Comparative transcriptomics identifies candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae)

Abstract

Background Fruits are the seed-bearing structures of flowering plants and are highly diverse in terms of morphology, texture and maturation. Dehiscent fruits split open upon maturation to discharge their seeds while indehiscent fruits are dispersed as a whole. Indehiscent fruits evolved from dehiscent fruits several times independently in the crucifer family (Brassicaceae). The fruits of Lepidium appelianum, for example, are indehiscent while the fruits of the closely related L. campestre are dehiscent. Here, we investigate the molecular and genetic mechanisms underlying the evolutionary transition from dehiscent to indehiscent fruits using these two Lepidium species as model system. Results We have sequenced the transcriptomes and small RNAs of floral buds, flowers and fruits of L. appelianum and L. campestre and analyzed differentially expressed genes (DEGs) and differently differentially expressed genes (DDEGs). DEGs are genes that show significantly different transcript levels in the same structures (buds, flowers and fruits) in different species, or in different structures in the same species. DDEGs are genes for which the change in expression level between two structures is significantly different in one species than in the other. Comparing the two species, the highest number of DEGs was found in flowers, followed by fruits and floral buds while the highest number of DDEGs was found in fruits versus flowers followed by flowers versus floral buds. Several gene ontology terms related to cell wall synthesis and degradation were overrepresented in different sets of DEGs highlighting the importance of these processes for fruit opening. Furthermore, the fruit valve identity genes FRUITFULL and YABBY3 were among the DEGs identified. Finally, the microRNA miR166 as well as the TCP transcription factors BRANCHED1 (BRC1) and TCP FAMILY TRANSCRIPTION FACTOR 4 (TCP4) were found to be DDEGs. Conclusions Our study reveals differences in gene expression between dehiscent and indehiscent fruits and uncovers miR166, BRC1 and TCP4 as candidate genes for the evolutionary transition from dehiscent to indehiscent fruits in Lepidium.

Evolution of Seed Dispersal Modes in the Orchidaceae: Has the Vanilla Mystery Been Solved?

“…Based on our phylogenetic reconstruction combined with dispersal features of fragrant Vanilla species (Figure 2), dehiscence appears to be more common and is likely to be the ancestral condition [65]. Recent evolutionary studies in other plant families suggest that indehiscent fruits evolved from dehiscent ancestors (e.g., Brassicaceae) [66][67][68]. Curiously, fruit dehiscence (and dispersal modes) appear not to be phylogenetically conserved, and both dehiscence and indehiscence may occur in different populations of a single species.…”

Differential Expression of miRNAs Involved in Response to Candidatus Liberibacter asiaticus Infection in Mexican Lime at Early and Late Stages of Huanglongbing Disease

“…Previously, the transcriptome of Paspalum notatum was used as a reference in ShortStack, obtaining a 30.3% reads alignment [45]. In addition, 24 miRNAs were detected in L. campestre small RNA data using the L. campestre genome; meanwhile, 29 miRNAs were identified in L. appelianum sRNA data using the L. appelianum transcriptome with ShortStack [46]. We detected 46 miRNAs in C. aurantifolia, corresponding to 29 known miRNAs and 17 novel miRNAs.…”

miR319-Regulated TCP3 Modulates Silique Development Associated with Seed Shattering in Brassicaceae

“…The miR319-targeted TCP genes control cell division arrest [25,27,28,[48][49][50]. In general, proteins encoded by genes expressed in the replum often negatively regulate genes expressed in the valves [1]. We found that these TCP genes were involved in development of repla because repla became wider in jaw-D mutant.…”

“…Angiosperms show various types of siliques, most of which are derived from the ovary walls and fertilized ovules. Their structures are conserved in Arabidopsis thaliana and some species of the Brassicaceae family, including cabbage, broccoli, Chinese cabbage (Brassica rapa), and rapeseed (Brassica napus) [1]. In Arabidopsis thaliana, siliques are composed of fertilized ovules and three major regions, namely the valves, repla, and valve margins.…”