Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation

Abstract

Many species from across the vascular plant tree‐of‐life have modified standard plant tissues into tubers, bulbs, corms, and other underground storage organs (USOs), unique innovations which allow these plants to retreat underground. Our ability to understand the developmental and evolutionary forces that shape these morphologies is limited by a lack of studies on certain USOs and plant clades. We take a comparative transcriptomics approach to characterizing the molecular mechanisms of tuberous root formation in Bomarea multiflora (Alstroemeriaceae) and compare these mechanisms to those identified in other USOs across diverse plant lineages; B. multiflora fills a key gap in our understanding of USO molecular development as the first monocot with tuberous roots to be the focus of this kind of research. We sequenced transcriptomes from the growing tip of four tissue types (aerial shoot, rhizome, fibrous root, and root tuber) of three individuals of B. multiflora. We identified differentially expressed isoforms between tuberous and non‐tuberous roots and tested the expression of a priori candidate genes implicated in underground storage in other taxa. We identify 271 genes that are differentially expressed in root tubers versus non‐tuberous roots, including genes implicated in cell wall modification, defense response, and starch biosynthesis. We also identify a phosphatidylethanolamine‐binding protein, which has been implicated in tuberization signalling in other taxa and, through gene‐tree analysis, place this copy in a phylogenetic context. These findings suggest that some similar molecular processes underlie the formation of USOs across flowering plants despite the long evolutionary distances among taxa and non‐homologous morphologies (e.g., bulbs vs. tubers). (Plant development, tuberous roots, comparative transcriptomics, geophytes).

Transcriptional dynamics in source‐sink tissues identifies molecular factors regulating the corm development process in saffron (Crocus sativus L.)

“…This HD3A/FT gene was only expressed in leaf tissues. The identification of FT homologs in this study supports the previous findings that suggest similar/shared molecular regulators involved in USO formation (Tribble et al 2021). Similarly, APETALA1‐like genes were up‐regulated during corm development in leaves, which are known to be involved in controlling photoperiod‐dependent control of plant growth (Azeez et al 2014).…”

“…Transcriptional regulation of corm development is not well studied. There exist a few studies in other geophytic plants concerning USO formation and many of them suggest that USO formation shares a common molecular mechanism for their formation (Tribble et al 2021). Although the formation of USOs can be driven by homologous molecular factors, the involvement of unique molecular factors cannot be neglected as many of the USOs have differences at the morphological and anatomical level.…”

Transcriptomic Effects of Acute Ultraviolet Radiation Exposure on Two Syntrichia Mosses

“…Sets of significantly increased or decreased transcripts at each time point in each species were compared and checked for overlap. Additionally, to test if distributions of Gene Ontology (GO; Gene Ontology Consortium, 2004) functional annotations were different for each set of significantly abundant transcripts from the overall pool of GO terms in the transcriptome, Fisher's exact tests were performed in R for each of the GO categories (Biological Processes, Molecular Functions, and Cellular Components) using a modified version of the protocol described by Tribble et al (2021). Additionally, individual GO terms that were enriched in each significantly differentially abundant transcript set relative to the whole transcriptome were detected using a maximum likelihood framework based on a binomial distribution as in Tribble et al (2021).…”

“…Furthermore, ELIPs function in photoprotection and in some plants the accumulation of ELIP transcripts is mediated by UVR8, the specialized UV-B receptor 8 (Hutin et al, 2003). Additionally, ELIPs, LEAs, and other genes with specific GO terms including: photosynthesis, response to light stimulus, response to stress, and photomorphogenesis were tested for differential transcript abundance as a group, relative to the distribution of differential abundance of all transcripts, following a modified version of the procedure described in Tribble et al (2021). In brief, for each group of n genes (e.g., ELIPs), n transcripts were randomly sampled 10,000 from the pool of all assayed transcripts.…”

Balancing read length and sequencing depth: Optimizing Nanopore long‐read sequencing for monocots with an emphasis on the Liliales

“…(Hernández et al, 2022 ), transcriptomes from eight taxa included in the One Thousand Plant Transcriptomes Project (1KP; Leebens‐Mack et al, 2019 ), and transcriptomes associated with tuber formation in Bomarea Mirb. (Tribble et al, 2021 ). Using long‐read sequencing technology to sequence the more repeat‐rich genomes of the Liliales and other taxa with giant genomes will help provide the necessary data to better investigate the tempo and mode of genome size evolution.…”