A high-quality Bougainvillea genome provides new insights into evolutionary history and pigment biosynthetic pathways in the Caryophyllales

Abstract

Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the world. However, the absence of genome data limits our understanding of the pathways involved in bract colouration and breeding. Here, we report a chromosome-level assembly of the giga-genome of Bougainvillea × buttiana ‘Mrs. Butt’, a cultivar thought to be the origin of many other Bougainvillea cultivars. The assembled genome is ~5 Gb with a scaffold N50 of 151,756,278 bp and contains 86,572 genes which undergone a recent WGD. We confirmed that multiple rounds of whole genome multiplication have occurred in the evolutionary history of the Caryophyllales, reconstructed the relationship in the Caryophyllales at whole genome level, and found discordance between species and gene trees as the result of complex introgression events. We investigated betalain and anthocyanin biosynthetic pathways and found instances of independent evolutionary innovations in the nine different Caryophyllales species. To explore the potential formation mechanism of diverse bract colours in Bougainvillea, we analyzed the genes involved in betalains and anthocyanins biosynthesis and found extremely low expression of ANS and DFR genes in all cultivars, which may limit anthocyanin biosynthesis. Our findings indicate that the expression pattern of the betalain biosynthetic pathway did not directly correlate with the bract colour, and the higher expression level in the betalain biosynthetic pathway is required for the coloured bract. The improved understanding of the correlation between gene expression and bract colour allows plant breeding outcomes to be predicted with greater certainty.

Transcriptome Profiling and Gene Network Analysis Revealed Regulatory Mechanisms of Bract Development in Bougainvillea glabra

“…Ornamental plant bracts are currently more studied mainly in pigments, For example, Bougainvillea is a woody plant of the Nyctaginaceae [12] , rich in colour, such as chalcone--avonone isomerase 1(CHI1), 4,5-DOPA dioxygenase extradiol (DOD) and avanone 3-hydroxylase(F3H), have all been shown to be involved in bract colour change [13,14] . But there is very little research on how bracts develop.…”

The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history

“…With the continuous update and development of sequencing technology, T2T genomes of many species have also been published, which will promote the continuous in-depth research of genomes ( Lan et al., 2023 , 2024 ). Plastome data is regularly used in phylogenomic and population genomic studies now due to the reliability of assembling these genomes and the large comparative databases for analyses ( Wang et al., 2023 ).…”