A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesis.
A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesis.
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DOI：
10.1038/s41438-021-00612-0
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发表时间：
2021-07-06
影响因子：
8.7
通讯作者：
Qin YH
中科院分区：
文献类型：
--
作者：
Chen JY;Xie FF;Cui YZ;Chen CB;Lu WJ;Hu XD;Hua QZ;Zhao J;Wu ZJ;Gao D;Zhang ZK;Jiang WK;Sun QM;Hu GB;Qin YH
火龙果（Hylocereus）是仙人掌科（Cactaceae）植物中最具经济价值的肉质果树，在世界范围内广泛种植，其果实中富含甜菜碱，因此引起了人们的广泛关注。尽管如此，缺乏火龙果参考基因组极大地阻碍了对其进化的研究，以及这种作物遗传改良的潜力。在此，我们采用了各种测序方法，即PacBio-SMRT，Illumina HiSeq配对末端，10× Genomics和Hi-C（高通量染色体构象捕获），以提供'GHB'火龙果（H. undatus，2n = 2x = 22条染色体）。组装后的火龙果基因组大小为1.41 Gb，骨架N50为~127.15 Mb。共获得27,753个蛋白质编码基因和896.31Mb的重复序列。undatus基因组进行了注释。火龙果经历了一个WGT（全基因组三倍），和最近的WGD（全基因组重复）发生后，伽马事件，这是常见的仙人掌科的其他物种。在H中共获得29，328个完整的LTR-RT（~696.45 Mb）。undatus，其中两个显著扩展的谱系Ty 1/copia和Ty 3/gypsy是扩展基因组的主要驱动因素。以‘GHB’ב大红’火龙果F_1群体为材料，构建了高密度遗传图谱。monacanthus）和它们的亲本，共鉴定了11个连锁群的20，872个bin标记（56，380个SNP）。更重要的是，通过转录组学和WGCNA（weighted gene coexpression network analysis）技术，从整体上揭示了火龙果甜菜色素生物合成的基因调控网络，包括结构基因和转录因子。我们的数据为促进火龙果的分子育种计划提供了宝贵的资源，并为其基因组进化以及可食用水果中甜菜色素生物合成的调节提供了新的见解。
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.
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