Differential activity of F-box genes and E3 ligases distinguishes sexual versus apomictic germline specification in Boechera

Abstract

A comprehensive tissue type-specific transcriptional study identifies 45 genes consistently differentially expressed during Boechera sexual as compared with apomictic germline specification, suggesting their relevance for apomixis.

Controlling Apomixis: Shared Features and Distinct Characteristics of Gene Regulation

“…Consistently, comparative transcriptome analysis in sexual and apomictic Boechera [103], Bohemeria tricuspis [97], and Hypericum perforatum [62] suggest that differential activity of genes involved in cell-cycle regulation, hormonal pathways, signal transduction, ubiquitinylation and protein degradation, and epigenetic regulatory pathway are involved in determining and sustaining megasporogenesis in either reproductive mode (Figure 3). To narrow down the number of candidate genes and to disentangle part of the effects of ploidy and species differences, differential expression analysis was recently applied to compare four apomictic versus two sexual Boechera accessions [103]. Thereby LAM and RNA-Seq have been combined to analyze gene expression in reproductive nucellus tissues harboring the AIC or MMC [103].…”

“…This discrepancy might potentially be explained by master regulators which control complex programs of gene activity. Transcriptional analyses to identify genes differentially expressed in sexual as compared to apomictic plants have been presented for a variety of species including Pennisetum ciliare and Pennisetum glaucum [83,84], Panicum maximum [85,86], Poa pratensis [87,88], Brachiaria brizantha [89,90], Paspalum notatum and Paspalum simplex [91][92][93][94], Eragostris curvula [95], Medicago falcata [96], Boehmeria tricuspis [97], Hypericum perforatum [62,98], Hieracium [99,100], Boechera [101][102][103], and also for Citrus [76] ( Table 2). These studies provide evidence for temporal deregulation of the gene regulatory processes governing sexual reproduction in apomicts and identify large numbers of up to hundreds of genes to be differentially expressed.…”

“…Novel insights have already been gained into the gene regulatory pathways governing the development of the sexual MMC and the cells of the mature female gametophyte in A. thaliana [79,[105][106][107], and the corresponding cells in the related triploid apomict Boechera gunnisoniana [80] (Table 2). Tissue type-specific transcriptome analysis targeting AIC/MMC and surrounding nucellus tissues furthermore allowed comparative analyses of gene expression and pathways relevant for megasporogenesis in different sexual as compared to apomictic Boechera accessions and in sexual versus aposporous Hypericum perforatum [62,103] (Table 2). LAM in combination with RNA-Seq recently has also shed light onto the cell type specification of the aposporous initial cell (AIC) as compared to early developing embryo sacs and somatic ovule tissues in Hieracium praealtum.…”

Differential Gene Expression Analysis and Cytological Evidence Reveal a Sexual Stage of an Amoeba with Multiparental Cellular and Nuclear Fusion

“…Enzyme Class (EC) distribution comparison of the two sets of DEGs showed that all the enzyme classes had more sequences in single samples than in fused samples except for the EC class Ligases (Fig 5). Various ligase enzymes were identified in fused samples including E3 ubiquitin-protein ligase previously shown to play a role in sexual development [47]. GO category representations in single samples were mostly dominated with metabolic activities (carbohydrate, lipid and protein), oxidation-reduction process, vesicle transport, cytoskeleton and cellular and intracellular movements (S7-S9 Figs).…”

“…These results can be interpreted as fused cells primarily engaged in ATP-mediated, DNA-related processes, likely reflecting their sexual nature. Among these, E3 ubiquitin ligase [47] and PHD-Finger [74] have been implicated to play a role in sexual development of plants. E3 ubiquitin ligase has a similar functional domain (i.e., RING-finger to Zip3), a meiosis specific gene and a member of the ZMM group known to play roles in crossover and SC assembly [54, 75].…”