Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts

Abstract

BackgroundPoinsettia is a popular and important ornamental crop, mostly during the Christmas season. Its bract coloration ranges from pink/red to creamy/white shades. Despite its ornamental value, there is a lack of knowledge about the genetics and molecular biology of poinsettia, especially on the mechanisms of color formation. We performed an RNA-Seq analysis in order to shed light on the transcriptome of poinsettia bracts. Moreover, we analyzed the transcriptome differences of red- and white-bracted poinsettia varieties during bract development and coloration. For the assembly of a bract transcriptome, two paired-end cDNA libraries from a red and white poinsettia pair were sequenced with the Illumina technology, and one library from a red-bracted variety was used for PacBio sequencing. Both short and long reads were assembled using a hybrid de novo strategy. Samples of red- and white-bracted poinsettias were sequenced and comparatively analyzed in three color developmental stages in order to understand the mechanisms of color formation and accumulation in the species.ResultsThe final transcriptome contains 288,524 contigs, with 33% showing confident protein annotation against the TAIR10 database. The BUSCO pipeline, which is based on near-universal orthologous gene groups, was applied to assess the transcriptome completeness. From a total of 1440 BUSCO groups searched, 77% were categorized as complete (41% as single-copy and 36% as duplicated), 10% as fragmented and 13% as missing BUSCOs. The gene expression comparison between red and white varieties of poinsettia showed a differential regulation of the flavonoid biosynthesis pathway only at particular stages of bract development. An initial impairment of the flavonoid pathway early in the color accumulation process for the white poinsettia variety was observed, but these differences were no longer present in the subsequent stages of bract development. Nonetheless, GSTF11 and UGT79B10 showed a lower expression in the last stage of bract development for the white variety and, therefore, are potential candidates for further studies on poinsettia coloration.ConclusionsIn summary, this transcriptome analysis provides a valuable foundation for further studies on poinsettia, such as plant breeding and genetics, and highlights crucial information on the molecular mechanism of color formation.

A Highly Mutable GST is Essential for Bract Colouration in Euphorbia Pulcherrima Willd. Ex Klotsch

“…In a previous study (Vilperte et al, 2019), we observed higher expression of an anthocyanin-related GSTlike gene in the red poinsettia variety 'Christmas Feelings' than in its white counterpart 'Christmas Feelings Pearl'. To investigate whether a similar phenomenon is observed in other red and white poinsettia pairs, we performed RT-qPCRs for six pairs of red-bracted poinsettia varieties and their independently generated white mutants.…”

“…As GST genes occur in large gene families, we wanted to analyse whether the poinsettia GST gene was related to other GST genes involved in anthocyanin transport to the vacuole. Therefore, we computed a phylogenetic tree from the deducted amino acid sequences of 95 GST family members from our previously assembled poinsettia transcriptome (Vilperte et al, 2019), as well as the Bract1 and anthocyanin-related GSTs from other species (CkmGST3, LcGST4, VvGST4, PhAN9, PpRiant1, PpRiant2, AtGSTF11 and AtTT19). Nine GST classes were identi ed among the poinsettia GSTs: Tau, Theta, Lambda, Zeta, Phi, tetrachlorohydroquinone dehalogenase (TCHQD), glutathionyl hydroquinone reductase (GHR), dehydroascorbate reductase (DHAR) and eukaryotic translation elongation factor 1B-γ (Ef1Bγ).…”

“…Anthocyanin-related GSTs play major roles in anthocyanin transport, since loss of function of these proteins leads to phenotypes with a lack of pigmentation, such as bz2 (Bronze-2) in maize, an9 (Anthocyanin 9) in petunia, tt19 (Transparent Testa 19) in Arabidopsis, 3 (Flavonoid3) in carnation, riant (regulator involved in anthocyanin transport) in peach, and rap (reduced anthocyanin in petioles) in strawberry (Alfenito et al;Marrs et al, 1995;Larsen et al, 2003;Kitamura et al, 2004;Cheng et al, 2015;Luo et al, 2018). In our previous study, an anthocyanin-related GST-like gene showed higher expression in a red poinsettia variety than in the white counterpart, thus making it a promising candidate responsible for the so-called 'white paradox' (Vilperte et al, 2019).…”

“…Therefore, green leaves and red bracts occur concomitantly and accumulate different groups of pigments, i.e., chlorophylls and anthocyanins (Pomar and Ros Barceló, 2007;Moustaka et al, 2018). Several anthocyanin types have been identi ed in poinsettia bracts and are responsible for its colouration range (Asen, 1958;Slatnar et al, 2013;Nitarska et al, 2018); however, molecular information is still limited for the species (Gu et al, 2018;Vilperte et al, 2019). Nonetheless, genes responsible for the biosynthesis of the anthocyanin pathway have been intensively characterized in a range of species, with its regulation being highly dependent on R2R3-MYB regulatory genes and MYB-bHLH-WD40 (MBW) regulatory complexes (Dubos et al, 2010;Petroni and Tonelli, 2011;Zhao and Tao, 2015).…”

A highly mutable GST is essential for bract colouration in Euphorbia pulcherrima Willd. Ex Klotsch

“…Therefore, green leaves and red bracts occur concomitantly and accumulate different groups of pigments, i.e., chlorophylls and anthocyanins [ 53 , 61 ]. Several anthocyanin types have been identified in poinsettia bracts and are responsible for its colouration range [ 3 , 55 , 66 ]; however, molecular information is still limited for the species [ 28 , 72 ]. Nonetheless, genes responsible for the biosynthesis of the anthocyanin pathway have been intensively characterized in a range of species, with its regulation being highly dependent on R2R3-MYB regulatory genes and MYB-bHLH-WD40 (MBW) regulatory complexes [ 16 , 58 , 76 ].…”