Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids

Abstract

Transcriptomic and genomic resources are a valuable tool for studying development within an evolutionary context, as they enable the search for candidate loci and their regulatory regions, contributing to the upgrading of study systems into model lineages. Thalictrum L. is an emerging model lineage within the Ranunculales (Damerval and Becker, 2017), the sister group to all other eudicots (Lane et al., 2018). The genus is therefore an extant representative of a privileged phylogenetic node, before a major evolutionary radiation within the flowering plants (Zeng et al., 2017). Thalictrum is a temperate genus of approximately 200 species with floral diversity that encompasses unisexual and windpollinated flowers, in association with polyploidy (Soza et al., 2012, 2013). Certain species, mainly T. thalictroides (L.) A. J. Eames & B. Boivin, are amenable to virus-induced gene silencing (Di Stilio et al., 2010), which has enabled functional studies of ABC model floral MADS-box genes (

Lineage‐Specific CYP80 Expansion and Benzylisoquinoline Alkaloid Diversity in Early‐Diverging Eudicots

“…Although the biosynthesis and evolution of well‐known BIA compounds, such as noscapine, morphine, and berberine, have been elucidated, how BIA diversity developed remains unclear. The genomic sequencing of various Ranunculales species, including Papaver , [ 23 ] Macleaya , [ 27 ] and Corydalis [ 31 ] from Papaveraceae; Coptis , [ 25 ] Thalictrum , [ 32 ] and Aquilegia [ 33 ] from Ranunculaceae; Epimedium [ 34 ] from Berberidaceae; Kingdonia [ 35 ] from Circaeasteraceae; and Akebia [ 36 ] from Lardizabalaceae, provides a critical foundation for comparative genomic studies aimed at understanding the biosynthesis and evolution of BIA diversity across different families. In this study, the high‐quality genome of Menispermum has helped fill a significant gap in the genomic information available for Menispermaceae, and thus presents a unique opportunity for exploring the molecular mechanisms underlying BIA diversity, particularly the specific evolution of bisBIAs and sinomenines in Menispermaceae.…”

California poppy (Eschscholzia californica), the Papaveraceae golden girl model organism for evodevo and specialized metabolism

“…Additionally to California poppy genome and transcriptome datasets being generated, these datasets are becoming available also for other Ranunculales, allowing comparative analyses. Several Ranunculales genomes have been published recently, some even at chromosome-level, including M. cordata (Liu et al, 2017), Coptis chinensis (Liu et al, 2021), P. somniferum (Guo et al, 2018), Papaver rhoeas, Papaver setigerum (Yang et al, 2021), and A. coerulea (Filiault et al, 2018), Aquilegia oxysepala (Xie et al, 2020), Thalictrum thalictroides (Arias et al, 2021), Kingdonia uniflora (Sun et al, 2020), Akebia trifoliata (Huang et al, 2021), and Corydalis tomentella (Xu et al, 2022).…”

“…While genome sequencing requires the extraction of a single sample of high molecular weight DNA, transcriptome analysis requires the collection of several biological replicates for many tissues, stages, and/or treatments, rendering this method more time consuming and laborious. While for Nigella damascena, A. coerulea, and T. thalictroides more extensive transcriptomes datasets have already been published facilitating gene identification in Ranunculales and gene expression analysis to a limited extent (Meaders et al, 2020;Zhang et al, 2020;Arias et al, 2021). However, the datasets often comprise only few tissues and an insufficient number of replicates to allow for digital gene expression analysis.…”

A cornucopia of diversity—Ranunculales as a model lineage

“…Table 1 shows that only two Ranunculales genomes match this criterion, these are P. somniferum (opium poppy) and Corydalis tomentella ( Guo et al , 2018 ; Xu et al , 2022 ). Genomes with lower BUSCO values are available for Thalictrum thalictroides , Coptis chinensis , Aquilegia coerulea , and Aquilegia oxysepala ( Ranunculaceae ), Kingdonia uniflora ( Circeasteraceae ), Akebia trifoliata ( Lardizabalaceae ), Epimedium pubescens ( Berberidaceae ), Eschscholzia californica , Corydalis tomentella , Papaver somniferum , Papaver rhoeas , Papaver setigerum , and Macleaya chordata ( Papaveraceae ) ( Liu et al , 2017 , 2021 ; Filiault et al , 2018 ; Hori et al , 2018 ; Sun et al , 2020 ; Xie et al , 2020 ; Arias et al , 2021 ; Chen et al , 2021 ; Huang et al , 2021 ; Yang et al , 2021 ; Shen et al , 2022 ).…”