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Article|06 Jul 2021|OPEN
A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesis
Jian-ye Chen1, Fang-fang Xie1, Yan-ze Cui2, Can-bin Chen1, Wang-jin Lu1, Xiao-Di Hu2, Qing-zhu Hua1, Jing Zhao2, Zhi-jiang Wu3, Dan Gao2, Zhi-ke Zhang1, Wen-kai Jiang2, Qing-ming Sun4, Gui-bing Hu1, & Yong-hua Qin1,
1State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Lingnan Guangdong Laboratory of Modern Agriculture, College of Horticulture, South China Agricultural University, 510642 Guangzhou, Guangdong, China
2Novogene Bioinformatics Institute, 100083 Beijing, China Full list of author information is available at the end of the article These authors contributed equally: Jian-ye Chen, Fang-fang Xie, Yan-ze Cui
3Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, Guangxi, China
4 Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences/Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA)/Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, 510640 Guangzhou, China

Horticulture Research 8,
Article number: 164 (2021)
doi: 10.1038/hortres.2021.164
Views: 227

Received: 14 Jan 2021
Revised: 20 May 2021
Accepted: 24 May 2021
Published online: 06 Jul 2021


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.