Transcriptome profiling of Desmos chinensis : revealing the molecular basis of dipartite perianth evolution in the early divergernt angiosperm family Annonaceae

Abstract

The development of a dipartite perianth (with morphologically distinct calyx and corolla) evolved independently in the Annonaceae and core eudicots, with bracteopetals and andropetals, respectively. Structural novelties seldom arise from completely new molecular origins: the convergent evolution of homoplastic structures—such as the evolution of petaloid organs—is hypothesized to share deep homology, with the adoption of similar molecular control but with variation in expression patterns. Little is known of the genetics of floral developmental in the early divergent angiosperm family Annonaceae. This research focuses on the organ-specific floral developmental genetics of Desmos chinensis (Annonaceae), which has a floral morphology typical for the family. A developmental study was performed to correlate morpho-anatomical changes of floral organs during floral development. The floral reproductive organs are initially protected by the bract and sepals, and then by petals later in bud development. Sepals reach morphological and functional maturity early in bud development, whereas petals differentiate and become functionally mature shortly before the anthesis. Conical epidermal cells do not develop in D. chinensis petals, despite being common in petals of other angiosperms. The perianth abscises before fruit development. This study enabled the identification floral development stages in D. chinensis for the downstream molecular study. Different developmental stages were sampled for each floral organ (as well as leaves) for transcriptome profiling with the application of high-throughput next generation sequencing. After comparing the results generated using different assembly pipelines, 22,112 de novo assembled transcripts were generated, contributing to c. 80% of transcriptome completeness. Most of these identified transcripts have at least one homology-based annotation and are functionally characterized. The majority of the transcripts are not specific to organs or developmental stages, although the expression levels differ among samples. Based on the digital gene expression level estimation, a large proportion of the D. chinensis transcriptome is responsible for various defense mechanisms, with some highly expressed in sepals. Transcripts related to glycolysis and secondary metabolite production are highly up-regulated in outer and inner petals. The expression data also suggests that circadian clock genes in D. chinensis might be responsible for petal maturation in response to photoperiodism. 33 homeotic MADS-box genes transcripts and isoforms were identified from the D. chinensis transcriptome. The identities of the MADS-box homologs were validated using Bayesian inference, maximum parsimony and maximum likelihood phylogenetic analyses, and with reference to the sequence similarity with other publicly available MADS-box sequences. There are more type II than type I MIKCc MADS-box genes expressed in the D. chinensis leaf and floral transcriptomes. The expression of B-class APETALA3 and E-class SEPALATA3 are spatially restricted and are not expressed in sepals, which might affect the formation of the functional transcription factor complex for petaloid organ development in the outermost perianth whorl, contributing to the development of a dipartite perianth in the Annonaceae. Molecular mechanisms that contribute to floral diversity in the family are yet to be discovered. The current organ-specific transcriptomics allow further application in

future developmental genetic studies of the Annonaceae, possibly with the integration of multi-omics approaches.