Expansion and evolutionary patterns of cysteine-rich peptides in plants

Abstract

BackgroundCysteine-rich peptides (CRPs) are gaining recognition as regulators of cell–cell communication in plants.ResultsWe identified 9556 CRPs in 12 plant species and analysed their evolutionary patterns. In most angiosperm plants, whole genome duplication and segmental duplication are the major factors driving the expansion of CRP family member genes, especially signal peptides. About 30% of the CRP genes were found clustered on the chromosomes, except in maize (Zea mays). Considerable collinearities between CRP genes between or within species reveal several syntenic regions on the chromosomes. Different subfamilies display diverse evolutionary rates, suggesting that these subfamilies are subjected to different selective pressures. CRPs in different duplication models also show contrasting evolutionary rates, although the underlying mechanism is unclear because of the complexity of gene evolution. The 1281 positively selected genes identified are probably generated within a certain period of time. While most of these belonged to maize and sorghum (Sorghum bicolor), new CRP functions would also be expected. Up-regulation of 10 CRPs was observed in self-pollinated pear pistils and pollen tubes under self S-RNase treatments in vitro. The expression divergence between different CRP gene duplication types suggests that different duplication mechanisms affected the fate of the duplicated CRPs.ConclusionOur analyses of the evolution of the CRP gene family provides a unique view of the evolution of this large gene family.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3948-3) contains supplementary material, which is available to authorized users.

Ectopic Expression of a Self-Incompatibility Module Triggers Growth Arrest and Cell Death in Vegetative Cells

“…PrsS and SPHs are members of the CRPs, which include the Brassica spp. pollen S-determinant SCR/SP11 (Schopfer et al, 1999;Takayama et al, 2000), defensins (Bircheneder and Dresselhaus, 2016), LUREs (Okuda et al, 2009;Takeuchi and Higashiyama, 2016), and rapid alkanization factors (RALFs; Pearce et al, 2001;Li and Yang, 2018), which are known to interact with receptors to activate diverse signaling networks involved in plant growth, defense, and reproduction (Wheeler et al, 2010;Marshall et al, 2011;Takeuchi and Higashiyama, 2016;Liu et al, 2017). Although comparatively few secreted peptides have been shown to interact with receptors in plants, genome analysis has revealed the existence of hundreds of predicted secreted proteins that may act as ligands (Lease and Walker, 2006).…”

“…PrpS encodes a novel integral membrane protein with several predicted transmembrane domains; PrsS encodes a small, secreted protein and is the founding member of the large family of S-protein homologs (SPHs), which are found in most dicotyledonous plants, some fungi, and metazoa (Rajasekar et al, 2019). This family of small, secreted proteins have features similar to cysteine-rich peptides (CRPs), which include ligands known to be involved in diverse signaling pathways (Wheeler et al, 2010;Marshall et al, 2011;Bircheneder and Dresselhaus, 2016;Liu et al, 2017). However, aside from PrsS, the functional roles of SPHs in plants remain to be established (Rajasekar et al, 2019).…”

In silicoCharacterization of Class II Plant Defensins fromArabidopsis thaliana

“…Still from the point of view of gene duplication and accumulation of mutations, in A. thaliana , the defensin gene differentiation occurred after ancestral gene duplication events (whole genome or single gene duplication), followed by species-specific functional diversification due to transcriptional divergences in tissue and levels of expression (Liu et al, 2017; Mondragón-Palomino et al, 2017). Considering that coding genes for A7REG2 and A7REG4 (AGI AT1G73603 and AT1G73607, respectively) are neighbors in chromosome 1 and are expressed in the same tissues with similar intensities (Figure 3), they could be a result of a process of subfunctionalization.…”

Plant Defense Proteins as Potential Markers for Early Detection of Forest Damage and Diseases

“…Total number of defensin and defensin-like genes predicted using standard homology-based genome annotation (brown) and AMP-targeted (orange) pipelines are given for selected herbaceous and woody plant species (species names in green and black, respectively). Information about the number of genes identified using the AMP-specific approaches is available for A. thaliana, A. halleri, and A. lyrata (Silverstein et al, 2005), M. truncatula (de Bang et al, 2017), T. aestivum (International Wheat Genome Sequencing, 2018), V. vinifera (Giacomelli et al, 2012), S. lycopersicum, P. persica, and P. trichocarpa (Liu et al, 2017). Stars indicate species, for which corresponding information is not available.…”