Whole-proteome tree of life suggests a deep burst of organism diversity
Jae Jin Choi and Sung-Hou Kim
PNAS first published February 4, 2020
Jae Jin Choi and Sung-Hou Kim
PNAS first published February 4, 2020
https://doi.org/10.1073/pnas.1915766117
Contributed by Sung-Hou Kim, December 11, 2019 (sent for review September 12, 2019; reviewed by Se-Ran Jun and Charles G. Kurland)
Significance
Tree of life (ToL) is a metaphorical tree that captures a simplified narrative of the evolutionary course and kinship among all living organisms of today. We have reconstructed a whole-proteome ToL for over 4,000 different extant species for which complete or near-complete genome sequences are available in public databases. The ToL suggests that 1) all extant organisms of this study can be grouped into 2 “Supergroups,” 6 “Major Groups,” or 35+ “Groups”; 2) the order of emergence of the “founders” of all the groups may be assigned on an evolutionary progression scale; and 3) all of the founders of the groups have emerged in a “deep burst” near the root of the ToL—an explosive birth of life’s diversity.
Abstract
An organism tree of life (organism ToL) is a conceptual and metaphorical tree to capture a simplified narrative of the evolutionary course and kinship among the extant organisms. Such a tree cannot be experimentally validated but may be reconstructed based on characteristics associated with the organisms. Since the whole-genome sequence of an organism is, at present, the most comprehensive descriptor of the organism, a whole-genome sequence-based ToL can be an empirically derivable surrogate for the organism ToL. However, experimentally determining the whole-genome sequences of many diverse organisms was practically impossible until recently. We have constructed three types of ToLs for diversely sampled organisms using the sequences of whole genome, of whole transcriptome, and of whole proteome. Of the three, whole-proteome sequence-based ToL (whole-proteome ToL), constructed by applying information theory-based feature frequency profile method, an “alignment-free” method, gave the most topologically stable ToL. Here, we describe the main features of a whole-proteome ToL for 4,023 species with known complete or almost complete genome sequences on grouping and kinship among the groups at deep evolutionary levels. The ToL reveals 1) all extant organisms of this study can be grouped into 2 “Supergroups,” 6 “Major Groups,” or 35+ “Groups”; 2) the order of emergence of the “founders” of all of the groups may be assigned on an evolutionary progression scale; 3) all of the founders of the groups have emerged in a “deep burst” at the very beginning period near the root of the ToL—an explosive birth of life’s diversity.
genome phylogeny, alignment-free, feature frequency profile, Jensen–Shannon divergence, genome tree
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