Industrial chicory genome gives insights into the molecular timetable of anther development and male sterility

Abstract

Industrial chicory (Cichorium intybus var. sativum) is a biannual crop mostly cultivated for extraction of inulin, a fructose polymer used as a dietary fiber. F1 hybrid breeding is a promising breeding strategy in chicory but relies on stable male sterile lines to prevent self-pollination. Here, we report the assembly and annotation of a new industrial chicory reference genome. Additionally, we performed RNA-Seq on subsequent stages of flower bud development of a fertile line and two cytoplasmic male sterile (CMS) clones. Comparison of fertile and CMS flower bud transcriptomes combined with morphological microscopic analysis of anthers, provided a molecular understanding of anther development and identified key genes in a range of underlying processes, including tapetum development, sink establishment, pollen wall development and anther dehiscence. We also described the role of phytohormones in the regulation of these processes under normal fertile flower bud development. In parallel, we evaluated which processes are disturbed in CMS clones and could contribute to the male sterile phenotype. Taken together, this study provides a state-of-the-art industrial chicory reference genome, an annotated and curated candidate gene set related to anther development and male sterility as well as a detailed molecular timetable of flower bud development in fertile and CMS lines.

Identification and characterization of CYP71 subclade cytochrome P450 enzymes involved in the biosynthesis of bitterness compounds in Cichorium intybus

“…Given their reported involvement in SL biosynthesis, our C. intybus var. sativum reference genome sequence (https:// bioinformatics.psb.ugent.be/orcae/overview/Cicin) (Waegneer et al, 2023) was used for genome-wide identification of members from the TPS and CYP gene families. In total, 447 C. intybus annotated genes were manually curated, respectively 51 TPSs and 396 CYPs, of which 87 (19%) were classified as pseudogenes.…”

“…An in-house generated C. intybus var. sativum reference genome sequence ( https://bioinformatics.psb.ugent.be/orcae/overview/Cicin ) ( Waegneer et al., 2023 ) was used for genome-wide identification of gene family members of the selected TPS and CYP gene families. First, the corresponding homology groups (HOMgroups) with all known orthologs of multiple species were extracted from the PLAZA dicots 4.0 database ( https://bioinformatics.psb.ugent.be/plaza ) ( Van Bel et al., 2018 ).…”

“…Industrial chicory and witloof reads were mapped on the CDS of an assembled and annotated reference genome of C. intybus var. sativum ( Waegneer et al., 2023 ), while lettuce reads were mapped on the CDS of the annotated reference genome of L. sativa ( Reyes-Chin-Wo et al., 2017 ), using BWA-MEM ( Li and Durbin, 2009 ) with default settings. Mapped reads were sorted using SAMtools ( Li et al., 2009 ) and reads with a mapping quality below 20 were discarded.…”

“…We used an annotated reference genome of C. intybus var. sativum ( Waegneer et al., 2023 ) to mine for all the corresponding genes of the two most important SL biosynthesis gene families, namely TPS s and CYP s. Using protein alignment and phylogenetic analysis, gene clades were delineated and clades were identified containing known members ( GAS , GAO , COS , KLS ) with a previously demonstrated biochemical activity in C. intybus or closely related plant species. Further, we performed a comprehensive transcriptome analysis of methyl jasmonate (MeJA)-treated samples of three species, C. intybus var.…”