional/methods , Information Storage and Retrieval/methods , Molecular Sequence DataABSTRACT
In order to study the phylogenetic relationships within the stramenopiles, and particularly among the heterokont algae, we have determined complete or nearly complete large-subunit ribosomal RNA sequences for different species of raphidophytes, phaeophytes, xanthophytes, chrysophytes, synurophytes and pinguiophytes. With the small- and large-subunit ribosomal RNA sequences of representatives for nearly all known groups of heterokont algae, phylogenetic trees were constructed from a concatenated alignment of both ribosomal RNAs, including more than 5,000 positions. By using different tree construction methods, inferred phylogenies showed phaeophytes and xanthophytes as sister taxa, as well as the pelagophytes and dictyochophytes, and the chrysophytes/synurophytes and eustigmatophytes. All these relationships are highly supported by bootstrap analysis. However, apart from these sister group relationships, very few other internodes are well resolved and most groups of heterokont algae seem to have diverged within a relatively short time frame.
Subject(s)
Eukaryota/classification , Eukaryota/genetics , Evolution, Molecular , Phylogeny , RNA, Ribosomal/genetics , Ribosomes/genetics , Ribosomes/chemistry , Sequence Alignment , Sequence Homology, Nucleic AcidABSTRACT
The European database on SSU rRNA can be consulted via the World WideWeb at http://rrna.uia.ac.be/ssu/ and compiles all complete or nearly complete small subunit ribosomal RNA sequences. Sequences are provided in aligned format. The alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure models and nucleotide variability maps, is also available.
Subject(s)
Databases, Nucleic Acid , RNA, Ribosomal/chemistry , RNA, Ribosomal/genetics , Animals , DNA, Ribosomal , Europe , Information Storage and Retrieval , Internet , Nucleic Acid Conformation , RNA, Archaeal/chemistry , RNA, Archaeal/genetics , RNA, Bacterial/chemistry , RNA, Bacterial/genetics , Sequence AlignmentABSTRACT
This paper reports the identification of bacterial endosymbionts inhabiting the leaf galls of Psychotria kirkii. A phylogenetic approach was used to reveal the identity of these as yet uncultivable bacterial endophytes. Based on the analysis of 16S rDNA sequences, evolutionary trees were constructed that place the endosymbiont in the genus Burkholderia. Low levels of sequence identity and rather large evolutionary distances to the closest validly named relatives indicate that these symbiotic bacteria represent a novel species. Until cultivation is successful or until more phenotypic data become available the provisional name 'Candidatus Burkholderia kirkii' sp. nov. is proposed.
