Genome sequence data availability
for the Japanese Red List

Updated on 2024-07-02

This page shows the availability of genome data for all organisms in the Japanese Red Lists (terrestrial list from 2020, and marine list from 2017). We used red list data from the Ministry of the Environment, Japan, taxonomy data from NCBI, iNaturalist, GBIF and COL, and genome data from NCBI Datasets (details). This page is placed in the public domain.

Citation: Kirill Kryukov, Naoyuki Nakahama, Shigehiro Kuraku (2024) “Genome assembly catalog for species in the Japanese Red List: unlocking endangered biodiversity through genomic inventory” [version 2; peer review: 2 approved] F1000Research, 2024, 13:583, https://doi.org/10.12688/f1000research.149793.2

Details by red list section: Mammals | Birds | Reptiles | Amphibians | Brackish and freshwater fishes | Insects | Molluscs | Other invertebrates | Vascular plants | Algae | Bryophytes | Lichen | Fungi | Saltwater fishes | Corals | Crustaceans | Cephalopods | Other marine invertebrates | All
Details by red list section: 哺乳類｜鳥類｜爬虫類｜両生類｜汽水・淡水魚類｜昆虫類｜貝類｜その他無脊椎動物｜維管束植物｜藻類｜蘚苔類｜地衣類｜菌類｜海産魚類｜サンゴ類｜甲殻類｜軟体動物（頭足類）｜その他無脊椎動物｜総計

Details by conservation status: EX | EW | CR | EN | CR+EN | VU | NT | DD | LP | All
Details by conservation status: 絶滅｜野生絶滅｜絶滅危惧IA類｜絶滅危惧IB類｜絶滅危惧I類｜絶滅危惧II類｜準絶滅危惧｜情報不足｜絶滅のおそれのある地域個体群｜総計

Statistics

Summary by conservation status (tsv) 🔗︎

Conservation StatusNumber
of entries		How many
are registered in
any taxonomy
(NCBI/iNat/GBIF/COL)		How many have
sequenced genomes
EX
絶滅		11196 (86.5%)
0 (0.0%)
EW
野生絶滅		1413 (92.9%)
0 (0.0%)
CR
絶滅危惧IA類		779719 (92.3%)
30 (3.9%)
EN
絶滅危惧IB類		805762 (94.7%)
20 (2.5%)
CR+EN
絶滅危惧I類		563482 (85.6%)
10 (1.8%)
VU
絶滅危惧II類		1,6251,504 (92.6%)
39 (2.4%)
NT
準絶滅危惧		1,5251,399 (91.7%)
36 (2.4%)
DD
情報不足		768695 (90.5%)
22 (2.9%)
LP
絶滅のおそれのある地域個体群		5449 (90.7%)
8 (14.8%)
Total
総計		6,2445,719 (91.6%)
165 (2.6%)

Summary by red list section (tsv) 🔗︎

Red
List		GroupNumber
of entries		How many
are registered in
any taxonomy
(NCBI/iNat/GBIF/COL)		How many have
sequenced genomes
Terrestrial Red List (2020)
レッドリスト（2020）		Mammals
哺乳類		7568 (90.7%)
16 (21.3%)
Birds
鳥類		154148 (96.1%)
30 (19.5%)
Reptiles
爬虫類		6261 (98.4%)
6 (9.7%)
Amphibians
両生類		6767 (100.0%)
0 (0.0%)
Brackish and freshwater fishes
汽水・淡水魚類		260239 (91.9%)
22 (8.5%)
Insects
昆虫類		877780 (88.9%)
5 (0.6%)
Molluscs
貝類		1,190973 (81.8%)
9 (0.8%)
Other invertebrates
その他無脊椎動物		152148 (97.4%)
5 (3.3%)
Vascular plants
維管束植物		2,1632,086 (96.4%)
25 (1.2%)
Algae
藻類		202152 (75.2%)
3 (1.5%)
Bryophytes
蘚苔類		282282 (100.0%)
1 (0.4%)
Lichen
地衣類		154141 (91.6%)
3 (1.9%)
Fungi
菌類		159150 (94.3%)
14 (8.8%)
Marine Red List (2017)
海洋生物レッドリスト（2017）		Saltwater fishes
海産魚類		218212 (97.2%)
20 (9.2%)
Corals
サンゴ類		1515 (100.0%)
2 (13.3%)
Crustaceans
甲殻類		173161 (93.1%)
0 (0.0%)
Cephalopods
軟体動物（頭足類）		33 (100.0%)
0 (0.0%)
Other marine invertebrates
その他無脊椎動物		3833 (86.8%)
4 (10.5%)
Total
総計		6,2445,719 (91.6%)
165 (2.6%)

