Genome sequence data availability
for the Japanese Red List

Updated on 2024-10-01

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		779721 (92.6%)
32 (4.1%)
EN
絶滅危惧IB類		805763 (94.8%)
20 (2.5%)
CR+EN
絶滅危惧I類		563483 (85.8%)
15 (2.7%)
VU
絶滅危惧II類		1,6251,504 (92.6%)
43 (2.6%)
NT
準絶滅危惧		1,5251,399 (91.7%)
38 (2.5%)
DD
情報不足		768695 (90.5%)
24 (3.1%)
LP
絶滅のおそれのある地域個体群		5449 (90.7%)
8 (14.8%)
Total
総計		6,2445,723 (91.7%)
180 (2.9%)

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		260240 (92.3%)
24 (9.2%)
Insects
昆虫類		877780 (88.9%)
5 (0.6%)
Molluscs
貝類		1,190974 (81.8%)
12 (1.0%)
Other invertebrates
その他無脊椎動物		152148 (97.4%)
5 (3.3%)
Vascular plants
維管束植物		2,1632,088 (96.5%)
27 (1.2%)
Algae
藻類		202152 (75.2%)
3 (1.5%)
Bryophytes
蘚苔類		282282 (100.0%)
2 (0.7%)
Lichen
地衣類		154141 (91.6%)
9 (5.8%)
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%)
21 (9.6%)
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		6,2445,723 (91.7%)
180 (2.9%)

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%)
61 (81.3%)
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		260219 (84.2%)
199 (76.5%)
225 (86.5%)
212 (81.5%)
240 (92.3%)
Insects
昆虫類		877348 (39.7%)
516 (58.8%)
702 (80.0%)
529 (60.3%)
780 (88.9%)
Molluscs
貝類		1,190512 (43.0%)
561 (47.1%)
963 (80.9%)
899 (75.5%)
974 (81.8%)
Other invertebrates
その他無脊椎動物		15291 (59.9%)
90 (59.2%)
145 (95.4%)
134 (88.2%)
148 (97.4%)
Vascular plants
維管束植物		2,1631,458 (67.4%)
1,429 (66.1%)
2,057 (95.1%)
1,961 (90.7%)
2,088 (96.5%)
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%)
77 (50.0%)
140 (90.9%)
105 (68.2%)
141 (91.6%)
Fungi
菌類		15977 (48.4%)
61 (38.4%)
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		1514 (93.3%)
15 (100.0%)
15 (100.0%)
15 (100.0%)
15 (100.0%)
Crustaceans
甲殻類		17396 (55.5%)
75 (43.4%)
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%)
21 (55.3%)
33 (86.8%)
33 (86.8%)
33 (86.8%)
Total
総計		6,2443,721 (59.6%)
3,787 (60.7%)
5,539 (88.7%)
4,993 (80.0%)
5,723 (91.7%)

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
VU
絶滅危惧II類		Vascular plants
維管束植物		Avicennia marina
ヒルギダマシ		GCA_042140295.12024-09-23National Science and Technology Development Agency
NT
準絶滅危惧		Lichen
地衣類		Solorina crocea (L.) Ach.
アカウラヤイトゴケ		GCA_964257125.12024-09-21Spribille Lab
VU
絶滅危惧II類		Lichen
地衣類		Flavocetraria cucullata (Bellardi) Kärnefelt & A.Thell
ウスキエイランタイ		GCA_964257225.12024-09-21Spribille Lab
CR+EN
絶滅危惧I類		Lichen
地衣類		Cornicularia normoerica (Gunnerus) Du Rietz
ミヤマヒジキゴケ		GCA_964254975.12024-09-21Spribille Lab
CR+EN
絶滅危惧I類		Lichen
地衣類		Usnocetraria oakesiana (Tuck.) M.J. Lai & J.C. Wei
オアケシゴケ		GCA_964254695.12024-09-21Spribille Lab
VU
絶滅危惧II類		Vascular plants
維管束植物		Tanacetum vulgare
エゾヨモギギク		GCA_964264315.12024-09-21WELLCOME SANGER INSTITUTE
VU
絶滅危惧II類		Vascular plants
維管束植物		Tanacetum vulgare
エゾヨモギギク		GCA_964264305.12024-09-21WELLCOME SANGER INSTITUTE
NT
準絶滅危惧		Lichen
地衣類		Parmotrema rampoddense (Nyl.) Hale
コナマツゲゴケ		GCA_964254915.12024-09-21Spribille Lab
CR
絶滅危惧IA類		Lichen
地衣類		Flavopunctelia flaventior (Stirt.) Hale
ハクテンヒメキウメノキゴケ		GCA_964257575.12024-09-21Spribille Lab
CR
絶滅危惧IA類		Saltwater fishes
海産魚類		Epinephelus lanceolatus
タマカイ		GCA_041903045.12024-09-12Yellow Sea Fisheries Research Institute
NT
準絶滅危惧		Brackish and freshwater fishes
汽水・淡水魚類		Misgurnus anguillicaudatus
ドジョウ		GCA_041755355.12024-09-05Huazhong Agricultural University
NT
準絶滅危惧		Brackish and freshwater fishes
汽水・淡水魚類		Misgurnus anguillicaudatus
ドジョウ		GCA_041755365.12024-09-05Huazhong Agricultural University
NT
準絶滅危惧		Brackish and freshwater fishes
汽水・淡水魚類		Misgurnus anguillicaudatus
ドジョウ		GCA_041755415.12024-09-05Huazhong Agricultural University
NT
準絶滅危惧		Brackish and freshwater fishes
汽水・淡水魚類		Misgurnus anguillicaudatus
ドジョウ		GCA_041755345.12024-09-05Huazhong Agricultural University
VU
絶滅危惧II類		Bryophytes
蘚苔類		Monosolenium tenerum Griff.
ヤワラゼニゴケ		GCA_041684035.12024-09-03Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences
DD
情報不足		Brackish and freshwater fishes
汽水・淡水魚類		Fibramia lateralis
ワキイシモチ		GCA_041296035.12024-08-15Iridian Genomes
DD
情報不足		Brackish and freshwater fishes
汽水・淡水魚類		Ellochelon vaigiensis
オニボラ		GCA_041107635.12024-08-08Iridian Genomes
CR
絶滅危惧IA類		Saltwater fishes
海産魚類		Thryssa baelama
オオイワシ		GCA_041045025.12024-08-05Iridian Genomes
DD
情報不足		Saltwater fishes
海産魚類		Okamejei kenojei
コモンカスベ		GCA_040805665.12024-07-22Northwestern Polytechnical University
VU
絶滅危惧II類		Vascular plants
維管束植物		Triglochin palustris
ホソバノシバナ		GCA_964197745.12024-07-06WELLCOME SANGER INSTITUTE

Submitters of sequenced genomes

Links