A genome Tree of Life for the Fungi kingdom

Abstract

Fungi belong to one of the largest and most diverse kingdoms of living organisms. The evolutionary kinship within a fungal population has so far been inferred mostly from the gene-information–based trees (“gene trees”), constructed commonly based on the degree of differences of proteins or DNA sequences of a small number of highly conserved genes common among the population by a multiple sequence alignment (MSA) method. Since each gene evolves under different evolutionary pressure and time scale, it has been known that one gene tree for a population may differ from other gene trees for the same population depending on the subjective selection of the genes. Within the last decade, a large number of whole-genome sequences of fungi have become publicly available, which represent, at present, the most fundamental and complete information about each fungal organism. This presents an opportunity to infer kinship among fungi using a whole-genome information-based tree (“genome tree”). The method we used allows comparison of whole-genome information without MSA, and is a variation of a computational algorithm developed to find semantic similarities or plagiarism in two books, where we represent whole-genomic information of an organism as a book of words without spaces. The genome tree reveals several significant and notable differences from the gene trees, and these differences invoke new discussions about alternative narratives for the evolution of some of the currently accepted fungal groups.

Human pantothenate kinase 4 is a pseudo‐pantothenate kinase

“…The topology of the fungi Clade 1 PANK subtree [Fig. (a)] is consistent with the established fungi tree of life . Clade 1 sequences from the “Monokaryotic” fungi taxa diverge at the root of the tree.…”

“…4(a)] is consistent with the established fungi tree of life. 29 Clade 1 sequences from the "Monokaryotic" fungi taxa diverge at the root of the tree. The monokaryotic fungi contain taxa that Archaeplastida (plants and algae) also encode only HsPANK4-related Clade1 kinases, which cluster together and share a common ancestor [ Fig.…”

Mitochondrial genome, comparative analysis and evolutionary insights into the entomopathogenic fungus Hirsutella thompsonii

“…To date, reference mitogenomes of 272 fungal species have been released in NCBI Organelle Genome Resources database (https:// www.ncbi.nlm.nih.gov/ genome/organelle/) as of June 2018. This number is, however, lower than the number of fungal species (over 400) with available nuclear genomes (Choi and Kim, 2017), let alone the vast number of described (~110 000) and estimated (1.5 million or more) fungal species (Dai et al, 2015). There is an urgent need for analyzing mitogenomes of more fungal lineages for insight into their evolution.…”

Insights from Ion Binding Site Network Analysis into Evolution and Functions of Proteins

“…They report a generative model, where power law behavior emerges on the level of protein domains. Qian et al also report a simple generative model, which reproduces the scale‐free properties of the relation between protein families and folds ,. Although existing studies provide possible mechanistic explanations on the level of protein domain networks, there are currently very few reports on evolution of protein binding sites.…”