DOI: 10.5061/dryad.wpzgmsc03
title: Insights from the developmental genes of sedges and grasses

description: The evolution of stomatal morphology is a defining trait among plant
 lineages. Grasses (Poaceae) have distinctive dumbbell-shaped stomata that
 enhance water-use efficiency compared to the more common kidney-shaped
 stomata. In the closely related sedges (Cyperaceae), both kidney-shaped
 and dumbbell-like stomata can be found. Dumbbell-like stomata in sedges
 share morphological features with grasses, suggesting potential
 conservation of developmental pathways. To investigate the evolution of
 dumbbell and dumbbell-like stomata, we analyzed genomic and transcriptomic
 data from 29 sedge species and 5 grass species. Using their predicted
 proteomes, we identified orthologues involved in stomatal development and
 reconstructed their phylogenetic histories. Among the 16 gene families
 analyzed, EPFL9, YODA, SCR, and SHR were expanded in grasses but not in
 sedges. POLAR, SPCH, and ABI were expanded in both lineages, seven
 families were conserved in both, BASL was lost in both, and, in the
 SCRM/ICE family, SCRM was lost while ICE was duplicated in sedges. Gene
 family expansion in grasses occurred primarily in genes involved in early
 stages of stomatal development, while gene families non-duplicated or
 independently expanded act in later stages. The non-duplicated or
 independently expanded genes shared by sedges and grasses contribute to
 development of the two lateral subsidiary cells as well as the guard
 cells, suggesting shared regulatory networks underlying the stomata
 morphology typical of the order Poales. Our study provides a crucial guide
 to further test functional proteins underlying paracytic dumbbell-like
 stomata development.
description: # Insights from the developmental genes of sedges and grasses ## Overview
 This repository contains datasets supporting the manuscript
 *"Decoding the evolution of dumbbell stomata: insights from the
 developmental genes of sedges and grasses"* (*Plant Gene*). The study
 investigates the evolution of stomatal developmental genes in sedges
 (Cyperaceae) and grasses (Poaceae). Data are provided to ensure
 reproducibility, facilitate reuse, and promote open science practices. ##
 Data Description ### 1. Proteomes (FASTA format) * **File:**
 `predicted_proteomes.tar.xz` * **Content:** Predicted proteomes from **45
 angiosperm species**. * **Species list:** * *Agave tequilana* * *Ananas
 comosus* * *Arabidopsis thaliana* * *Asparagus officinalis* *
 *Brachypodium distachyon* * *Carex alatauensis* * *Carex breviculmis* *
 *Carex capillaris* * *Carex capillifolia* * *Carex cristatella* * *Carex
 kokanica* * *Carex littledalei* * *Carex myosuroides* * *Carex nigra* *
 *Carex nudicarpa* * *Carex pseuduncinoides* * *Carex rigescens* * *Carex
 sargentiana* * *Carex scoparia* * *Carex tibetikobresia* * *Cyperus
 alternifolius* * *Cyperus brevifolius* * *Cyperus difformis* * *Cyperus
 esculentus* * *Cyperus iria* * *Cyperus papyrus* * *Dioscorea alata* *
 *Eleocharis dulcis* * *Eriophorum vaginatum* * *Eucalyptus grandis* *
 *Hordeum vulgare* * *Joinvillea ascendens* * *Juncus effusus* * *Juncus
 inflexus* * *Lepidosperma gibsonii* * *Mapania palustris* * *Musa
 acuminata* * *Oreobolus obtusangulus* * *Oryza sativa* * *Rhynchospora
 breviuscula* * *Rhynchospora pubera* * *Rhynchospora tenuis* * *Setaria
 viridis* * *Sorghum bicolor* * *Zea mays* * **Source:** Publicly available
 predicted proteomes and transcriptomes. ### 2. Stomatal Development Gene
 Families (FASTA format) * **File:** `protein_families.tar.xz` *
 **Content:** Curated sequences of stomatal development-related genes
 identified in this study, grouped by family: * **ABI1** * **EPFL9** *
 **FAMA** * **MUTE** * **NAP1** * **PAN1** * **PAN2** * **PIR121** *
 **POLAR** * **SCAR** * **SCRM** * **SCR** * **SHR** * **SPCH** * **YODA**
 ### 3. Multiple Sequence Alignments (FASTA format) * **File:**
 `protein_alingments.tar.xz` * **Content:** Alignments generated using: *
 **MAFFT** for local pairwise alignment. * **trimAl** with `-gappyout` flag
 for alignment trimming. ### 4. Phylogenetic Trees (Newick format) *
 **File:** `nwk_trees.tar.xz` * **Content:** Maximum-likelihood trees
 inferred with **IQ-TREE**. ## Contact * **Corresponding Author:** Alison
 P. A. Menezes ([alisonpam@gmail.com](mailto:alisonpam@gmail.com)), ORCID:
 [0000-0002-8036-6576](https://orcid.org/0000-0002-8036-6576) *
 **Affiliation:** University of Naples Federico II * **Code/scripts:**
 Available at
 [https://github.com/alisonpelri/stomata_project](https://github.com/alisonpelri/stomata_project).