How to build a fruit: Transcriptomics of a novel fruit type in the Brassiceae

Abstract

Comparative gene expression studies are invaluable for predicting how existing genetic pathways may be modified or redeployed to produce novel and variable phenotypes. Fruits are ecologically important organs because of their impact on plant fitness and seed dispersal, modifications in which results in morphological variation across species. A novel fruit type in the Brassicaceae known as heteroarthrocarpy enables distinct dispersal methods in a single fruit through segmentation via a lateral joint and variable dehiscence at maturity. Given the close relationship to Arabidopsis, species that exhibit heteroarthrocarpy are powerful models to elucidate how differences in gene expression of a fruit patterning pathway may result in novel fruit types. Transcriptomes of distal, joint, and proximal regions from Erucaria erucarioides and Cakile lanceolata were analyzed to elucidate within fruit and between species differences in whole transcriptome, gene ontology, and fruit patterning expression profiles. Whole transcriptome expression profiles vary between fruit regions in patterns that are consistent with fruit anatomy. These transcriptomic variances do not correlate with changes in gene ontology, as they remain generally stable within and between both species. Upstream regulators in the fruit patterning pathway, FILAMENTOUS FLOWER and YABBY3 , are expressed in the distal and proximal regions of E . erucarioides , but not in the joint, implicating alterations in the pathway in heteroarthrocarpic fruits. Downstream gene, INDEHISCENT , is significantly upregulated in the abscissing joint region of C . lanceolata , which suggests repurposing of valve margin genes for novel joint disarticulation in an otherwise indehiscent fruit. In summary, these data are consistent with modifications in fruit patterning genes producing heteroarthrocarpic fruits through different components of the pathway relative to other indehiscent, non-heteroarthrocarpic, species within the family. Our understanding of fruit development in Arabidopsis is now extended to atypical siliques within the Brassicaceae, facilitating future studies on seed shattering in important Brassicaceous crops and pernicious weeds.

Zahora, a new monotypic genus from tribe Brassiceae (Brassicaceae) endemic to the Moroccan Sahara

“…Therefore, Zahora might be an interesting study object to investigate the evolution of dehiscent and indehiscent fruit types in Brassicacae. There is some important progress to unravel the molecular mechanisms of this important trait in Brassicaceae (Carey et al 2019), and its ecological and evolutionary relevance has been documented recently for crucifer genera Lepidium L. (Sperber et al 2017) and Aethionema W.T. Aiton (Lenser et al 2016, Mérai et al 2019).…”

Nectary development in Cleome violacea

“…Nectary tissue was excised, flash frozen in liquid nitrogen, and stored at -80°C. Following: Carey et al, (2019) , RNA was extracted from manually-ground frozen tissue using a Qiagen RNeasy micro kit (Hilden, Germany) and cDNA was generated using the Illumina TruSeq stranded mRNA LT sample prep kit RS-122-2101 (California, U.S.). In this case, mRNA for each sample was isolated using nucleomag beads (Macherey-Nagel, Düren, Germany).…”

“…Raw reads were downloaded from the TCAG webserver and processed as in ( Carey et al., 2019 ) using updated software ( Table S1 ). The raw reads are available at the Sequence Read Archive (SRA) database (BioProject: PRJNA912718).…”

Identification of Candidate Chromosome Region Related to Melon (Cucumis melo L.) Fruit Surface Groove Trait Through Biparental Genetic Mapping and Genome-Wide Association Study

“…The roles vary widely among family members. A comparative analysis of Brassica plants shows that changes in the expression of the MADS-box transcription factor can control the change from cracking to noncracking in fruits of related species ( Muhlhausen et al, 2013 ; Carey et al, 2019 ). This may also be the reason why melons with the characteristics of fruit surface grooves do not easily crack, but the specific regulatory mechanism needs further research.…”