1.Whole-genome sequencing and analysis of the Chinese herbal plant .
Yisong LIU ; Qi TANG ; Pi CHENG ; Mingfei ZHU ; Hui ZHANG ; Jiazhe LIU ; Mengting ZUO ; Chongyin HUANG ; Changqiao WU ; Zhiliang SUN ; Zhaoying LIU
Acta Pharmaceutica Sinica B 2020;10(2):374-382
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.