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Species Profile Genome Assembly

Species Profile

Genus Panax
Species Panax japonicus C.A.Mey.var.Major
Common name Bead ginseng
Synonyms Panax major Ting
Chromosome 2n=2x=24
Utilization medicinal
Distribution 1700-3600m a.l.s.; Forests.Cultivated in Sichuan,Gansu,Guizhou,Henan,Hubei,Shanxi,Sichuan,Xizang,Yunnan,China;Native to SW China,N Myanmar,Nepal,N Vietnam.
Description

Herbs, perennial,ca.80cm tall.Rhizome beadlike,internodes usually long and thin such as rope;Sometimes part of the nodules are densely shaped like bamboo whip,palmately compound leaves with 3-5 whorled stem apices;Petiole ca.9cm;Leaflets usually 5,smaller on either side,petioles 5-15mm long,central leaflets elliptic or elliptically ovate,10-13mm long,5-7cm wide,apex long acuminate,base suborbicular or cuneate,margin finely serrate,margin and both surfaces sparsely bristled.Umbel simple,sometimes its subumbels 1 or more small umbels;The flowers are small and pale green;Calyx apex 5-cuspate;Petals 5,ovate-triangular,apex acute;Stamens 5,filaments short;Ovary inferior,style usually 2,disjunct.Fruit is drupe berry,round,bright red when ripe.Flowering from July to August,fruiting from August to October.

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

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)