Computational protocol: Whole Genome Sequencing of the Symbiont Pseudovibrio sp. from the Intertidal Marine Sponge Polymastia penicillus Revealed a Gene Repertoire for Host-Switching Permissive Lifestyle

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[…] Whole genome sequencing was performed using the Illumina’s HiSeq 2000 Sequencing System. Paired-end read library (2 ×100 nt) construction with an insert size of ∼300 bp and sequencing were performed at Macrogen, South Korea. The sequencing reads were assembled using de novo short read sequence assembler, Velvet 1.2.10 (). Illumina reads were quality filtered by discarding the reads with a Phred quality score below 30. Adapter sequences were trimmed off raw reads with cutadapt () retrieving a total of 77492810 reads. The best possible k-mer coverage of reads (k = 99) for the current genome assembly was opted from VelevetK. Overall, 271 contigs of >1,400-fold coverage were retrieved and annotated using the Prokka v1.10 () annotation pipeline. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession LCWX00000000. The version described in this article is version LCWX01000000.Prokka depends on many external feature prediction tools for genome annotation. Coding sequence (CDS) predication was carried out by Prodigal v2.60 (). We compiled a core database for assigning the function to the predicted CDS using a set of trustworthy curated data set comprising annotated bacterial proteins obtained from the current release of UniProt Knowledgebase, UniProtKB Release 2014_10 (). Ribosomal RNA (rRNA), transfer RNA (tRNA) genes, and noncoding RNA were predicted using RNAmmer v1.2 (), ARAGORN v1.2.36 (), and Infernal v1.1 (), respectively. SignalP v4.1 was used for the prediction of signal peptides ().Other genomes from the genus Pseudovibrio (FO-BEG and JE062) used for comparative purposes in this study were downloaded from NCBI ftp (ftp://ftp.ncbi.nih.gov/genomes/). The predicted ORFs were assigned to Clusters of Orthologous Groups of proteins (COGs) using WebMGA server () with RPSBLAST v2.2.15 (). […]

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