Moss phylogeny reconstruction using nucleotide pangenome of complete Mitogenome sequences

Abstract

Stability of composition and sequence of genes was shown earlier in 13 mitochondrial genomes of mosses (Rensing, S. A., et al. (2008) Science, 319, 64-69). It is of interest to study the evolution of mitochondrial genomes not only at the gene level, but also on the level of nucleotide sequences. To do this, we have constructed a "nucleotide pangenome" for mitochondrial genomes of 24 moss species. The nucleotide pangenome is a set of aligned nucleotide sequences of orthologous genome fragments covering the totality of all genomes. The nucleotide pangenome was constructed using specially developed new software, NPG-explorer (NPGe). The stable part of the mitochondrial genome (232 stable blocks) is shown to be, on average, 45% of its length. In the joint alignment of stable blocks, 82% of positions are conserved. The phylogenetic tree constructed with the NPGe program is in good correlation with other phylogenetic reconstructions. With the NPGe program, 30 blocks have been identified with repeats no shorter than 50 bp. The maximal length of a block with repeats is 140 bp. Duplications in the mitochondrial genomes of mosses are rare. On average, the genome contains about 500 bp in large duplications. The total length of insertions and deletions was determined in each genome. The losses and gains of DNA regions are rather active in mitochondrial genomes of mosses, and such rearrangements presumably can be used as additional markers in the reconstruction of phylogeny.

Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate vast taxonomic diversity, open genomes and an abundance of carbohydrate-active enzyme family isoforms

“…It is inevitable that some degree of subjectivity is seen with respect to taxonomy, and consequently the same group of organisms can be sorted and arranged in many different ways [4,11]. More recently, pangenomic analyses (those which look at shared core genes, accessory genes that confer variability, and the combination of these as the pangenome) have also been suggested as potential methods for defining bacterial species [12][13][14].…”

Coordinate systems for supergenomes

“…So far, this approach has been applied only to closely related procaryotic genomes. Prime examples are a detailed comparative analysis of the transcriptome of multiple isolates of Campylobacter jejuni [ 18 ] or the reconstruction of the phylogeny of mosses from the “nucleotide pangenome” of mitogenomic sequences [ 19 ]. We remark that some approaches to “pangenomes” are concerned with gMSAs of (usually large numbers of) closely related isolates; most of this literature, however, treats pangenomes as sets of orthologous genes [ 20 ].…”