Integration of the metabolome and transcriptome reveals indigo biosynthesis in Phaius flavus flowers under freezing treatment.

Background: Indigo-containing plant tissues change blue after a freezing treatment, which is accompanied by changes in indigo and its related compounds. Phaius flavus is one of the few monocot plants containing indigo. The change to blue after freezing was described to explore the biosynthesis of indigo in P. flavus. Methods: In this study, we surveyed the dynamic change of P. flavus flower metabolomics and transcriptomics. Results: The non-targeted metabolomics and targeted metabolomics results revealed a total of 98 different metabolites, the contents of indole, indican, indigo, and indirubin were significantly different after the change to blue from the freezing treatment. A transcriptome analysis screened ten different genes related to indigo upstream biosynthesis, including three anthranilate synthase genes, two phosphoribosyl-anthranilate isomerase genes, one indole-3-glycerolphosphate synthase gene, five tryptophan synthase genes. In addition, we further candidate 37 cytochrome P450 enzyme genes, one uridine diphosphate glucosyltransferase gene, and 24 ß-D-glucosidase genes were screened that may have participated in the downstream biosynthesis of indigo. This study explained the changes of indigo-related compounds at the metabolic level and gene expression level during the process of P. flavus under freezing and provided new insights for increasing the production of indigo-related compounds in P. flavus. In addition, transcriptome sequencing provides the basis for functional verification of the indigo biosynthesis key genes in P. flavus.

The genome sequence of star fruit (Averrhoa carambola).

Oxalidaceae is one of the most important plant families in horticulture, and its key commercially relevant genus, Averrhoa, has diverse growth habits and fruit types. Here, we describe the assembly of a high-quality chromosome-scale genome sequence for Averrhoa carambola (star fruit). Ks distribution analysis showed that A. carambola underwent a whole-genome triplication event, i.e., the gamma event shared by most eudicots. Comparisons between A. carambola and other angiosperms also permitted the generation of Oxalidaceae gene annotations. We identified unique gene families and analyzed gene family expansion and contraction. This analysis revealed significant changes in MADS-box gene family content, which might be related to the cauliflory of A. carambola. In addition, we identified and analyzed a total of 204 nucleotide-binding site, leucine-rich repeat receptor (NLR) genes and 58 WRKY genes in the genome, which may be related to the defense response. Our results provide insights into the origin, evolution and diversification of star fruit.

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

Floral color polymorphism can provide great insight into species evolution from a genetic and ecological standpoint. Color variations between species are often mediated by pollinators and are fixed characteristics, indicating their relevance to adaptive evolution, especially between plants within a single population or between similar species. The orchid genus Pleione has a wide variety of flower colors, from violet, rose-purple, pink, to white, but their color formation and its evolutionary mechanism are unclear. Here, we selected the P. limprichtii population in Huanglong, Sichuan Province, China, which displayed three color variations: Rose-purple, pink, and white, providing ideal material for exploring color variations with regard to species evolution. We investigated the distribution pattern of the different color morphs. The ratio of rose-purple:pink:white-flowered individuals was close to 6:3:1. We inferred that the distribution pattern may serve as a reproductive strategy to maintain the population size. Metabolome analysis was used to reveal that cyanindin derivatives and delphidin are the main color pigments involved. RNA sequencing was used to characterize anthocyanin biosynthetic pathway-related genes and reveal different color formation pathways and transcription factors in order to identify differentially-expressed genes and explore their relationship with color formation. In addition, qRT-PCR was used to validate the expression patterns of some of the genes. The results show that PlFLS serves as a crucial gene that contributes to white color formation and that PlANS and PlUFGT are related to the accumulation of anthocyanin which is responsible for color intensity, especially in pigmented flowers. Phylogenetic and co-expression analyses also identified a R2R3-MYB gene PlMYB10, which is predicted to combine with PlbHLH20 or PlbHLH26 along with PlWD40-1 to form an MBW protein complex (MYB, bHLH, and WDR) that regulates PlFLS expression and may serve as a repressor of anthocyanin accumulation-controlled color variations. Our results not only explain the molecular mechanism of color variation in P. limprichtii, but also contribute to the exploration of a flower color evolutionary model in Pleione, as well as other flowering plants.

The complete chloroplast genome of Pleione pleionoides (Orchidaceae).

Pleione pleionoides is a vulnerable orchid with significant ornamental values. Here, we report the first complete chloroplast genome of P. pleionoides. The circular genome was 159,468 bp in length and consisted of a pair of inverted repeats (IR 26,651 bp), which were separated by a large single copy region (LSC 87,461 bp) and a small single copy region (SSC 18,705 bp). It contained 115 unique genes, including 87 protein-coding genes, 38 tRNAs, and 8 rRNAs. The maximum likelihood phylogenetic analysis indicated that P. pleionoides and P. bulbocodioides cluster together and closely related to P. formosana.

Next-generation sequencing yields the complete chloroplast genome of Pleione chunii, a vulnerable orchid in China.

Pleione chunii is a vulnerable epiphytic orchid with significant ornamental value. Here, we report the first complete chloroplast genome of P. chunii. The circular genome was 158,880 bp in length and consisted of a pair of inverted repeats (IR 26,465 bp), which were separated by a large single copy region (LSC 87,259 bp) and a small single copy region (SSC 18,691 bp). It contained 115 unique genes, including 87 protein-coding genes, 38 tRNAs, and eight rRNAs. The maximum-likelihood phylogenetic analysis indicated that P. chunii was sister to P. bulbocodioides and P. formosana.