Tree-thinkers Lab✨分子生命史研究室
@kurakulabmsm.bsky.social
Molecular Life History Lab led by Shigehiro Kuraku at National Institute of Genetics in Mishima, Japan. Home of Squalomix & MedakaBase フィールド&分子生物学実験寄り動物ゲノム情報学&分子進化学研究とリテラシー普及@遺伝研
Huge congrats to Sean & Tatiana on their new
@cp-iscience.bsky.social paper!
doi.org/10.1016/j.is...
Tracing the Kazald quartet from sharks to tetrapods—a fantastic milestone for Sean’s PhD journey in Europe. @squalomix4earth.bsky.social pride ! 🦈🧬
@cp-iscience.bsky.social paper!
doi.org/10.1016/j.is...
Tracing the Kazald quartet from sharks to tetrapods—a fantastic milestone for Sean’s PhD journey in Europe. @squalomix4earth.bsky.social pride ! 🦈🧬
February 12, 2026 at 3:49 PM
Huge congrats to Sean & Tatiana on their new
@cp-iscience.bsky.social paper!
doi.org/10.1016/j.is...
Tracing the Kazald quartet from sharks to tetrapods—a fantastic milestone for Sean’s PhD journey in Europe. @squalomix4earth.bsky.social pride ! 🦈🧬
@cp-iscience.bsky.social paper!
doi.org/10.1016/j.is...
Tracing the Kazald quartet from sharks to tetrapods—a fantastic milestone for Sean’s PhD journey in Europe. @squalomix4earth.bsky.social pride ! 🦈🧬
ここから来年度への研究室の外向き（国内）発信のラフな予定です
3月2日 メダカの会でゲノム情報リソース紹介
3月31日 ワークショップ「生命の樹」を主催（まだ参加受付中）
4月 大学院説明会にて研究室紹介
開催日未定 研究会「自然と社会を読み解く分子進化学のフロンティア」を主催
開催日未定 研究会「生命科学を支える分子系統学 2026」を主催
3月2日 メダカの会でゲノム情報リソース紹介
3月31日 ワークショップ「生命の樹」を主催（まだ参加受付中）
4月 大学院説明会にて研究室紹介
開催日未定 研究会「自然と社会を読み解く分子進化学のフロンティア」を主催
開催日未定 研究会「生命科学を支える分子系統学 2026」を主催
February 12, 2026 at 3:40 PM
ここから来年度への研究室の外向き（国内）発信のラフな予定です
3月2日 メダカの会でゲノム情報リソース紹介
3月31日 ワークショップ「生命の樹」を主催（まだ参加受付中）
4月 大学院説明会にて研究室紹介
開催日未定 研究会「自然と社会を読み解く分子進化学のフロンティア」を主催
開催日未定 研究会「生命科学を支える分子系統学 2026」を主催
3月2日 メダカの会でゲノム情報リソース紹介
3月31日 ワークショップ「生命の樹」を主催（まだ参加受付中）
4月 大学院説明会にて研究室紹介
開催日未定 研究会「自然と社会を読み解く分子進化学のフロンティア」を主催
開催日未定 研究会「生命科学を支える分子系統学 2026」を主催
Reposted by Tree-thinkers Lab✨分子生命史研究室
What on earth is a 'fish'?
Inspired by @hankgreen.bsky.social's video 'Sharks Aren't Fish' we've put together this link where you can explore the bony vertebrates on OneZoom (in turquoise), as well as some of his standout examples of thats-not-really-a-fish (in red)
www.onezoom.org/life/@Chorda...
Inspired by @hankgreen.bsky.social's video 'Sharks Aren't Fish' we've put together this link where you can explore the bony vertebrates on OneZoom (in turquoise), as well as some of his standout examples of thats-not-really-a-fish (in red)
www.onezoom.org/life/@Chorda...
July 28, 2025 at 11:33 AM
What on earth is a 'fish'?
Inspired by @hankgreen.bsky.social's video 'Sharks Aren't Fish' we've put together this link where you can explore the bony vertebrates on OneZoom (in turquoise), as well as some of his standout examples of thats-not-really-a-fish (in red)
www.onezoom.org/life/@Chorda...
Inspired by @hankgreen.bsky.social's video 'Sharks Aren't Fish' we've put together this link where you can explore the bony vertebrates on OneZoom (in turquoise), as well as some of his standout examples of thats-not-really-a-fish (in red)
www.onezoom.org/life/@Chorda...
Reposted by Tree-thinkers Lab✨分子生命史研究室
Interested in the newest developments in orthology? Check out the last Quest for Orthologs (QfO9) meeting report:
link.springer.com/article/10.1...
