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

文献类型： 外文期刊

第一作者： Chen, Jian-ye

作者： Chen, Jian-ye;Xie, Fang-fang;Chen, Can-bin;Lu, Wang-jin;Hua, Qing-zhu;Zhang, Zhi-ke;Hu, Gui-bing;Qin, Yong-hua;Cui, Yan-ze;Hu, Xiao-di;Zhao, Jing;Gao, Dan;Jiang, Wen-kai;Wu, Zhi-jiang;Sun, Qing-ming

作者机构：

期刊名称：HORTICULTURE RESEARCH （ 影响因子：6.793； 五年影响因子：6.589 ）

ISSN： 2662-6810

年卷期： 2021 年 8 卷 1 期

页码：

收录情况： SCI

摘要： 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, 10x 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 1.41Gb, with a scaffold N50 of similar to 127.15Mb. In total, 27,753 protein-coding genes and 896.31Mb 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 (similar to 696.45Mb) 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'x'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.

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