Phylogenetic and Biological Significance of Evolutionary Elements from Metazoan Mitochondrial Genomes

Abstract

The evolutionary history of living species is usually inferred through the phylogenetic analysis of molecular and morphological information using various mathematical models. New challenges in phylogenetic analysis are centered mostly on the search for accurate and efficient methods to handle the huge amounts of sequence data generated from newer genome sequencing. The next major challenge is the determination of relationships between the evolution of structural elements and their functional implementation, which is largely ignored in previous analyses. Here, we described the discovery of structural elements in metazoan mitochondrial genomes, termed key K-strings, that can serve as a basis for phylogenetic tree construction. Although comprising only a small fraction (0.73%) of all K-strings, these key K-strings are pivotal to the tree construction because they allow for a significant reduction in the computational time required to construct phylogenetic trees, and more importantly, they make significant improvement to the results of phylogenetic inference. The trees constructed from the key K-strings were consistent overall to our current view of metazoan phylogeny and exhibited a more rational topology than the trees constructed by using other conventional methods. Surprisingly, the key K-strings tended to accumulate in the conserved regions of the original sequences, which were most likely due to strong selection pressure. Furthermore, the special structural features of the key K-strings should have some potential applications in the study of the structures and functions relationship of proteins and in the determination of evolutionary trajectory of species. The novelty and potential importance of key K-strings lead us to believe that they are essential evolutionary elements. As such, they may play important roles in the process of species evolution and their physical existence. Further studies could lead to discoveries regarding the relationship between evolution and processes of speciation.

Resolution of deep divergence of club fungi (phylum Basidiomycota)

“…Instead of exploiting site substitution, CVTree profiles difference of sequences through the effective frequency of short strings. As a good independent verification of standard phylogenetic reconstruction, this method and its variants have been successfully used to resolve the evolutionary relationships of many major divisions of life, including virus [23], archaea and bacteria [24], fungi [25] and animals [26].…”

Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea)

“…Most angiosperm chloroplasts contain 74 protein-coding genes; an additional three are found in a few species [25][26][27][28]. The four Castanea cp genomes we sequenced revealed 84 predicted protein-coding genes (77 unigenes were predicted to be protein coding).…”

“…Chloroplast genomes can provide species identification, sequences or SNPs to establish intra or interspecies differences, and they are often used for phylogeny and population genetic analysis [19][20][21][22]. Whole organelle sequences can potentially be used as "super barcodes" to differentiate lineages or varieties in breeding programs [23][24][25][26][27][28].…”

CVTree: A Parallel Alignment-Free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes

“…And the similarity between the two sequences was measured by the cosine of two CVs. The classical CVTree method was first developed to infer evolutionary relatedness of Bacteria and Archaea [11−14], and then successfully applied to fungi [15] , [16] , viruses [17] , chloroplasts [18] , and mitochondria [19] , as well as metagenomes [20] , [21] . After the proposal of the classical CVTree method, there are three versions of CVTree web server were released successively by our group [22−24].…”