Computational protocol: Complete Genome Sequence of Porphyrobacter sp. Strain CACIAM 03H1, a Proteobacterium Obtained from a Nonaxenic Culture of Microcystis aeruginosa

Similar protocols

Protocol publication

[…] Porphyrobacter is one of the five genera affiliated with the family Erythrobacteraceae, which was proposed in 2005 based on phylogenetic studies of the Alphaproteobacteria class. Erythrobacteraceae members are Gram-negative, aerobic, rod-shaped or pleomorphic coccoid, and non-spore-forming bacteria. Furthermore, they are chemo-organotrophic and most often associated with freshwater environments ().Since the availability of genomic data from Amazonian proteobacteria is scarce, we recovered the complete genome of a Porphyrobacter sp., which was obtained from a culture of Microcystis aeruginosa sp. strain CACIAM 03 (BioSample SAMN05467875). This cyanobacterium was isolated from a water sample from the Tucuruí Hydroelectric Power station reservoir (3°50′04.9″S, 49°42′32.2″W) in Pará, Brazil.After DNA extraction of the nonaxenic culture, two sequencing runs were performed on the GS FLX 454 (Roche Life Sciences) platform using nonpaired libraries, and one sequencing run was carried out on the Illumina MiSeq platform using a paired-end library with 150-bp read length. All the raw reads were quality filtered, with a minimum Phred score of 20. A coassembly of all reads was performed by the assembly software Newbler version 2.9 () (which was parameterized with a minimum overlap of 40 bp, minimum overlap identity of 90%, heterozygote mode, and extend low-depth overlap options on), producing 1,484 scaffolds.MaxBin 2.2.1 () was used to bin the set of assembled scaffolds. To classify taxonomically the obtained bins, we performed a BLASTp search for each bin in the sequences containing hidden Markov models for essential genes identified by MaxBin 2.2.1 against the NCBI nonredundant database. The results were visualized on MegaN 5.11.3 ().The bin identified as Porphyrobacter contained 6 scaffolds with an N50 value of 1,078,724 bp, totaling 3.5 Mb. To obtain the complete genome of Porphyrobacter sp. strain CACIAM 03H1, we aligned the scaffolds with the Porphyrobacter sp. strain LM 6 genome using Mauve 2.4.0 (). Then, a manual gap closure step was done mapping the reads to the sequence with Geneious R9 ().The complete genome sequence has 3.5 Mb, 105 single-copy marker genes (104 unique), and 67.6% GC content and was estimated to be 97.2% complete. An automatic annotation process using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) () identified 3,281 coding sequences (CDSs), 44 tRNAs, 3 rRNAs, and 4 noncoding RNAs (ncRNAs). Overall, the data presented here will improve genomic information about Erythrobacteraceae members. Furthermore, it should provide further insights with regard to aerobic anoxygenic phototrophic metabolism, physiological nature, and biotechnological purposes. […]

Pipeline specifications

Software tools Newbler, MaxBin, BLASTP, MEGAN, Mauve, Geneious, PGAP
Databases BioSample
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Microcystis aeruginosa