Ilex crenata
Thunb. · speciesAt a glance
Sources12 archives
Databases and archives Ilex crenata's data was compiled from.
WikipediaWikimedia Foundation11 languages↗
BioWikiNetmultilingual Wikipediamultilingual↗
GBIFGlobal Biodiversity Information Facility4 200 records↗
ENAEuropean Nucleotide Archive · EMBL-EBI31 eDNA detections↗
BOLD SystemsCentre for Biodiversity Genomics10 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 & karyotypeEvery layer below draws on the sources above — open one to explore it, or use ← → to move between tabs.
Ilex crenata, the Japanese holly or box-leaved holly (Japanese: イヌツゲ inutsuge) is a species of flowering plant in the family Aquifoliaceae, native to eastern China, Japan, Korea, Taiwan, and Sakhalin. It is an evergreen shrub or small tree growing to a height of 3–5 m (rarely 10 m) tall, with a trunk diameter up to 20 cm. The leaves are glossy dark green, small, 10–30 mm long and 10–17 mm broad, with a crenate (wavy) margin, sometimes spiny. The plants are dioecious (having separate male and female plants), with white, four-lobed flowers. The fruit is a black drupe (stone fruit) 5 mm diameter, containing four seeds. It grows well in acidic soil, between a pH of 3.7 and 6.0.Osaka hundred trees: Ilex crenata (in Japanese; google translation)Okayama Science University: Ilex crenata (in Japanese; google translation)Huxley, A., ed. (1992). New RHS Dictionary of Gardening. Macmillan .
No narrative description available for this taxon yet.
Size & morphology8
Life cycle & reproduction27
Habitat & environment27
Physiology & chemistry21
Uses & economy13
Other traits7
Compounds documented for Ilex crenata across natural-product and food-composition databases — not just the ~150 nutrients on a classic label ("nutritional dark matter").
Compound class profile5 classes
Documented compounds65 total
| Compound | Class | Amount | Source |
|---|---|---|---|
| (10S,11R,12R,13S,14R)-10,11-dihydroxy-14-(2-hydroxy-3,4-dimethoxyphenyl)-8-methoxy-N,N-dimethyl-13-phenyl-4,6,15-trioxatetracyclo[7.6.0.03,7.010,14]pentadeca-1,3(7),8-triene-12-carboxamide | present | NPASS | |
| (10S,11R,12R,13S,14R)-14-(3,4-dimethoxyphenyl)-10,11-dihydroxy-8-methoxy-N,N-dimethyl-13-phenyl-4,6,15-trioxatetracyclo[7.6.0.03,7.010,14]pentadeca-1,3(7),8-triene-12-carboxamide | present | NPASS | |
| (1S,12R,20R,21R,22S)-20-hydroxy-3,16,17-trimethoxy-N,N-dimethyl-22-phenyl-5,7,11,19-tetraoxahexacyclo[10.7.3.01,12.02,10.04,8.013,18]docosa-2,4(8),9,13(18),14,16-hexaene-21-carboxamide | present | NPASS | |
| (1S,2R,3R,4aR,6aR,6aS,6bR,8aR,10S,12aR,14bS)-1-hydroxy-1,2,6a,6b,9,9,12a-heptamethyl-3-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-10-[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy-2,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylic acid | present | LOTUS | |
| (1S,2R,3R,4aR,6aR,6aS,6bR,8aS,10S,12aR,14bR)-1-hydroxy-1,2,6a,6b,9,9,12a-heptamethyl-3-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-10-[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy-2,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylic acid | present | LOTUS | |
| (2R)-N-[(2R)-1-[(1R,12R,13S,14R,15S)-1,15-dihydroxy-3-methoxy-12-(4-methoxyphenyl)-13-phenyl-5,7,11-trioxatetracyclo[10.2.1.02,10.04,8]pentadeca-2,4(8),9-triene-14-carbonyl]pyrrolidin-2-yl]-2-methylbutanamide | present | NPASS | |
| (2S,4aS,4bR,6aR,8S,10aR,10bR,12R)-12-hydroxy-4a,4b,7,7,10a-pentamethyl-2-[(3R)-3-methyl-4-oxopentyl]-8-[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy-4,5,6,6a,8,9,10,10b,11,12-decahydro-3H-chrysene-2-carboxylic acid | present | LOTUS | |
| (2S,4aS,4bR,6aR,8S,10aR,10bR,12R)-8-[(2S,3R,4S,5S)-4,5-dihydroxy-3-[(2R,3R,4S,5R,6R)-2,3,5-trihydroxy-6-(hydroxymethyl)oxan-4-yl]oxyoxan-2-yl]oxy-12-hydroxy-4a,4b,7,7,10a-pentamethyl-2-[(3R)-3-methyl-4-oxopentyl]-4,5,6,6a,8,9,10,10b,11,12-decahydro-3H-chrysene-2-carboxylic acid | present | LOTUS | |
| (2S,4aS,4bR,6aR,8S,10aS,10bR)-4a,4b,7,7,10a-pentamethyl-2-[(3R)-3-methyl-4-oxopentyl]-8-[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy-4,5,6,6a,8,9,10,10b-octahydro-3H-chrysene-2-carboxylic acid | present | LOTUS | |
| (2S,4aS,4bR,6aR,8S,10aS,10bR)-8-[(2S,3R,4S,5S)-3,5-dihydroxy-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-4a,4b,7,7,10a-pentamethyl-2-[(3R)-3-methyl-4-oxopentyl]-4,5,6,6a,8,9,10,10b-octahydro-3H-chrysene-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 Ilex crenata 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 Ilex crenata 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 341×CCDB · book-fedorov
