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NPG-explorer: a new tool for nucleotide pangenome construction and analysis of closely related prokaryotic genomes

Boris Nagaev and Andrei Alexeevski

Genomes of closely related bacteria have highly similar sequences of orthologous fragments but usually undergo multiple rearrangements, long deletions, insertions of mobile elements and occasionally horizontally transferred regions.

We developed a new tool, Nucleotide PanGenome explorer (NPG-explorer), designed for aligning and analysis of a number of input closely related genomes. NPG-explorer constructs nucleotide pangenome - a set of aligned blocks, each block consisting of orthologous fragments. Fragments having no orthologs are considered dummy blocks of one fragment. Each nucleotide from input genomes belongs to exactly one block of NPG (it is a reason for NPG terminology). Minimum length of block (default 100 bp) and minimum identity (default 90%) are algorithm parameters. NPG-explorer iterates block detection algorithm until the following criterion is satisfied: BLAST search all-against-all block consensuses detects no hits of appropriate size and identity.

In addition NPG-explorer provides: (1) Multiple alignments of input chromosomes represented by a sequence of block identifiers. These alignments allow to detect chromosomal rearrangements. (2) File with consensus sequences of all blocks and file with description of all mutations with respect to consensuses. Thus, all input genome sequences can be completely reconstructed from these two files. (3) Phylogenetic trees of core blocks and of whole genomes. Core blocks are those that contain exactly one fragment of each genome. These trees are computed on the base of diagnostic positions in block alignments. (4) All gene annotations, mapped on blocks. This data are useful for detection and correction mis-annotations, gene corruption etc.

NPG-visualization tool presents interactively a list of blocks, the alignment with mapped genes, alignments of block identifiers.

NPG-explorer is written in C++ and is licensed under the GNU GPL. Simple script language for program modules invocation is introduced.

NPG-explorer was applied to 17 genomes of Brucella genus, each genome consists of about 3 Mb. NPG-explorer worked approximately one hour on Intel Core i5 computer. Among 527 detected blocks with two or more fragments there are 270 core blocks, they cover 95% of nucleotides. Average sequence similarity in core blocks is 99.2%. Phylogenetic tree of genomes computed by NPG-explorer by using diagnostic positions is in agreement with published data for 10 Brucella genomes [1]. Detected 25787 point mutations and 2334 deletions of more than two bp describes the evolution of sequences within blocks. The program found large translocation from first to second chromosome in Brucella suis ATCC 23445 and large inversion in chromosome 2 of Brucella abortus, also described earlier [2].

The work was supported by RFBR grants 14-04-01693, 13-07-00969.

[1] Wattam et al., J.Bacteriology, 191:3569-79 (2009)
[2] Tsoktouridis et al., J.Bacteriology, 185:6130-6 (2003)