Comparison of taxonomies (tsv) 🔗︎

Red
List		GroupNumber
of entries		How many
are registered in
NCBI taxonomy		How many
are registered in
iNat taxonomy		How many
are registered in
GBIF taxonomy		How many
are registered in
COL taxonomy		How many
are registered in
any taxonomy
(NCBI/iNat/
GBIF/COL)
Terrestrial Red List (2020)
レッドリスト（2020）		Mammals
哺乳類		7550 (66.7%)
65 (86.7%)
66 (88.0%)
60 (80.0%)
68 (90.7%)
Birds
鳥類		154125 (81.2%)
137 (89.0%)
143 (92.9%)
142 (92.2%)
148 (96.1%)
Reptiles
爬虫類		6244 (71.0%)
58 (93.5%)
60 (96.8%)
58 (93.5%)
61 (98.4%)
Amphibians
両生類		6765 (97.0%)
65 (97.0%)
65 (97.0%)
62 (92.5%)
67 (100.0%)
Brackish and freshwater fishes
汽水・淡水魚類		260217 (83.5%)
200 (76.9%)
225 (86.5%)
212 (81.5%)
239 (91.9%)
Insects
昆虫類		877344 (39.2%)
515 (58.7%)
702 (80.0%)
529 (60.3%)
780 (88.9%)
Molluscs
貝類		1,190505 (42.4%)
562 (47.2%)
963 (80.9%)
898 (75.5%)
973 (81.8%)
Other invertebrates
その他無脊椎動物		15291 (59.9%)
89 (58.6%)
145 (95.4%)
134 (88.2%)
148 (97.4%)
Vascular plants
維管束植物		2,1631,445 (66.8%)
1,423 (65.8%)
2,057 (95.1%)
1,960 (90.6%)
2,086 (96.4%)
Algae
藻類		202126 (62.4%)
69 (34.2%)
126 (62.4%)
0 (0.0%)
152 (75.2%)
Bryophytes
蘚苔類		282199 (70.6%)
139 (49.3%)
280 (99.3%)
274 (97.2%)
282 (100.0%)
Lichen
地衣類		15476 (49.4%)
76 (49.4%)
140 (90.9%)
105 (68.2%)
141 (91.6%)
Fungi
菌類		15977 (48.4%)
60 (37.7%)
147 (92.5%)
147 (92.5%)
150 (94.3%)
Marine Red List (2017)
海洋生物レッドリスト（2017）		Saltwater fishes
海産魚類		218192 (88.1%)
207 (95.0%)
212 (97.2%)
211 (96.8%)
212 (97.2%)
Corals
サンゴ類		1513 (86.7%)
15 (100.0%)
15 (100.0%)
15 (100.0%)
15 (100.0%)
Crustaceans
甲殻類		17395 (54.9%)
74 (42.8%)
157 (90.8%)
147 (85.0%)
161 (93.1%)
Cephalopods
軟体動物（頭足類）		33 (100.0%)
3 (100.0%)
3 (100.0%)
3 (100.0%)
3 (100.0%)
Other marine invertebrates
その他無脊椎動物		3826 (68.4%)
20 (52.6%)
33 (86.8%)
33 (86.8%)
33 (86.8%)
Total
総計		6,2443,693 (59.1%)
3,777 (60.5%)
5,539 (88.7%)
4,990 (79.9%)
5,719 (91.6%)

Comparison with the IUCN Red List (tsv) 🔗︎

Conservation Status
in the Japanese
Red List		Conservation Status
in the IUCN Red List
EXEWCRENVUNTLCDD—All
EX
絶滅		6051014985111
EW
野生絶滅		010000111114
CR
絶滅危惧IA類		10382283668633779
EN
絶滅危惧IB類		00859148508658805
CR+EN
絶滅危惧I類		2031171732500563
VU
絶滅危惧II類		002194526105191,4091,625
NT
準絶滅危惧		001212919150201,2851,525
DD
情報不足		304182296918625768
LP
絶滅のおそれのある地域個体群		0001112022954
Total
総計		12161152126684721175,2356,244

