TreeBASE Search-Matrices for study 13547

@ARTICLE{TreeBASE2Ref21466, author = {Pieter De Maayer and Wai Yin Chan and Jochen Blom and Stephanus N Venter and Brion Duffy and Theo HM Smits and Teresa A Coutinho}, title = {The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification}, year = {2012}, keywords = {}, doi = {}, url = {http://}, pmid = {}, journal = {BMC Genomics}, volume = {}, number = {}, pages = {}, abstract = {Background: Pantoea spp. are frequently isolated from a wide range of ecological niches and have various biological roles, as plant epi- or endophytes, biocontrol agents, plant-growth promoters or as pathogens of both plant and animal hosts. This suggests that members of this genus have undergone extensive genotypic diversification. One means by which this occurs among bacteria is through the acquisition and maintenance of plasmids. Here, we have analyzed and compared the genomes of a large plasmid common to all sequenced Pantoea spp. Results and discussion: The Large Pantoea Plasmid (LPP-1) ranges in size from ~281 to 794 kb and carries between 238 and 750 protein coding sequences (CDS). A core set of proteins, conserved among all LPP-1 genomes, includes those required for thiamine and pigment biosynthesis. Phylogenetic analysis reveals that these plasmids have arisen from an ancestral plasmid, which has undergone extensive diversification. Analysis of the proteins encoded on LPP-1 also showed that these plasmids contribute to a wide range of Pantoea phenotypes, including the transport and catabolism of various substrates, inorganic ion assimilation, resistance to antibiotics and heavy metals, colonization and persistence in the host and environment, pathogenesis and antibiosis. Conclusions: LPP-1 is universal to all Pantoea spp. whose genomes have been sequenced to date and is derived from an ancestral plasmid. LPP-1 encodes a large array of proteins that have played a major role in the adaptation of the different Pantoea spp. to their various ecological niches and their specialization as pathogens, biocontrol agents or benign saprophytes found in many diverse environments. } }

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Matrices for Study 13547

Citation title: "The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification".

Study name: "The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification".

This study is part of submission 13547 (Status: Published).

Matrices

ID	Matrix Title	Description	Data type	NTAX	NCHAR	Taxa
M14842	Chromosomal concatenated house-keeping protein matrix	Data matrix for the concatenated amino acid sequences of the four chromosomal housekeeping genes atpD, gyrB, infB and rpoB	Amino Acid	25	882	View Taxa
M14843	Chromosomal concatenated plasmid protein matrix	Data matrix for the concatenated amino acid sequences of twenty genes on the LPP-1 plasmid	Amino Acid	20	6838	View Taxa