Organ-specific transcriptome profiling of metabolic and pigment biosynthesis pathways in the floral ornamental progenitor species Anthurium amnicola Dressler

Abstract

Anthurium amnicola Dressler possesses a number of desirable and novel ornamental traits such as a purple-colored upright spathe, profuse flowering, and floral scent, some of which have been introgressed into modern Anthurium cultivars. As a first step in identifying genes associated with these traits, the transcriptome from root, leaf, spathe, and spadix from an accession of A. amnicola was assembled, resulting in 28,019 putative transcripts representing 19,458 unigenes. Genes involved in pigmentation, including those for the metabolism of chlorophyll and the biosynthesis of carotenoids, phenylpropanoids, and flavonoids were identified. The expression levels of one MYB transcription factor was highly correlated with naringenin 3-dioxygenase (F3H) and dihydroflavonol-4-reductase (DFR) in leaves, whereas a bHLH transcription factor was highly correlated with flavonoid 3′-monooxygenase (F3′H) and a DFR in spathes, suggesting that these two transcription factors might regulate flavonoid and anthocyanin synthesis in A. amnicola. Gene sequence and expression data from four major organs of A. amnicola provide novel basal information for understanding the genetic bases of ornamental traits and the determinants and evolution of form and function in the Araceae.Anthurium is a major cut flower and potted plant with a long and important history of breeding, selection, and cultivation in Hawaii. Today, the largest production comes from the Netherlands, with significant production and research in Hawaii and other tropical and subtropical areas. A popular attraction is its colorful spathe, a modified leaf that is associated with the spadix, an organ often also found in varied colors housing numerous bisexual, protogynous flowers. The major spathe color classes red, pink, orange, coral, and purple are from variations in anthocyanin type and levels and white coloration represents loss of pigment. Further, green coloration is thought to occur from variations in chlorophyll production, while brown coloration is likely derived from variations in anthocyanin and chlorophyll content [1][2][3][4][5] .The genus Anthurium consists of as many as 1,500 species found between Southern Mexico and Northern Argentina and is the largest genus in the Araceae family 6 . A limited sampling revealed that Anthurium species possess medium-sized genomes ranging from between 2 to 10 Gbp per haploid genome 7 . A majority of the modern Anthurium cultivars in the market today descend from historical or recent hybrids between species 8 particularly with A. andraeanum, which is characterized by the commercially popular heart-shaped spathe. Spathe and

Decoding the gene coexpression network underlying the ability of Gevuina avellana to live in diverse light conditions

“…In general, transcriptomic responses and gene coexpression networks have the capacity to greatly enhance ecological investigations of species distribution and community structure (Proost & Mutwill, ; Swenson et al ., ). Moreover, the use of gene coexpression networks has provided consistent relationships between transcriptional profiles and phenotypic traits (Suzuki et al ., ; Zinkgraf et al ., ). Our findings revealed a dynamic molecular regulation of the photosynthetic machinery and carbon assimilation pathways as well as of the photoprotective and antioxidant system, which is tightly coordinated with the prevailing light environment in which G. avellana grows.…”

Decoding the gene co-expression network underlying the ability of Gevuina avellana Mol. to live in diverse light conditions

“…The combination of WGCNA and the IGRAPH packages for network construction using this subset of genes produced a robust community structure whose properties and memberships were effective in identifying co-expression patterns with an appropriate biological relevance for the photochemical responses of G. avellana . In general, the use of gene co-expression networks has provided consistent relationships between transcriptional profiles and phenotypic traits (Zinkgraf et al, 2017; Suzuki et al, 2017). Our results revealed a dynamic molecular regulation of the photosynthetic machinery and carbon assimilation pathways as well as of the photoprotective and antioxidant system which is tightly coordinated with the prevailing light environment where this tree grows.…”

Peer Review #1 of "Co-expression clustering across flower development identifies modules for diverse floral forms in Achimenes (Gesneriaceae) (v0.1)"

“…However, this approach may greatly over-simplify the nature of transcriptional regulation in these species. Organ-and structure-specific expression studies may have greater power to detect floral formspecific differences, both in terms of the number of differentially expressed genes, and coexpression network structure (Hollender et al 2014;Suzuki et al 2017;Shahan et al 2018). As a result, our data likely represents an underestimate of the true number of modules.…”