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Pipeline publication

[…] from a frost-plant-tissue sample in the process of screening for ice-nucleating bacteria in China (). The strain showed remarkable nematicidal activity against Caenorhabditis elegans (unpublished data). To identify the potential nematode-virulent factors, we sequenced and annotated the genome of A. johnsonii MB44., Genomic DNA was extracted using a bacterial DNA kit (GBCBIO), and DNA quantity was determined with a Nanodrop spectrometer (Thermo Scientific, Wilmington, NC, USA). The genome sequencing of A. johnsonii MB44 was performed via Illumina HiSeq 2000 platform using the paired-end strategy (2 × 125 bp). A total of 8,593,104 reads with approximately 137-fold coverage were assembled via ABySS version 1.3.7 () using a k-mer size of 90. Through the data assembly, 75 contigs with a total length of 3,357,599 bp and an average G+C content of 41.37 were obtained, and the contig N50 was found to be 106,230 bp., The annotation of the genome was performed by the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/), which predicted 3,277 genes, including 3,064 coding sequences (CDS), 21 rRNAs, and 81 tRNAs. A total of 58.00% of CDSs could be assigned to the cluster of orthologous groups of proteins (COG) database, and 3 clusters of regularly interspaced short palindromic repeat (CRISPR) repeats were found using CRISPRFinder (). The 16S rRNA gene sequence of A. johnsonii MB44 was 99.65% identical to the type strain A. johnsonii ATCC 17909T. The average nucleotide identity (ANI) using the online calculator (http://enve-omics.ce.gatech.edu/ani/index) revealed a two-way ANI value of 95.65% between A. johnsonii MB44 and A. johnsonii ATCC 17909T, which suggests that these two strains belong to same speices., We used the software MP3 () to predict virulent proteins in this genomic data and 108 potential virulent proteins were found. In addition, this genome encodes some proteins that are homologous to the known virulent proteins in A. baumannii, such as the outer membrane protein A, the phospholipase D, and penicillin-binding protein 7/8 (). The genome of MB44 also contains genes involved in the biosynthesis of siderophore and capsular polysaccharide, which are important virulence factors associated with the killing of C. elegans (, ). The genome information of A. johnsonii MB44 may accelerate our understanding of the molecular mechanism of its ability to infect nematodes., This whole-genome shotgun project was depos […]

Pipeline specifications

Software tools ABySS, PGAP, CRISPRFinder, MP3