Global Analysis of Proline-Rich Tandem Repeat Proteins Reveals Broad Phylogenetic Diversity in Plant Secretomes
(A) Dendrogram showing the evolutionary relationships among major plant divisions as well as the distribution of EXTAs identified in this study and in previous literature , , . (To reflect results of a recent phylogenetic analysis , the large divisions, super-rosids and super-asterids are shown rather than rosids, asterids, and other phylogenetic groups). (B) Heat map showing phylogenetic distributions of 18 secreted Pro-rich TRP classes, 17 of which are represented by more than a single plant family (abbreviated names are described in Text S2, and Tables S6, S7, S8). TRP classes are divided into the extensin superfamily, the non-extensin core modules, and the less conserved TRP classes found in >1 plant family. Dark-green rectangles represent TRP classes in which at least one known protein sequence or full-length ORF with a predicted secretion signal was found in the corresponding TRP class and plant phylogenetic group. Light-green rectangles with a horizontal line pattern represent TRP classes in which at least one putative member is present in the corresponding phylogenetic group (e.g. lacking a full-length sequence). Gray rectangles with a diagonal line pattern represent the putative moss AGPA and EXTB sequences (the AGPA is not predicted to be GPI-anchored; the EXTB sequence is not predicted to be secreted and has a TR domain that encompasses only half of the sequence). (C) Phylogenetic sampling bias of all ESTs and protein sequences (from Table S1) either captured by our TR taxonomy (Tables S3, S4, S5) or representing secreted Pro-rich TRPs (Table S2), shown as a log-scale histogram.