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.
Highlights
Pitaya or pitahaya (Hylocereus), referred to as dragon fruit, is one of the most important and widely spread fruit crops in tropical and subtropical countries
Two distinct peaks of 0.3 and 0.7 appeared in the distribution of the 4dTv (4-fold transversion substitution rate) values between the H. undatus gene pairs (Supplementary Fig. 5B), indicating that the common ancestor of H. undatus, S. oleracea, and B. vulgaris had a WGT event and that a recent WGD event occurred in pitaya (Supplementary Figs. 5–6)
ADH1, CYP76AD1-1, and DODA1 were highly expressed in the red pulp, resulting in more betalains being produced in red pulp than in white pulp (Supplementary Fig. 17B). These findings suggested that the clustering of ADH1, CYP76AD1-1, and DODA1 located on chromosome 3 is likely responsible for the genetic stability of betalain heredity, and their differential expressions are accountable for different betalain biosynthesis contents in white and red pulp
Summary
Pitaya or pitahaya (Hylocereus), referred to as dragon fruit, is one of the most important and widely spread fruit crops in tropical and subtropical countries. Pitaya likely originated from rainforests in tropical and subtropical areas of Latin America (Mexico and Colombia), and it is a globally important fruit crop[1,2]. Two types of pitaya fruit, namely, H. undatus (red peel with white pulp) and H. monacanthus (red peel with red pulp), are commercially produced at a large scale as fruit crops in Central America, Southeast Asia, and China[2]. A total of 12,946 scientific plant names at the rank of the species for the family Cactaceae have been recorded in the working list of plants
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
