A Full-Length Reference Floral Transcriptome ofBoehmeria tricuspisProvides Insights into Apomeiosis and Polyploidy

Abstract

Boehmeria tricuspis (Hance) Makino constitutes a hardy herbaceous or shrubby perennial native to East Asia that includes different ploidy levels and reproductive modes (diplosporous to sexual). Although several apomeiosis-associated genes have been described, the genetic control and molecular mechanisms underlying apomeiosis remain poorly understood. Moreover, the basis of the correlation between polyploidy and apomixis has not yet been clarified. We utilized long-read sequencing to produce a full-length reference floral transcriptome of B. tricuspis. Based on the generated database, gene expression of the female flowers of different ploidy levels and reproductive mode cytotypes was compared. Overall, 1,387 genes related to apomeiosis, 217 genes related to ploidy, and 9 genes associated with both apomixis and ploidy were identified. Gene Ontology analyses of this set of transcripts indicated reproductive genes, especially those related to “cell differentiation” and “cell cycle process,” as significant factors regulating apomeiosis. Furthermore, our results suggested that different expressions of stress response genes might be important in the preparation for apomeiosis transition. In addition, our observations indicated that the expression of apomeiosis may not depend on polyploidy but rather on deregulation of the sexual pathway in B. tricuspis.

Endosperm variability: from endoreduplication within a seed to higher ploidy across species, and its competence

“…Inheritance of aposporous apomixis has been studied in Pennisetum , Panicum and Brachiaria and reported to be determined by a single dominant locus (Sherwood et al, 1994; Valle et al, 1994; Savidan, 2000). Genes (protein coding and lncRNA) and epigenetic mechanisms regulating apomixis are well documented (Guerin et al, 2000; Albertini et al, 2005; Laspina et al, 2008; Garcia-Aguilar et al, 2010; Polegri et al, 2010; Ortiz et al, 2013; Hand and Koltunow, 2014; Podio et al, 2014a,b; Felitti et al, 2015; Ortiz et al, 2017; Selva et al, 2017; Tang et al, 2017; Bocchini et al, 2018; Ochogavía et al, 2018; Tang et al, 2019; de Oliveira et al, 2020). However, complete molecular regulatory mechanisms are yet to be revealed and would help fertilize agricultural crops innovatively through fixing the hybrid heterotic vigour in order to propagate indefinitely with enhanced productivity (Dujardin and Hanna, 1983; Khush, 1994; Ramulu et al, 1999; Spillane et al, 2001, 2004; Ortiz et al, 2013; Brukhin, 2017).…”

“…Comparison between nearest taxa variables for apomictic behaviour helped identify a set of genes including AGO9 (Olmedo-Monfil et al, 2010), CASEIN KINASE (Depetris et al, 2018), LORELEI (Felitti et al, 2011), a MAP3K coding gene QUI-GON-JINN (Mancini et al, 2018), THAUMATIN-LIKE , COPIA , CCD , LEISHMANOLYSIN - LIKE PEPTIDASE and FAR1-RELATED (Ortiz et al, 2017), ORC3 (Siena et al, 2016), DORN1 and eATP pathway (Choi et al, 2014; Felitti et al, 2015), AMP SYNTHASE , EF-1α , COP9 SIGNALOSOME and ACETOLACTATE SYNTHASE (Cervigni et al, 2008), long non-coding RNAs like N13 (Ochogavía et al, 2018) and QGJ (Mancini et al, 2018), and small RNAs like ATHILA , LINE and ATLANTYS (Olmedo-Monfil et al, 2010), involved in the regulatory processes for apomictic expression. In addition, some recent reports have identified apomixis-related genes in Paspalum (de Oliveira et al, 2020) and Boehmeria (Tang et al, 2019), which provide insight in genetic control of apomeiosis and polyploidy events leading to apomixis behaviour (Savidan, 2000; Hand and Koltunow, 2014). Also, regulatory mechanisms modulated at the transcriptional, translational and post-translational levels dissecting the apomictic trait, including epigenetic regulation, signal transduction and evolutionary aspects have been covered in detail (Ortiz et al, 2013; Brukhin, 2017; Schmidt, 2020).…”

Differential Proteomic Analysis to Identify Proteins Associated with Apomeiosis in Boehmeria tricuspis (Hance) Makino Using an iTRAQ-Based Strategy

“…Four cytotypes of B. tricuspis (JG1, JG2, ZJJ, and HD) were used, whose reproductive modes and ploidy levels were reported previously. 12 Briefly, diploid JG1 was sexual, whereas JG2 was at the same ploidy level, and tetraploid HD was facultative apomictic. Triploid ZJJ was an obligate apomictic.…”

“…The database was set up from the full-length reference floral transcriptome. 12 Only the proteins with unique peptides ≥1 and a Score Sequest HT >0 were considered reliable proteins for further analysis. After removing the invalid values and the antilibrary data, the differential abundance proteins (DAPs) were identified according to the fold change ≥1.5 or ≤0.67 and at an unadjusted significance level p < 0.05.…”

“…10 Particularly, our prior study has confirmed that Boehmeria tricuspis (Hance) Makino, a native species of China, is an agamic complex that includes different reproductive patterns (i.e., facultative and obligate apomictic and sexual) and ploidy levels (2×, 3×, and 4×). 11,12 In diplosporous apomixis, the embryo develops from an unreduced megaspore mother cell only through mitotic divisions in a process termed apomeiosis. Thus, apomeiosis is the first stage following parthenogenesis and the formation of a viable endosperm and is an essential prerequisite of apomictic development.…”