Changes of red list coverage with genome data over time 🔗︎

20 most recent genomes 🔗︎

Conservation
Status		Red List SectionOrganismAccessionDateSubmitter
DD
情報不足		Birds
鳥類		Anser cygnoides
サカツラガン		GCA_040182565.12024-06-14Jiangsu Agri-animal Husbandry Vocational College
CR
絶滅危惧IA類		Mammals
哺乳類		Dugong dugon
ジュゴン		GCA_040182945.12024-06-14Institute of Deep-sea Science and Engineering
DD
情報不足		Brackish and freshwater fishes
汽水・淡水魚類		Anguilla bicolor pacifica
ニューギニアウナギ		GCA_039654925.22024-06-14ChungAng University
DD
情報不足		Saltwater fishes
海産魚類		Heptranchias perlo
エドアブラザメ		GCA_035084135.22024-06-14Vertebrate Genomes Project
LP
絶滅のおそれの
ある地域個体群		Mammals
哺乳類		Cervus nippon
馬毛島のニホンジカ		GCA_040085125.12024-06-06Northeast Forestry University
VU
絶滅危惧II類		Vascular plants
維管束植物		Moehringia trinervia
タチハコベ		GCA_964106765.12024-06-06WELLCOME SANGER INSTITUTE
VU
絶滅危惧II類		Vascular plants
維管束植物		Moehringia trinervia
タチハコベ		GCA_964106845.12024-06-03WELLCOME SANGER INSTITUTE
VU
絶滅危惧II類		Mammals
哺乳類		Nyctalus aviator
ヤマコウモリ		GCA_036971965.22024-05-31Northeast Normal University
CR
絶滅危惧IA類		Vascular plants
維管束植物		Elymus sibiricus
エゾムギ		GCA_039707655.12024-05-20Northwest Institute of Plateau Biology, Chinese Academy of Sciences
NT
準絶滅危惧		Fungi
菌類		Piptoporus quercinus (Schrad.) P.Karst.
コカンバタケ		GCA_964035675.12024-05-02WELLCOME SANGER INSTITUTE
NT
準絶滅危惧		Fungi
菌類		Piptoporus quercinus (Schrad.) P.Karst.
コカンバタケ		GCA_964035665.12024-05-01WELLCOME SANGER INSTITUTE
NT
準絶滅危惧		Molluscs
貝類		Corbicula japonica
ヤマトシジミ		GCA_038501625.12024-04-29ChungAng University
VU
絶滅危惧II類		Birds
鳥類		Anas formosa
トモエガモ		GCA_038406215.12024-04-22Iridian Genomes
LP
絶滅のおそれの
ある地域個体群		Mammals
哺乳類		Cervus nippon
馬毛島のニホンジカ		GCA_038088365.12024-04-17northwestern polytechnology university
VU
絶滅危惧II類		Other invertebrates
その他無脊椎動物		Ryuthela nishihirai sensu lato
オキナワキムラグモ（広義）		GCA_038380435.12024-04-17Trier University
DD
情報不足		Fungi
菌類		Boletus edulis Bull.
ヤマドリタケ		GCA_038093215.12024-04-12University of Utah
DD
情報不足		Fungi
菌類		Boletus edulis Bull.
ヤマドリタケ		GCA_038089135.12024-04-12University of Utah
CR
絶滅危惧IA類		Mammals
哺乳類		Apodemus agrarius
セスジネズミ		GCA_964023405.12024-04-12Centro Nacional de Análisis Genómico
EN
絶滅危惧IB類		Birds
鳥類		Platalea minor
クロツラヘラサギ		GCA_037975005.12024-04-05The Chinese University of Hong Kong
VU
絶滅危惧II類		Brackish and freshwater fishes
汽水・淡水魚類		Oryzias latipes
ミナミメダカ		GCA_040372325.12024-04-04Environmental Genomics Office, Biodiversity Division, National Institute for Environmental Studies

Submitters of sequenced genomes

Links