Abstract
The fasciclin-like arabinogalactan proteins (FLAs) play important roles in plant development and adaptation to the environment. FLAs contain both fasciclin domains and arabinogalactan protein (AGP) regions, which have been identified in several plants. The evolutionary history of this gene family in plants is still undiscovered. In this study, we identified the FLA gene family in 13 plant species covering major lineages of plants using bioinformatics methods. A total of 246 FLA genes are identified with gene copy numbers ranging from one (Chondrus crispus) to 49 (Populus trichocarpa). These FLAs are classified into seven groups, mainly based on the phylogenetic analysis of plant FLAs. All FLAs in land plants contain one or two fasciclin domains, while in algae, several FLAs contain four or six fasciclin domains. It has been proposed that there was a divergence event, represented by the reduced number of fasciclin domains from algae to land plants in evolutionary history. Furthermore, introns in FLA genes are lost during plant evolution, especially from green algae to land plants. Moreover, it is found that gene duplication events, including segmental and tandem duplications are essential for the expansion of FLA gene families. The duplicated gene pairs in FLA gene family mainly evolve under purifying selection. Our findings give insight into the origin and expansion of the FLA gene family and help us understand their functions during the process of evolution.
Highlights
The cell wall plays an important role in plant growth and development by providing structural support and protection, and acting as a filtering mechanism
We first used the Hidden Markov Model (HMM) profile of fasciclin downloaded from Pfam to identify the proteins with fasciclin domains from 13 plant species (C. crispus, Chlamydomonas reinhardtii, Chara braunii, Marchantia polymorpha, Physcomitrella patens, Selaginella moellendorffii, Picea abies, Amborella trichopoda, Brachypodium distachyon, O. sativa, A. thaliana, E. grandis, and P. trichocarpa) [31,32,33,34,35,36,37,38,39,40,41,42,43]
Green algae Fasciclin-like arabinogalactan protein (AGP) (FLAs) genes contained a large number of introns, while most land plants FLA genes contained one intron or even had no intron (Table S1). It seemed that introns in FLA genes were lost during plant evolution, especially from green algae to land plants
Summary
The cell wall plays an important role in plant growth and development by providing structural support and protection, and acting as a filtering mechanism. Hydroxyproline-rich glycoproteins (HRGPs) are a major group of cell wall glycoproteins that play important roles in plant growth and development [3]. The majority of plant fasciclin-like proteins are FLAs and the functions of FLAs are related to many important processes in development and stress responses, such as contributing to biophysical properties (e.g., swelling and interpolymer connectivity), affecting secondary cell wall formation and structure, acting in male gametophyte development, influencing organ formation, and sensing salt stress in roots [18]. It was proposed that a conserved group of FLAs with a single fasciclin domain was specific to the evolution of flowering plant secondary cell wall formation and properties through phylogenetic analysis of >100 FLA mature proteins [30]. Our study shows that there is a reduction in the number of fasciclin domains in FLAs from algae to land plants, which indicates that the reduced number of fasciclin domains plays a crucial role in land plant evolution
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