Transcriptional analysis of Ceratopteris richardii young sporophyte reveals conservation of stem cell factors in the root apical meristem

Abstract

Gene expression in roots has been assessed in different plant species in studies ranging from complete organs to specific cell layers, and more recently at the single cell level. While certain genes or functional categories are expressed in the root of all or most plant species, lineage-specific genes have also been discovered. An increasing amount of transcriptomic data is available for angiosperms, while a limited amount of data is available for ferns, and few studies have focused on fern roots. Here, we present a de novo transcriptome assembly from three different parts of the Ceratopteris richardii young sporophyte. Differential gene expression analysis of the root tip transcriptional program showed an enrichment of functional categories related to histogenesis and cell division, indicating an active apical meristem. Analysis of a diverse set of orthologous genes revealed conserved expression in the root meristem, suggesting a preserved role for different developmental roles in this tissue, including stem cell maintenance. The reconstruction of evolutionary trajectories for ground tissue specification genes suggests a high degree of conservation in vascular plants, but not for genes involved in root cap development, showing that certain genes are absent in Ceratopteris or have intricate evolutionary paths difficult to track. Overall, our results suggest different processes of conservation and divergence of genes involved in root development.

Transcriptomic analyses in the gametophyte of Dryopteris affinis: apomixis and more

“…In addition, a couple of proteins: UBIQUITIN-SPECIFIC PROTEASE 26 (UBP26), a heterochromatin silencing, and whose loss-of-function mutants show embryonic arrest (Sridhar et al, 2007); and PLETHORA 2 (PLT2), involved in the establishment of the stem cell niche in embryogenesis (Smith and Long, 2010), and which belongs to a large family of transcription factors known to regulate plant development. Our result agrees with other studies, such as those carried out by Youngstrom et al, (2019) and Aragón-Raygoza et al, (2022), who have detected the protein PLT2 in gametophytes and sporophytes of the fern C. richardii . Finally, quite a few proteins belonging to the DEAD box helicase family were found: MATERNAL EFFECT EMBRYO ARREST 5 (MEE5), 63 (MEE63), and 58 (MEE58), all important in embryogenesis.…”

“…Auxins and cytokinins are suggested to be involved in stablishing polarity in the syncytial gametophyte, in many plant species (Terceros et al, 2020). In ferns, in a study carried out in young sporophytes of the fern C. richardii , it was detected the expression of PIN3 gene in the root tip, given the directional movement characteristic of auxin transport (Aragón-Raygoza et al, 2022). Recently, in gametophytes of the fern C. richardii , Whithers et al, (2023) demonstrated that correct auxin transport is involved in meristem positioning and regeneration, as they observed that upon destruction of a marginal meristem cell, cell proliferation ceased in this area, and an auxin synthesis gene was no longer expressed, but with the addition of auxins, such as indolacetic or 2, 4-dichlorophenoxyacetic acids, the meristem shifted position to the apex of the gametophytes.…”

“…In fact, they occupy one of the last positions in the race to decipher genome sequencing because of their high chromosome number and large genome size (Barker and Wolf, 2010). To our knowledge, the genomes of only four fern species are accessible, which are Alsophila spinulosa, Azolla filiculoides , C. richardii , and Salvinia cucullata (Aragón-Raygoza et al, 2022). Thanks to the advent of next-generation sequencing methodologies, more genomes are expected to be deciphered soon, as predicted by Kinosian and Wolf (2022).…”

Proteome and Interactome Linked to Metabolism, Genetic Information Processing, and Abiotic Stress in Gametophytes of Two Woodferns

“…sinense [23]. In addition, some molecular studies were performed on the fern Ceratopteris richardii [5,24]; in one of them, sex determination was found to be accompanied by changes in the transcriptome driving epigenetic reprogramming of the young gametophyte [25]; in another, the WUSCHEL-related homeobox (WOX) gene, which promotes cell division in gametophytes and organ development in sporophytes, was characterized for the first time in ferns [26]; and finally, transcriptional analysis of the young sporophyte showed the conservation of stem cell factors in the root apical meristem [27]. More recently, other studies on ferns were carried out.…”