Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.
Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
Sci Rep. 2021 Jul 22;11(1):14944. doi: 10.1038/s41598-021-93495-z.
Picrorhiza kurrooa is an endangered medicinal herb which is distributed across the Himalayan region at an altitude between 3000-5000 m above mean sea level. The medicinal properties of P. kurrooa are attributed to monoterpenoid picrosides present in leaf, rhizome and root of the plant. However, no genomic information is currently available for P. kurrooa, which limits our understanding about its molecular systems and associated responses. The present study brings the first assembled draft genome of P. kurrooa by using 227 Gb of raw data generated by Illumina and PacBio RS II sequencing platforms. The assembled genome has a size of n = ~ 1.7 Gb with 12,924 scaffolds. Four pronged assembly quality validations studies, including experimentally reported ESTs mapping and directed sequencing of the assembled contigs, confirmed high reliability of the assembly. About 76% of the genome is covered by complex repeats alone. Annotation revealed 24,798 protein coding and 9789 non-coding genes. Using the assembled genome, a total of 710 miRNAs were discovered, many of which were found responsible for molecular response against temperature changes. The miRNAs and targets were validated experimentally. The availability of draft genome sequence will aid in genetic improvement and conservation of P. kurrooa. Also, this study provided an efficient approach for assembling complex genomes while dealing with repeats when regular assemblers failed to progress due to repeats.
波棱瓜子是一种濒危的药用植物，分布于喜马拉雅山脉海拔 3000-5000 米的地区。波棱瓜子的药用特性归因于存在于植物的叶、根茎和根中的单萜类苦味素。然而，目前波棱瓜子没有基因组信息，这限制了我们对其分子系统和相关反应的理解。本研究利用 Illumina 和 PacBio RS II 测序平台产生的 227 Gb 原始数据，首次组装了波棱瓜子的基因组草图。组装的基因组大小为 n = ~1.7 Gb，有 12924 个支架。四项四核组装质量验证研究，包括实验报告的 ESTs 映射和组装的连续体定向测序，证实了组装的高度可靠性。大约 76%的基因组仅由复杂重复序列组成。注释揭示了 24798 个蛋白质编码基因和 9789 个非编码基因。利用组装的基因组，共发现了 710 个 miRNA，其中许多与分子对温度变化的反应有关。miRNA 和靶标得到了实验验证。基因组草图的可用性将有助于波棱瓜子的遗传改良和保护。此外，这项研究提供了一种有效的方法来组装复杂的基因组，同时在常规组装器因重复而无法进行时处理重复。
