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Species Profile Genome Assembly

Species Profile

Genus Panax
Species Panax bipinnatifidus Seen
Common name Yuyesanqi
Synonyms Panax japonicus var. bipinnatifidus; Panax pseudoginseng var. bipinnatifidus; Panax sinensis; Panax pseudo-ginseng subsp.himalaicus
Chromosome
Utilization medicinal
Distribution Forests,1900-3200m.Distributing in Xizang (Nyalam,Yadong,Chauna,Mirin),Yunnan,Sichuan,Hubei (Padong),Shaanxi (Taibai Mountain) and Gansu (Xihe),China;Nepal,India;Myanmar,Vietnam(Hoang Lien Son)
Description

Herbs, perennial.50–100 cm tall; Horizontal rhizomes, slender and elongated internodes; tuber variable in shapes, persistent in older rhizomes; Dark brown stem; Leaves 4–7 foliate,10–30 cm long,petioles 6–12 cm long; petiolules 0.5–1.5 cm long; leaflets oblong–lanceolate to lanceolate, 9–18 cm long, 1.5–3.0 cm wide; apex long acuminate to 3.0 cm; singly or doubly serrate; setose on adaxial surface; base round, subcordate, obtuse and oblique.Peduncle length is longer than leaf length, 15–40 cm long. Flowers are bracts lanceolate, 0.3–0.6 cm long, deciduous; pedicels 0.7–2.0 cm long; sepals triangular; petals lanceolate or traingular, ± 2 mm long; anther elliptic, ± 2 mm long. Fruits are sub-globose, lower half red and upper half black; seeds large, ovoid, 5–7 mm long.

References

QIN Haining, et al, 2021, China Checklist of Higher Plants, In the Biodiversity Committee of Chinese Academy of Sciences ed., Catalogue of Life China: 2021 Annual Checklist, Beijing, China.Bhusan G,Pardeep K,B.,Amit K,R.,et al.Major ginsenoside contents in rhizomes of Panax sokpayensis and Panax bipinnatifidus[J]Natural Product Research.Nat Prod Res.2018,1.32(2):234-238;Zhao R,Shan XX,Yang JW,et al.Analysis of Botanical Characters and Growth Dynamic in Panax Japonicus C.A.Mey.Var.bipinnatifidus (Seem.) C.Y.Wu et K.M.Feng[J].Journal of Yunnan College of Traditional Chinese Medicine,2012,35(02):24-27+45.;Ji Y, Liu C, Yang Z, et al.Testing and using complete plastomes and ribosomal DNA sequences as the next generation DNA barcodes in Panax (Araliaceae)[J]. Mol Ecol Resour. 2019,9.19(5):1333-1345.

Genome assembly

Items 2017a 2017b 2020a 2020b 2021a 2017 2018
Plant material Notoginseng Notoginseng Notoginseng Notoginseng Notoginseng 4nullyearoldP. ginseng line IR826 P.Ginsengcultivar “Chunpoong”
Size of raw data(Gb) 385.28 1837.6 178.19 240.22 424 391.46 746 Gb pairednullend and 365 Gb matenullpaired raw data
Total length of contigs (Gb) 1.53 1.99 - 2.25 2.4 3.00 2.99
Number of contigs 225513 563700 - - 2993 39.48kb -
Contig N50 13.16 kb 15.99 kb 1.12 Mb 220.89kb 1.45Mb 21.98Kb 13.2 kb
Longest contig (bp) 120.91 kb 199.81 kb 13.35 Mb 7.10Mb - 574.18Kb -
Number of scaffolds 76517 122131 13292 219 5218 9072 9845
Scaffold N50 157.81 kb 96.16 kb 216.47Mb 173.39 Mb 196.33 Mb 108.71kb 158 kb
Longest scaffold (bp) 1.19 Mb 834.33 kb 295.55 Mb 219.05Mb 460.99kb 1303.41kb 3.64Mb
GC content (%) 34.85 28.65 34.45 34.02 34.43 42 35
Number of genes 34369 36790 37606 39452 47870 42006 59352
Average gene length (bp) 2705 3307 5060 3883 - - -
Complete BUSCOs (%)(Genome) - 94.5 96.6 89.3 95.4 - -
BUSCOs (%)(Gene set) 71.3 74.1 - 82.5 94 69.9 94.6
Average CDS length (bp) 957 942 1203 1002 1444 - 1120
Average exon length (bp) 251.39 211.92 231 224.65 293.09 - -
Average exon number per gene 3.8 4.45 5.21 4.5 4.9 - -
Average transcript length (bp) 2,705 (UTR excluded) 3307 3759 5060 5183 - -
Percentage of repeat sequences (%) 61.31 81.26 85.85 79.07 88.2 62.17 -
Percentage of LTRnullRTs (%) 57.41 66.72 58.88 - 81.2 83.5 -
Reference (Zhang et al., 2017) (Chen et al., 2017) (Jiang et al.,2020) (Fan et al.,2020) (Yang et al.,2021) (Xu et al.,2017) (Jayakodi et al.,2017)