Callicarpa japonica
Thunb. · speciesAt a glance
Sources13 archives
Databases and archives Callicarpa japonica's data was compiled from.
WikipediaWikimedia Foundation8 languages↗
BioWikiNetmultilingual Wikipediamultilingual↗
GBIFGlobal Biodiversity Information Facility6 133 records↗
ENAEuropean Nucleotide Archive · EMBL-EBI45 eDNA detections↗
BOLD SystemsCentre for Biodiversity Genomics5 specimens↗
NCBIUS National Library of Medicinesequences↗
LOTUSNatural Products (Wikidata)compounds↗
NPASSNat. Product Activity & Species Sourcecompounds↗
GRIN TaxonomyUSDA-ARSdistribution & uses↗
Open Tree of LifeOpenTreephylogeny backbone↗
CCDBChromosome Counts DB · Tel Aviv U.genome & karyotype↗
PloiDBPloidy Databasegenome & karyotype
GLoBIGlobal Biotic Interactionsbiotic interactions↗Every layer below draws on the sources above — open one to explore it, or use ← → to move between tabs.
Callicarpa japonica, commonly known as East Asian beautyberry or Japanese beautyberry, is a plant in the mint family. It is a deciduous shrub, most notable for producing purple drupes (its "berries") in the fall. The flowers can range from pink through white. This species is native to China, Japan, Korea, Ryukyu Islands, and Taiwan.Kew World Checklist of Selected Plant Families It considered to be a common species in Japan. It is cultivated as an ornamental bush, and it is very popular in gardens and parks. The fruits are not edible for humans, but are food of birds and deer. The leaves can be used to make herbal tea.
No narrative description available for this taxon yet.
Size & morphology7
Life cycle & reproduction4
Diet & foraging1
Habitat & environment7
Physiology & chemistry3
Compounds documented for Callicarpa japonica across natural-product and food-composition databases — not just the ~150 nutrients on a classic label ("nutritional dark matter").
Compound class profile5 classes
Documented compounds84 total
| Compound | Class | Amount | Source |
|---|---|---|---|
| (+)-Intermedeol | present | LOTUS | |
| (+)-taxifolin | present | NPASS | |
| (-)-Humulene epoxide II | present | LOTUS | |
| (1aR,4aR,7S,7aS,7bR)-1,1,7-Trimethyl-4-methylidenedecahydro-1H-cyclopropa[e]azulen-7-ol | present | LOTUS | |
| (1aS,4aS,7S,7aR,7bS)-1,1,7-trimethyl-4-methylidene-1a,2,3,4a,5,6,7a,7b-octahydrocyclopropa[h]azulen-7-ol | present | LOTUS | |
| (1R,3E,7E,11R)-1,5,5,7-tetramethyl-12-oxabicyclo[9.1.0]dodeca-3,7-diene | present | LOTUS | |
| (1R,8S,9R,16R,18S,27S)-9-(3,4-dihydroxyphenyl)-5,8,16,21,23-pentahydroxy-2,10,17,26-tetraoxaheptacyclo[14.11.1.01,13.03,12.06,11.018,27.020,25]octacosa-3(12),4,6(11),13,20,22,24-heptaen-15-one | present | NPASS | |
| (1S,2E,10R)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene | present | LOTUS | |
| (1S,2R,4aR,8aR)-1,2,3,4,4a,7,8,8a-Octahydro-1,2,4a,5-tetramethyl-1-naphthaleneacetaldehyde | present | LOTUS | |
| (2R,3R,4S,5R,6S)-3,4,5-trihydroxy-6-[5-hydroxy-2-(4-hydroxyphenyl)-4-oxochromen-7-yl]oxyoxane-2-carboxylic acid | present | LOTUS |
A DNA barcode is a short, standardised stretch of genes that works like a fingerprint — enough to tell one species from another. Below is the molecular trace Callicarpa japonica has left across the world's sequence archives.
At a glance
★ the standard DNA barcode for this group — the short region actually read to tell this species apart. The rest are extra genes sequenced along the way.
The complete instruction manual Callicarpa japonica carries — its genome. We read it from three angles — how big it is, how the DNA is packed into chromosomes, and how completely it has been sequenced — and explain how to read each value as you go.