n 182×CCDB · book-ipcn67-71 · CCDB · book-ipcn75-78
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 type4 200 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 institutions78 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 |
|---|---|
| Odawara, JP | 127 |
| Nagano City, JP | 56 |
| Sanda, JP | 56 |
| Bando, JP | 46 |
| KURAlocation not on record | 40 |
| Chiba, JP | 36 |
| Beijing, CN | 27 |
| Nagatoro-machi, Chichibu-gun, JP | 23 |
| Taipei, TW | 23 |
| Osaka, JP | 16 |
| FFPRIlocation not on record | 15 |
| Kochi, JP | 13 |
| Bronx, US | 12 |
| Saint Louis, US | 12 |
| KR | 12 |
| Bangkok, TH | 11 |
| Hangzhou, CN | 10 |
| University of Stellenboschlocation not on record | 10 |
| Fukushima Universitylocation not on record | 10 |
| Nanjing, CN | 10 |
| TAIElocation not on record | 10 |
| Vancouver, CA | 10 |
| Zhejiang Universitylocation not on record | 9 |
| Moscow State Universitylocation not on record | 9 |
| Shanghai, CN | 8 |
| Obihiro Centennial City Museumlocation not on record | 8 |
| Guangzhou, CN | 8 |
| Philadelphia, US | 8 |
| Taipei, TW | 7 |
| WTUlocation not on record | 7 |
| Guilin, CN | 7 |
| Herbarium of the Department of Botany, University of Tokyolocation not on record | 6 |
| MeiseBGlocation not on record | 6 |
| Knoxville, US | 6 |
| Nanjing, CN | 6 |
| Sagamihara, JP | 6 |
| University of New Hampshirelocation not on record | 6 |
| Burlington, US | 5 |
| Tianjin Natural History Museumlocation not on record | 5 |
| Elocation not on record | 5 |
| Angwin, US | 5 |
| Chapel Hill, US | 5 |
| KOMlocation not on record | 5 |
| Edinburgh, GB | 5 |
| GBS RAN - Glavny Botanichesky Sad Rossijskoj Akademii Nauklocation not on record | 5 |
| Fort Worth, US | 4 |
| Chongqing Museumlocation not on record | 4 |
| LDlocation not on record | 4 |
| Cambridge, US | 4 |
| College Park, US | 4 |
| Taipei, TW | 4 |
| SLU Artdatabankenlocation not on record | 3 |
| Millersville, US | 3 |
| Henderson State Universitylocation not on record | 3 |
| Kew, GB | 3 |
| Herbarium of South China Botanical Gardenlocation not on record | 3 |
| FJFClocation not on record | 3 |
| Riverside, US | 3 |
| Gijón, ES | 2 |
| Columbia, US | 2 |
| Anhui Normal Universitylocation not on record | 2 |
| Guangzhou, CN | 2 |
| Western Carolina Universitylocation not on record | 2 |
| Appalachian State Universitylocation not on record | 2 |
| Lanzhou, CN | 2 |
| Wlocation not on record | 2 |
| Richmond, US | 2 |
| Minia, EG | 2 |
| Bothell, US | 2 |
| EL PASO, US | 2 |
| Christchurch, NZ | 2 |
| Canadian Department of Agriculturelocation not on record | 2 |
| Florida Museum of Natural History- Zoology, Paleontology & Paleobotanylocation not on record | 2 |
| Zhejiang Museum of Natural Historylocation not on record | 2 |
| Allentown, US | 2 |
| New Haven, US | 2 |
| Kingston, US | 2 |
| James F. Matthews Center for Biodiversity Studieslocation not on record | 2 |
| Emporia, US | 1 |
| Chongqing, CN | 1 |
| San Sebastián, ES | 1 |
| Fujian Institute of Subtropical Botanylocation not on record | 1 |
| Stockholm, SE | 1 |
| Chicago, US | 1 |
| Xinxiang, CN | 1 |
| National Institute of Biological Resourceslocation not on record | 1 |
| Gifu prefectural Museumlocation not on record | 1 |
| Vitoria, ES | 1 |
| Museum Of Natural And Environmental History, Shizuokalocation not on record | 1 |
| Dekalb, US | 1 |
| Long Beach, US | 1 |
| Fairfax, US | 1 |
| Rotorua, NZ | 1 |
| Tomioka, JP | 1 |
| Johnson City, US | 1 |
| Honolulu, US | 1 |
| Clemson, US | 1 |
| Pullman, US | 1 |
| DOI/NPS, Colonial National Historical Parklocation not on record | 1 |
| Institut de Biologia Evolutiva, (CSIC-UPF)location not on record | 1 |
| Flagstaff, US | 1 |
| Dover, US | 1 |
| Norfolk, US | 1 |
| Corvallis, US | 1 |
| Wellington, NZ | 1 |
| Beijing Natural History Museumlocation not on record | 1 |
| Kyoto Universitylocation not on record | 1 |
| Awka, NG | 1 |
| Frankfurt am Main | 1 |
| Jiangxi College of Traditional Chinese Medicinelocation not on record | 1 |
| Philadelphia, US | 1 |
| Santa Barbara, US | 1 |
| Cape Town, ZA | 1 |
| Institute for Agricultural Bacteriology and Fermentation Biologylocation not on record | 1 |
| Staten Island, US | 1 |
| Victoria, CA | 1 |
| Washington, US | 1 |
| Wuzhou, CN | 1 |
| DOI/NPS, Little Rock Central High School National Historic Sitelocation 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 Ilex crenata 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.