Sex Determination in Ceratopteris richardii Is Accompanied by Transcriptome Changes That Drive Epigenetic Reprogramming of the Young Gametophyte

Abstract

The fern Ceratopteris richardii is an important model for studies of sex determination and gamete differentiation in homosporous plants. Here we use RNA-seq to de novo assemble a transcriptome and identify genes differentially expressed in young gametophytes as their sex is determined by the presence or absence of the male-inducing pheromone called antheridiogen. Of the 1,163 consensus differentially expressed genes identified, the vast majority (1,030) are up-regulated in gametophytes treated with antheridiogen. GO term enrichment analyses of these DEGs reveals that a large number of genes involved in epigenetic reprogramming of the gametophyte genome are up-regulated by the pheromone. Additional hormone response and development genes are also up-regulated by the pheromone. This C. richardii gametophyte transcriptome and gene expression dataset will prove useful for studies focusing on sex determination and differentiation in plants.

Keywords: Ceratopteris; Genetics of Sex; RNA-seq; antheridiogen; epigenetics; gametophyte; gibberellin; sex determination; transcriptome.

Figure 1

Ceratopteris gametophyte development. (a) SEM of spores three days after inoculation showing trilete markings. (b-d) SEMs of 4.5d, 6d and 14d gametophytes grown in the presence of $A_{CE}$. (e-g) SEMs of 4.5d, 6d and 14d gametophytes grown in the absence of $A_{CE}$. The mature hermaphrodite (g) has a meristem notch (mn), archegonia (ar) and antheridia (an) while the mature male (d) has only antheridia (an). Bars = 0.15mm.

Figure 2

MA plot showing the $lo{g}_2$ Fold change vs. the baseMean (normalized average expression), as calculated by DESeq (Anders and Huber 2010). Genes which are more highly expressed in $+A_{CE}$ treatment are shown in blue whereas those more highly expressed in $-A_{CE}$ treatement are shown in purple. The majority (88%) of differentially expressed genes were more highly expressed in $A_{CE}$ treated gametophytes.

Figure 3

Functionally grouped Biological Process GO terms specific for $A_{CE}$-up regulated DEGs. The size of each node represents the term enrichment significance. Node labels are shown in the bar graph in Figure S2.