Comparative genomics of Prauserella sp. Am3, an actinobacterium isolated from root nodules of Alnus nepalensis in India
A novel actinomycete strain, assigned as Am3, was isolated from the root nodules of Alnus nepalensis at Mirik hills, India. Analysis of the 16s rRNA gene sequence placed this new strain within the genus Prauserella. The genome was sequenced by Illumina sequencing and resulting 5.33-Mbp high quality draft genome sequenced with a G + C content of 70.0 % and 4828 candidate protein-encoding genes. Phylogenetically, Prauserella clusters very close to Amycolatopsis and was previously placed under the genus Amycolatopsis. Our main focus was to reveal the genomic similarities and dissimilarities of the newly sequenced Prauserella sp. Am3 with the type strain, Prauserella rugosa DSM 43194 T, and to determine its relationship with Amycolatopsis, which is happened to be the closest genus of Prauserella. Taking an in silico approach, bioinformatic analysis revealed that the core genome of Amycolatopsis and Prauserella contained 1589 genes. The two Prauserella genomes shared approximately 4224 genes, and 237 and 245 unique genes were found in the P. rugosa and Prauserella sp. Am3 genomes, respectively. Analysis of various phylogenetic trees including a 16s rRNA gene tree, MLSA protein-based tree and concatenated core-genome-based tree, placed both Prauserella genomes together with Amycolatopsis halophila YIM 93233 as its closest neighbor. Blast Matrix analysis of the predicted proteomes revealed about 86 % homology between the two Prauserella genomes. Analysis of the strand variation property revealed the absence of replication-transcriptional selection. Overall, a high degree of similarity was found between the two Prauserella genomes and a high percentage of similarity occurred among the Prauserella genomes and Amycolatopsis halophila.
Digital Object Identifier (DOI)
Bose, D., I. Sarkar, R. Labar, R. Oshone, S. Ghazal, K. Morris, F. Abebe-Akele, W.K. Thomas, A. Sen and L.S. Tisa. 2016. Comparative genomics of Prauserella sp. Am3, an actinobacterium isolated from root nodules of Alnus nepalensis in India. Symbiosis 70:49-58 (doi: 10.1007/s13199-016-0401-3)
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