Comparative phylogeny and evolutionary analysis of Dicer-like protein family in two plant monophyletic lineages

Background: Small RNAs (sRNAs) that do not get untranslated into proteins exhibit a pivotal role in the expression regulation of their cognate gene(s) in almost all eukaryotic lineages, including plants. Hitherto, numerous protein families such as Dicer, a unique class of Ribonuclease III, have been reported to be involved in sRNAs processing pathways and silencing. In this study, we aimed to investigate the phylogenetic relationship and evolutionary history of the DCL protein family.

Results: Our results illustrated the DCL family of proteins grouped into four main subfamilies (DCLs 1-4) presented in either Eudicotyledons or Liliopsids. The accurate observation of the phylogenetic trees supports the independent expansion of DCL proteins among the Eudicotyledons and Liliopsids species. They share the common origin, and the main duplication events for the formation of the DCL subfamilies occurred before the Eudicotyledons/Liliopsids split from their ancestral DCL. In addition, shreds of evidence revealed that the divergence happened when multicellularization started and since the need for complex gene regulation considered being a necessity by organisms. At that time, they have evolved independently among the monophyletic lineages. The other finding was that the combination of DCL protein subfamilies bears several highly conserved functional domains in plant species that originated from their ancestor architecture. The conservation of these domains happens to be both lineage-specific and inter lineage-specific.

Conclusions: DCL subfamilies (i.e., DCL1-DCL4) distribute in their single clades after diverging from their common ancestor and before emerging into higher plants. Therefore, it seems that the main duplication events for the formation of the DCL subfamilies occurred before the Eudicotyledons/Liliopsida split and before the appearance of moss, and after the single-cell green algae. We also observed the same trends among the main DCL subfamilies from functional unit composition and architecture. Despite the long evolutionary course from the divergence of Liliopsida lineage from the Eudicotyledons, a significant diversifying force to domain composition and orientation was absent. The results of this study provide a deeper insight into DCL protein evolutionary history and possible sequence and structural relationships between DCL protein subfamilies in the main higher plant monophyletic lineages; i.e., Eudicotyledons and Liliopsida.