Data_Sheet_2_Molecular Traits and Functional Analysis of the CLAVATA3/Endosperm Surrounding Region-Related Small Signaling Peptides in Three Species of Gossypium Genus.xlsx

The CLAVATA3/endosperm surrounding region-related (CLE) small peptides are a group of C-terminally encoded and post-translationally modified signal molecules involved in regulating the growth and development of various plants. However, the function and evolution of these peptides have so far remained elusive in cotton. In this study, 55, 56, and 86 CLE genes were identified in the Gossypium raimondii, Gossypium arboreum, and Gossypium hirsutum genomes, respectively, and all members were divided into seven groups. These groups were distinctly different in their protein characteristics, gene structures, conserved motifs, and multiple sequence alignment. Whole genome or segmental duplications played a significant role in the expansion of the CLE family in cotton, and experienced purifying selection during the long evolutionary process in cotton. Cis-acting regulatory elements and transcript profiling revealed that the CLE genes of cotton exist in different tissues, developmental stages, and respond to abiotic stresses. Protein properties, structure prediction, protein interaction network prediction of GhCLE2, GhCLE33.2, and GhCLE28.1 peptides were, respectively, analyzed. In addition, the overexpression of GhCLE2, GhCLE33.2, or GhCLE28.1 in Arabidopsis, respectively, resulted in a distinctive shrub-like dwarf plant, slightly purple leaves, large rosettes with large malformed leaves, and lack of reproductive growth. This study provides important insights into the evolution of cotton CLEs and delineates the functional conservatism and divergence of CLE genes in the growth and development of cotton.

CLAVATA3/胚乳周围区域相关（CLE）小肽是一类由C端编码且经过翻译后修饰的信号分子，参与调控多种植物的生长发育过程。然而，目前此类小肽在棉花中的功能与演化机制仍尚不明确。本研究分别在雷蒙德氏棉（Gossypium raimondii）、亚洲棉（Gossypium arboreum）和陆地棉（Gossypium hirsutum）的基因组中鉴定出55、56和86个CLE基因，且所有家族成员可划分为7个组群。这些组群在蛋白特征、基因结构、保守基序以及多序列比对结果上均存在显著差异。全基因组复制或片段复制在棉花CLE基因家族的扩张过程中发挥了重要作用，且该家族在棉花的长期演化过程中经历了纯化选择。顺式作用调控元件分析与转录组表达谱分析显示，棉花CLE基因在不同组织、不同发育阶段均有表达，且能响应非生物胁迫。本研究分别对GhCLE2、GhCLE33.2及GhCLE28.1这三种小肽的蛋白特性、结构预测以及蛋白互作网络预测进行了分析。此外，在拟南芥中分别过表达GhCLE2、GhCLE33.2或GhCLE28.1，均会导致植株出现独特的灌丛状矮化表型、叶片略带紫色、形成带有大量畸形叶片的大型莲座丛，且无法进行生殖生长。本研究为棉花CLE基因家族的演化提供了重要见解，并阐明了CLE基因在棉花生长发育过程中的功能保守性与分化情况。