Chromosomes & ploidyhow the DNA is packaged
2n is the full chromosome count in a normal body cell; n is a gamete (egg or sperm), which carries half. Ploidy is how many complete chromosome sets each cell holds — 2× (diploid) is typical for animals, while higher levels (polyploidy) are common in plants. Click any value below to see the underlying records and sources.
2n 161×CCDB · book-atlas-flowering-plants
2n 181×CCDB · book-atlas-flowering-plants
n 181×CCDB · book-ipcn65
diploid inferred1×PloiDB · genus-scale
How far back this lineage goes — and how we know. Everything here is measured in Ma, short for “mega-annum”: millions of years ago. The chart reads left to right like a calendar of the Earth, from the deep past on the left to today at the right edgetop to bottom like a core drilled through the Earth, from the deep past at the top down to today at the bottom.
At a glance
When this lineage existed
How to read this: the coloured strip along the bottomdown the left is the geological calendar — the standard epochs (Pliocene, Pleistocene…) every museum uses, shown so you can see which chapter of Earth's history this lineage lived in. This lineage is a young one, so the strip is zoomed in to epochs — the finer subdivisions inside a period. The orange marker is the DNA clock: DNA accumulates mutations at a roughly steady rate, so comparing this species' DNA with its relatives estimates when the lineage split off — independently of any fossil.
Record type6 133 records
Origin
Range
Wildobservation + sensor
Human sightings and records, or camera-trap / sensor detections — someone (or a device) saw or captured the species in the wild.
Museum / Voucheredphysical evidence
Backed by a physical specimen — a herbarium sheet, sample or voucher held in a collection. “Vouchered” means supported by material evidence, not just an observation.
Cultivated / Captivenot free-living
A living individual in a botanical garden, zoo or nursery — cultivated or kept, not free-living.
Wildobservation + sensor
Human sightings and records, or camera-trap / sensor detections — someone (or a device) saw or captured the species in the wild.
Holding institutions60 of 119 geolocated
Institutions and collections holding physical, vouchered specimens of this species — click a row to fly to it on the map.
| Institution | Specimens |
|---|---|
| Sanda, JP | 236 |
| Nagano City, JP | 217 |
| Odawara, JP | 215 |
| Shinshu Universitylocation not on record | 213 |
| Bando, JP | 171 |
| Toyama, JP | 152 |
| KR | 146 |
| Chiba, JP | 116 |
| Kochi, JP | 115 |
| Nagatoro-machi, Chichibu-gun, JP | 112 |
| Beijing, CN | 84 |
| Herbarium of the Department of Botany, University of Tokyolocation not on record | 74 |
| KURAlocation not on record | 65 |
| Fukushima Universitylocation not on record | 58 |
| Sendai, JP | 54 |
| Wuhan, CN | 49 |
| JP | 48 |
| Tokushima, JP | 45 |
| FFPRIlocation not on record | 36 |
| NSMKlocation not on record | 32 |
| Osaka, JP | 31 |
| Hangzhou, CN | 30 |
| Hiratsuka City Museumlocation not on record | 30 |
| Kyoto Universitylocation not on record | 28 |
| Korea National Arboretumlocation not on record | 23 |
| Ishikawa Museum of Natural Historylocation not on record | 22 |
| Bronx, US | 21 |
| National Institute of Biological Resourceslocation not on record | 19 |
| KOMlocation not on record | 18 |
| Akita Prefectural Museumlocation not on record | 18 |
| Sugadaira Research Station, Mountain Science Center, University of Tsukubalocation not on record | 16 |
| Taipei, TW | 16 |
| Iwate Prefectural Museumlocation not on record | 15 |
| Institute for Agricultural Bacteriology and Fermentation Biologylocation not on record | 15 |
| Philadelphia, US | 14 |
| Guangzhou, CN | 14 |
| Zhejiang Universitylocation not on record | 14 |
| Nanjing, CN | 13 |
