Transcriptome Analysis of a Petal Anthocyanin Polymorphism in the Arctic Mustard, Parrya nudicaulis

Abstract

Angiosperms are renown for their diversity of flower colors. Often considered adaptations to pollinators, the most common underlying pigments, anthocyanins, are also involved in plants’ stress response. Although the anthocyanin biosynthetic pathway is well characterized across many angiosperms and is composed of a few candidate genes, the consequences of blocking this pathway and producing white flowers has not been investigated at the transcriptome scale. We take a transcriptome-wide approach to compare expression differences between purple and white petal buds in the arctic mustard, Parrya nudicaulis, to determine which genes’ expression are consistently correlated with flower color. Using mRNA-Seq and de novo transcriptome assembly, we assembled an average of 722 bp per gene (49.81% coding sequence based on the A. thaliana homolog) for 12,795 genes from the petal buds of a pair of purple and white samples. Our results correlate strongly with qRT-PCR analysis of nine candidate genes in the anthocyanin biosynthetic pathway where chalcone synthase has the greatest difference in expression between color morphs (P/W = ∼7×). Among the most consistently differentially expressed genes between purple and white samples, we found 3× more genes with higher expression in white petals than in purple petals. These include four unknown genes, two drought-response genes (CDSP32, ERD5), a cold-response gene (GR-RBP2), and a pathogen defense gene (DND1). Gene ontology analysis of the top 2% of genes with greater expression in white relative to purple petals revealed enrichment in genes associated with stress responses including cold, drought and pathogen defense. Unlike the uniform downregulation of chalcone synthase that may be directly involved in the loss of petal anthocyanins, the variable expression of several genes with greater expression in white petals suggest that the physiological and ecological consequences of having white petals may be microenvironment-dependent.

Comparative Transcriptomics Provides Insight into Floral Color Polymorphism in a Pleione limprichtii Orchid Population

“…Color changes are related to flower pigment content. To date, the molecular mechanism of flower color transition has been investigated in several species, owing to the main floral pigments having been well characterized in many plants [8][9][10][11][12][13] providing sufficient information for studying floral color formation in non-model species and the opportunity to explore the relationship between phenotypic evolution and color variations.…”

Transcriptome analysis of terpene chemotypes of Melaleuca alternifolia across different tissues

“…The analysis of the whole transcriptome can reveal the set of genes associated with distinctive polymorphisms that are common in nature. For example, such analyses have helped to elucidate the genetic basis of anthocyanin polymorphism in the mustard Parrya nudicaulis (Butler, Dick, Carlson, & Whittall, ), behavioral castes in Hymenoptera (Feldmeyer, Elsner, & Foitzik, ; Ferreira et al, ; Wang et al, ), and the mutations in the cavefish morphs of Astyanax mexicanus (Hinaux et al, ).…”

Unexpected predicted length variation for the coding sequence of the sleep related gene, BHLHE41 in gorilla amidst strong purifying selection across mammals

“…To confirm that there were no homologous sequences with known 3D structures in other species or sequences with alternative gene annotations, we conducted a BLAST search using the human BHLHE41 sequence and filtered for results with known 3D structures. The best-hit had an E-value of 0.042, which is substantially above the commonly used threshold for homology (<10 −3 ; [34]), thus we conclude that no 3D structures for BHLHE41 are currently available.…”