Key Laboratory of Crop biology of Anhui Province, Anhui Agricultural University, Hefei, China.
School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China.
Gigascience. 2018 Jun 1;7(6). doi: 10.1093/gigascience/giy067.
Luo-han-guo (Siraitia grosvenorii), also called monk fruit, is a member of the Cucurbitaceae family. Monk fruit has become an important area for research because of the pharmacological and economic potential of its noncaloric, extremely sweet components (mogrosides). It is also commonly used in traditional Chinese medicine for the treatment of lung congestion, sore throat, and constipation. Recently, a single reference genome became available for monk fruit, assembled from 36.9x genome coverage reads via Illumina sequencing platforms. This genome assembly has a relatively short (34.2 kb) contig N50 length and lacks integrated annotations. These drawbacks make it difficult to use as a reference in assembling transcriptomes and discovering novel functional genes.
Here, we offer a new high-quality draft of the S. grosvenorii genome assembled using 31 Gb (∼73.8x) long single molecule real time sequencing reads and polished with ∼50 Gb Illumina paired-end reads. The final genome assembly is approximately 469.5 Mb, with a contig N50 length of 432,384 bp, representing a 12.6-fold improvement. We further annotated 237.3 Mb of repetitive sequence and 30,565 consensus protein coding genes with combined evidence. Phylogenetic analysis showed that S. grosvenorii diverged from members of the Cucurbitaceae family approximately 40.9 million years ago. With comprehensive transcriptomic analysis and differential expression testing, we identified 4,606 up-regulated genes in the early fruit compared to the leaf, a number of which were linked to metabolic pathways regulating fruit development and ripening.
The availability of this new monk fruit genome assembly, as well as the annotations, will facilitate the discovery of new functional genes and the genetic improvement of monk fruit.
罗汉果（Siraitia grosvenorii），又称罗汉果，是葫芦科的一员。由于其无热量、极其甜的成分（罗汉果苷）的药理学和经济潜力，罗汉果已成为研究的重要领域。它也常用于中药治疗肺充血、喉咙痛和便秘。最近，罗汉果的参考基因组可用，通过 Illumina 测序平台，从 36.9x 基因组覆盖读数组装。该基因组组装的 contig N50 长度相对较短（34.2kb），并且缺乏集成注释。这些缺点使得在组装转录组和发现新的功能基因时难以使用。
在这里，我们提供了一个使用 31 Gb（约 73.8x）长的单分子实时测序读数组装的高质量的 S. grosvenorii 基因组的新草案，并使用约 50 Gb Illumina 配对末端读数进行了抛光。最终的基因组组装约为 469.5 Mb，contig N50 长度为 432,384 bp，代表了 12.6 倍的改进。我们进一步用综合证据注释了 237.3 Mb 的重复序列和 30,565 个共识蛋白编码基因。系统发育分析表明，S. grosvenorii 与葫芦科的成员大约在 4090 万年前分化。通过全面的转录组分析和差异表达测试，我们在早期果实中鉴定出 4606 个上调基因与叶相比，其中一些与调节果实发育和成熟的代谢途径有关。
这种新的罗汉果基因组组装以及注释的可用性将有助于发现新的功能基因和罗汉果的遗传改良。
