The evolutionary history of plant T2/S-type ribonucleases
- Published
- Accepted
- Subject Areas
- Evolutionary Studies, Genetics, Genomics, Molecular Biology, Plant Science
- Keywords
- self-incompatibility, S-RNase, self-incompatibility RNase, homology, gametophytic self-incompatibility, GSI, gene family, evolution, T2-RNase, plants
- Copyright
- © 2017 Ramanauskas et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. The evolutionary history of plant T2/S-type ribonucleases. PeerJ Preprints 5:e3171v1 https://doi.org/10.7287/peerj.preprints.3171v1
Abstract
A growing number of T2/S-RNases are being discovered in plant genomes. Members of this protein family have a variety of known functions, but the vast majority are still uncharacterized. We present data and analyses of phylogenetic relationships among T2/S-RNases, and pay special attention to the group that contains the female component of the most widespread system of self-incompatibility in flowering plants. The returned emphasis on the initially identified component of this mechanism yields important conjectures about its evolutionary context. First, we find that the clade involved in self-rejection (class III) is found exclusively in core eudicots, while the remaining clades contain members from other vascular plants. Second, certain features, such as intron patterns, isoelectric point, and conserved amino acid regions, help differentiate S-RNases, which are necessary for expression of self-incompatibility, from other T2/S-RNase family members. Third, we devise and present a set of approaches to clarify new S-RNase candidates from existing genome assemblies. We use genomic features to identify putative functional and relictual S-loci in genomes of plants with unknown mechanisms of self-incompatibility. The widespread occurrence of possible relicts suggests that the loss of functional self-incompatibility may leave traces long after the fact, and that this manner of molecular fossil-like data could be an important source of information about the history and distribution of both RNase-based and other mechanisms of self-incompatibility. Finally, we release a public resource intended to aid the search for S-locus RNases, and help provide increasingly detailed information about their taxonomic distribution.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Supplemental information
- A list of ENTREZ search terms used to obtain T2/S-RNase sequences from GenBank.
- List of species removed from the dataset.
- Gene tree of T2/S-RNases in land plants with tip names and other annotations.
- The relationship between calculated pI values and experimental pH optima for several T2/S-RNases in land plants.
- Gene tree of F-box-containing genes near T2/S-RNase loci.
- Table of GenBank accessions used.
- Table of the referenced functional T2/S-RNase studies.
- Table of genomes used.