A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesis

Abstract

Pitaya (Hylocereus) is the most economically important fleshy-fruited tree of the Cactaceae family that is grown worldwide, and it has attracted significant attention because of its betalain-abundant fruits. Nonetheless, the lack of a pitaya reference genome significantly hinders studies focused on its evolution, as well as the potential for genetic improvement of this crop. Herein, we employed various sequencing approaches, namely, PacBio-SMRT, Illumina HiSeq paired-end, 10× Genomics, and Hi-C (high-throughput chromosome conformation capture) to provide a chromosome-level genomic assembly of 'GHB' pitaya (H. undatus, 2n = 2x = 22 chromosomes). The size of the assembled pitaya genome was 1.41 Gb, with a scaffold N50 of ~127.15 Mb. In total, 27,753 protein-coding genes and 896.31 Mb of repetitive sequences in the H. undatus genome were annotated. Pitaya has undergone a WGT (whole-genome triplication), and a recent WGD (whole-genome duplication) occurred after the gamma event, which is common to the other species in Cactaceae. A total of 29,328 intact LTR-RTs (~696.45 Mb) were obtained in H. undatus, of which two significantly expanded lineages, Ty1/copia and Ty3/gypsy, were the main drivers of the expanded genome. A high-density genetic map of F1 hybrid populations of 'GHB' × 'Dahong' pitayas (H. monacanthus) and their parents were constructed, and a total of 20,872 bin markers were identified (56,380 SNPs) for 11 linkage groups. More importantly, through transcriptomic and WGCNA (weighted gene coexpression network analysis), a global view of the gene regulatory network, including structural genes and the transcription factors involved in pitaya fruit betalain biosynthesis, was presented. Our data present a valuable resource for facilitating molecular breeding programs of pitaya and shed novel light on its genomic evolution, as well as the modulation of betalain biosynthesis in edible fruits.

Fig. 1. Landscape of H. undatus genome.

Track a, the eleven chromosomes (in Mb scale). The density of genes (Track b) and TEs (Track c) across chromosomes. Track d, the GC contents. Colored lines in the center represent syntenic links between the chromosomes

Fig. 2. Species trees and LTR insertion times of H. undatus.

A Species tree and divergence times of H. undatus and the other species. B Species tree and expansion-contraction in gene families. The green and red numbers present expanded and contracted gene families, respectively. MRCA stands for the most recent common ancestor. C Distribution of insertion times for LTR-RTs

Fig. 3. Genes involved in the betalain biosynthesis cascade.

A The development of ‘Guanhuabai’ (GHB) and ‘Guanhuahong’ (GHH) pitaya pulp. B The betacyanin and betaxanthin contents of ‘GHB’ and ‘GHH’ pitaya pulp. C The expression profiles of genes related to betalain biosynthesis according to the RNA-Seq datasets of ‘GHB’ and ‘GHH’ pitaya pulp. The gene IDs are in brackets. Spon, spontaneous. Bar = 2 cm

Fig. 4. Transcriptional regulation of betalain biosynthetic genes.

A WGCNA dendrogram indicating the expression of 23 different gene modules in all 8 pitaya samples. B Trait and module association analyses. Different colors designate the 23 different modules. C Heatmap of three highly correlated modules, including light cyan (145 genes), grey60 (112 genes), and blue (825 genes) modules

Fig. 5. Transcriptional modulation of betalain biosynthetic genes.

A The coexpression network connecting the structural genes in betalain biosynthesis with the transcription factors representing the modulation of betalain biosynthetic genes. Expression associations between TFs and catechin-associated genes (colored solid hexagons) are indicated with colored lines according to weight. B Heatmap of MYBs, bHLHs, AP2-EREBPs, and HBs, which had the maximum number in the coexpression network. Orange circles indicate candidate TFs highly expressed at 25 d and/or 32 d in ‘GHH’ pitaya