Computational protocol: Genome Sequence of Mycoplasma meleagridis Type Strain 17529

Similar protocols

Protocol publication

[…] Mycoplasma meleagridis is usually reported as a specific pathogen of turkeys that causes embryo mortality, skeletal abnormalities, and poor growth performance in the infected progeny (). Nevertheless, its occasional isolation from chickens showing signs of respiratory disease and/or egg production losses suggests that M. meleagridis might also be a pathogen in chickens. This assumption was formally demonstrated in 2011 and opened many questions about transmission and adaptation to chickens as a new host (). To start answering these questions, the availability of the complete genome sequence of M. meleagridis was required. Here, we determined the complete genome sequence of M. meleagridis type strain ATCC 25294, originally isolated from infected turkeys.The genome sequencing of M. meleagridis ATCC 25294 strain was achieved at the Genome-Transcriptome facility of Bordeaux (http://www.pgtb.u-bordeaux2.fr) using the Illumina MiSeq version 2 sequencer and by combining mate-pair and paired-end libraries. De novo assembly was performed at the Bordeaux Bioinformatics Center (http://www.cbib.u-bordeaux2.fr/) using CLC and ABySS softwares. Coding sequences (CDSs) were predicted with the fully automated Rapid Annotations using Subsystems Technology (RAST) server (). This initial annotation was improved by manual curation. The RNAmmer 2.1 software () was run to verify rRNAs, and the Aragorn software () was used to predict tRNAs and transfer-messenger RNAs (tmRNAs). The annotated genome was integrated into the MolliGen database (http://cbi.labri.fr/outils/molligen/), which is dedicated to the comparative genomics of Mollicutes genomes (). Analysis of the M. meleagridis genome was supported by tools available in RAST/SEED and MolliGen.De novo assembly of the M. meleagridis genome resulted in 22 contigs organized in 7 scaffolds. The genome sequence is composed of 634,182 bp, with an overall G+C content of 26.02%. It contains 505 predicted CDSs, representing a coding density of 91.49%. The M. meleagridis genome includes one copy each of the 16S and 23S rRNA genes and two copies of the 5S rRNA gene. A set of 33 tRNA genes, corresponding to all amino acids, was also characterized.The origin of replication of M. meleagridis has not been experimentally identified. However, as described for other bacterial genomes, the tandem arrangement of the dnaA (MMELEA_00800) and dnaN (MMELEA_00810) genes was found (, ).A phylogenetic tree inferred from the 16S rRNA gene sequences of multiple mycoplasma species showed that M. meleagridis belongs to the Hominis group of mycoplasmas. Analysis of the M. meleagridis genome revealed that the arginine dihydrolase pathway is complete. Indeed, the genes arcA, arcB, and arcC encoding arginine deiminase (MMELEA_04580), ornithine carbamoyltransferase (MMELEA_04570), and carbamate kinase (MMELEA_04560), respectively, were identified. This finding is in accordance with the ability of M. meleagridis to alkalinize culture medium containing arginine ().This is the first genome sequence of the M. meleagridis species, which will be helpful for a better understanding of the genetic basis of the virulence of the pathogen. Further genome sequencing of M. meleagridis strains isolated from chickens will be necessary to address the question of host specificity. […]

Pipeline specifications

Software tools RAST, RNAmmer, ARAGORN
Databases MolliGen
Applications Genome annotation, Phylogenetics
Organisms Meleagris gallopavo
Diseases Mycoplasma Infections, Genetic Diseases, Inborn