The Selaginella rhizophore has a unique transcriptional identity compared with root and shoot meristems

Abstract

Summary The genus Selaginella resides in an early branch of the land plant lineage that possesses a vasculature and roots. The majority of the Selaginella root system is shoot borne and emerges through a distinctive structure known as the rhizophore, the organ identity of which has been a long‐debated question. The rhizophore of Selaginella moellendorffii – a model for the lycophytes – shows plasticity to develop into a root or shoot up until 8 d after angle meristem emergence, after which it is committed to root fate. We subsequently use morphology and plasticity to define the stage of rhizophore identity. Transcriptomic analysis of the rhizophore during its plastic stage reveals that, despite some resemblance to the root meristem, rhizophore gene expression patterns are largely distinct from both shoot and root meristems. Based on this transcriptomic analysis and on historical anatomical work, we conclude that the rhizophore is a distinct organ with unique features.

Gene expression data support the hypothesis that Isoetes rootlets are true roots and not modified leaves

“…If I. echinospora rootlets were modified leaves, as predicted by the modified shoot hypothesis, we might expect gene expression signatures to be similar in the rootlets and leaves. To test this hypothesis, we compared gene expression in rootlets, leaves and corms using a principal coordinate analysis (PCoA), because similar approaches have proved successful for the investigation of lycophyte root transcriptomes 36 , 37 . The two leaf replicates, two corm replicates and the single rootlet sample were plotted on the first two PCoA axes [which together account for 98.6% of the variance in the sample (Fig.…”

“…Using these 1737 orthologs we compared gene expression between the different species. We compared average gene expression between I. echinospora rootlets and leaves (this study) with the published gene expression in roots and leaves of S. moellendorffii 36 and roots and “aerial parts” of Arabidopsis thaliana (based on EMBL-EBI accession E-GEOD-53197) (Supplementary Table S1 ). To compare gene expression between these different species and organs we subjected the gene expression dataset to a PCoA.…”

Gene expression data support the hypothesis that Isoetes rootlets are true roots and not modified leaves

“…Using these 1,737 orthologs we compared gene expression between the different species. We compared average gene expression between I. echinospora rootlets and leaves (this study) with the published gene expression in roots and leaves of S. moellendorffii 38 and roots and “aerial parts” of Arabidopsis thaliana (based on EMBL-EBI accession E-GEOD-53197). To compare gene expression between these different species and organs we subjected the gene expression dataset to a PCoA.…”

“…ROOT HAIR DEFECTIVE SIX-LIKE ( RSL ) genes positively regulate the development of root hairs in euphyllophytes including A. thaliana 39–42 and are expressed in S. moellendorffii roots 43,44 . RSL genes are markers for vascular plant roots because they are expressed at a much higher level in roots of A. thaliana (EMBL-EBI accession E-GEOD-53197) and S. moellendorffii 45 than in leaves and shoots (Supplementary Table S1). We searched the I. echinospora transcriptome for RSL genes using the BLAST algorithm with RSL-specific queries.…”

“…Using these 1,737 orthologs we contrasted gene expression between the different species. We investigated average genes expression between I. echinospora rootlets and leaves (this study) with the published average gene expression between roots and leaves of S. moellendorffii 38 and A. thaliana. A. thaliana gene expression was based on average gene expression in “aerial part” and “root” of 17 different natural accessions (EMBL-EBI accession E-GEOD-53197).…”