| Elocation not on record | 13 |
| Nanjing, CN | 12 |
| Cambridge, US | 11 |
| Toyota city nature sanctuarylocation not on record | 10 |
| Tomioka, JP | 10 |
| Changsha, CN | 9 |
| Taipei, TW | 9 |
| Zhengzhou, CN | 8 |
| Taipei, TW | 8 |
| Kew, GB | 7 |
| Sagamihara, JP | 7 |
| J.F.Oberlin Universitylocation not on record | 7 |
| KIWElocation not on record | 7 |
| WNNUlocation not on record | 6 |
| Yangling, CN | 6 |
| Angwin, US | 6 |
| Kagoshima, JP | 6 |
| Central China Agricultural Universitylocation not on record | 6 |
| KIRMlocation not on record | 5 |
| Guilin, CN | 4 |
| Chengdu, CN | 4 |
| Bangkok, TH | 4 |
| Yunnan Universitylocation not on record | 3 |
| Seoul, KR | 3 |
| SJNAlocation not on record | 3 |
| Zhuzhou, CN | 3 |
| Otaru, JP | 3 |
| Guiyang, CN | 3 |
| Adam Mickiewicz University in Poznańlocation not on record | 3 |
| JBRJlocation not on record | 2 |
| Jiujiang Forestry Institutelocation not on record | 2 |
| Wlocation not on record | 2 |
| DOI/NPS, Mississippi National River & Recreation Arealocation not on record | 2 |
| Auckland, NZ | 2 |
| Edinburgh, GB | 2 |
| DNSMlocation not on record | 2 |
| Shanghai, CN | 2 |
| Hangzhou Normal Collegelocation not on record | 2 |
| Awka, NG | 2 |
| SMMUlocation not on record | 2 |
| BISHlocation not on record | 2 |
| DMZ botanic gardenlocation not on record | 2 |
| Nagasaki University - Fisherieslocation not on record | 2 |
| Burlington, US | 2 |
| Obihiro Centennial City Museumlocation not on record | 2 |
| Kunming, CN | 2 |
| Shanghai, CN | 2 |
| Honolulu, US | 2 |
| Xiamen, CN | 2 |
| Chongqing Museumlocation not on record | 1 |
| Institut de Biologia Evolutiva, (CSIC-UPF)location not on record | 1 |
| PRClocation not on record | 1 |
| DOI/NPS, Colonial National Historical Parklocation not on record | 1 |
| The Sandakan Herbarium, Forest Research Centrelocation not on record | 1 |
| Jiangxi College of Traditional Chinese Medicinelocation not on record | 1 |
| “Manash Kozybayev North Kazakhstan University" NPLClocation not on record | 1 |
| Ann Arbor, US | 1 |
| Macomb, US | 1 |
| ENHMlocation not on record | 1 |
| Herbarium of South China Botanical Gardenlocation not on record | 1 |
| Wellington, NZ | 1 |
| Dekalb, US | 1 |
| Beijing Natural History Museumlocation not on record | 1 |
| Xinxiang, CN | 1 |
| Jackson, US | 1 |
| Columbia, US | 1 |
| ifplocation not on record | 1 |
| Chapel Hill, US | 1 |
| University of Stellenboschlocation not on record | 1 |
| Berlin, DE | 1 |
| South China Normal Universitylocation not on record | 1 |
| Chongqing Natural History Museumlocation not on record | 1 |
| Central China Normal Universitylocation not on record | 1 |
| SDFlocation not on record | 1 |
| Museum Of Natural And Environmental History, Shizuokalocation not on record | 1 |
| Capital Normal Universitylocation not on record | 1 |
| nlocation not on record | 1 |
| Fort Worth, US | 1 |
| MAlocation not on record | 1 |
| College Park, US | 1 |
| Southwest Forestry Collegelocation not on record | 1 |
Cultivated / Captivenot free-living
A living individual in a botanical garden, zoo or nursery — cultivated or kept, not free-living.
Where the DNA of Callicarpa japonica was picked up in samples of water, soil or air — nobody saw the organism, only its DNA left behind. A trace is a clue that the species was near, not a confirmed sighting.
Signal
Where its DNA was found
How strong is each trace?
Modelled climatemodelled
How to read this: each dot is one detection of this species' DNA in an environmental sample. The confidence meter weighs how many independent studies and places back up the signal — one detection in one study is a hint; many across several studies is solid. Records dated before 2008 (when eDNA methods began) are treated as likely mislabeled and left off the map.