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中草药植物的全基因组测序与分析

Whole-genome sequencing and analysis of the Chinese herbal plant .

作者信息

Liu Yisong, Tang Qi, Cheng Pi, Zhu Mingfei, Zhang Hui, Liu Jiazhe, Zuo Mengting, Huang Chongyin, Wu Changqiao, Sun Zhiliang, Liu Zhaoying

机构信息

Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha 410128, China.

Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China.

出版信息

Acta Pharm Sin B. 2020 Feb;10(2):374-382. doi: 10.1016/j.apsb.2019.08.004. Epub 2019 Aug 16.

DOI:10.1016/j.apsb.2019.08.004
PMID:32082980
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7016290/
Abstract

BACKGROUND

() (2n = 2x = 16) is genus of flowering plants belonging to the Gelsemicaeae family.

METHOD

Here, a high-quality genome assembly using the Oxford Nanopore Technologies (ONT) platform and high-throughput chromosome conformation capture techniques (Hi-C) were used.

RESULTS

A total of 56.11 Gb of raw GridION X5 platform ONT reads (6.23 Gb per cell) were generated. After filtering, 53.45 Gb of clean reads were obtained, giving 160 × coverage depth. The genome assemblies 335.13 Mb, close to the 338 Mb estimated by k-mer analysis, was generated with contig N50 of 10.23 Mb. The vast majority (99.2%) of the assembled sequence was anchored onto 8 pseudo-chromosomes. The genome completeness was then evaluated and 1338 of the 1440 conserved genes (92.9%) could be found in the assembly. Genome annotation revealed that 43.16% of the genome is composed of repetitive elements and 23.9% is composed of long terminal repeat elements. We predicted 26,768 protein-coding genes, of which 84.56% were functionally annotated.

CONCLUSION

The genomic sequences of could be a valuable source for comparative genomic analysis in the Gelsemicaeae family and will be useful for understanding the phylogenetic relationships of the indole alkaloid metabolism.

摘要

背景

（）（2n = 2x = 16）是属于钩吻科的开花植物属。

方法

在此，使用牛津纳米孔技术（ONT）平台和高通量染色体构象捕获技术（Hi-C）进行了高质量的基因组组装。

结果

总共产生了56.11 Gb的原始GridION X5平台ONT读数（每个细胞6.23 Gb）。过滤后，获得了53.45 Gb的干净读数，覆盖深度为160倍。生成的基因组组装体大小为335.13 Mb，接近通过k-mer分析估计的338 Mb，重叠群N50为10.23 Mb。绝大多数（99.2%）的组装序列被锚定到8条假染色体上。然后评估基因组完整性，在组装体中可发现1440个保守基因中的1338个（92.9%）。基因组注释显示，43.16%的基因组由重复元件组成，23.9%由长末端重复元件组成。我们预测了26768个蛋白质编码基因，其中84.56%具有功能注释。

结论

（）的基因组序列可能是钩吻科比较基因组分析的宝贵资源，将有助于理解吲哚生物碱代谢的系统发育关系。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/7219ae4eac05/sc1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/a58a659e30bb/fx1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/3de4f35bbe07/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/bb1090440ea9/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/e3ee998d7ab0/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/7fa7fbf59ec3/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/d6692da03d49/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/7219ae4eac05/sc1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/a58a659e30bb/fx1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/3de4f35bbe07/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/bb1090440ea9/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/e3ee998d7ab0/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/7fa7fbf59ec3/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/d6692da03d49/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/7016290/7219ae4eac05/sc1.jpg

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