#orthology #function #domains #AI #paralogy
Thanks to @sinamajidian.bsky.social and all co-authors for their valuable contribution.
link.springer.com/article/10.1...
#orthology #function #domains #AI #paralogy
Thanks to @sinamajidian.bsky.social and all co-authors for their valuable contribution.
November 18, 2025 at 11:52 AM
Interested in the newest developments in orthology? Check out the last Quest for Orthologs (QfO9) meeting report:
link.springer.com/article/10.1...
#orthology #function #domains #AI #paralogy
Thanks to @sinamajidian.bsky.social and all co-authors for their valuable contribution.
link.springer.com/article/10.1...
#orthology #function #domains #AI #paralogy
Thanks to @sinamajidian.bsky.social and all co-authors for their valuable contribution.
Reposted by Tree-thinkers Lab✨分子生命史研究室
Folks, it is finally out! Our paper on T2T assemblies of the zebrafish genome is on BioRxiv:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 17, 2025 at 11:22 PM
Folks, it is finally out! Our paper on T2T assemblies of the zebrafish genome is on BioRxiv:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Tree-thinkers Lab✨分子生命史研究室
REGISTRATION IS NOW OPEN!!
Start your countdown; #WCMB2026 is happening exactly one year from now!
Register here: wcmb2026.org/registration
@unoceandecade.bsky.social @vliz.be #marinebiodiversity
Start your countdown; #WCMB2026 is happening exactly one year from now!
Register here: wcmb2026.org/registration
@unoceandecade.bsky.social @vliz.be #marinebiodiversity
Register here
wcmb2026.org
November 17, 2025 at 4:18 PM
REGISTRATION IS NOW OPEN!!
Start your countdown; #WCMB2026 is happening exactly one year from now!
Register here: wcmb2026.org/registration
@unoceandecade.bsky.social @vliz.be #marinebiodiversity
Start your countdown; #WCMB2026 is happening exactly one year from now!
Register here: wcmb2026.org/registration
@unoceandecade.bsky.social @vliz.be #marinebiodiversity
Reposted by Tree-thinkers Lab✨分子生命史研究室
国立遺伝学研究所は、遺伝形質研究系教授または准教授を公募します。2025年12月24日（水）正午必着。採用条件は微生物あるいは微生物に関連した生命現象を対象とする研究分野で優れた業績を持ち、遺伝研核生物リソースを発展させられること。ご応募お待ちしています。募集要項 www.nig.ac.jp/nig/ja/2025/...
遺伝形質研究系 教授又は准教授 公募 応募締切：2025年12月24日(水)正午必着 | 国立遺伝学研究所
遺伝学の中核拠点として生命システムの解明を目指す先端研究や共同利用・共同研究を推進しています。また、総研大 先端学術院 遺伝学コースを併設し大学院教育を行っています。
www.nig.ac.jp
October 27, 2025 at 2:32 AM
国立遺伝学研究所は、遺伝形質研究系教授または准教授を公募します。2025年12月24日（水）正午必着。採用条件は微生物あるいは微生物に関連した生命現象を対象とする研究分野で優れた業績を持ち、遺伝研核生物リソースを発展させられること。ご応募お待ちしています。募集要項 www.nig.ac.jp/nig/ja/2025/...
Reposted by Tree-thinkers Lab✨分子生命史研究室
Lagman, Bergqvist & Kuraku analysed opsin gene evolution in jawless vertebrates, confirming tandem duplications of visual opsins before the vertebrate radiation.
🔗 doi.org/10.1093/molbev/msaf231
#evobio #molbio #opsins
🔗 doi.org/10.1093/molbev/msaf231
#evobio #molbio #opsins
Tandem Gene Clusters as Phylogenetic Anchors Reveal the Hidden History of Vertebrate Visual Opsins
Abstract. The expansion of the visual opsin gene family was a crucial event in the diversification of vertebrate vision in evolution. Additional expansions
doi.org
October 13, 2025 at 8:33 AM
Lagman, Bergqvist & Kuraku analysed opsin gene evolution in jawless vertebrates, confirming tandem duplications of visual opsins before the vertebrate radiation.
🔗 doi.org/10.1093/molbev/msaf231
#evobio #molbio #opsins
🔗 doi.org/10.1093/molbev/msaf231
#evobio #molbio #opsins
Reposted by Tree-thinkers Lab✨分子生命史研究室
Thanks to our whole EBP community for making this milestone possible.
| @bat1kgenomes.bsky.social |
@kurakulabmsm.bsky.social | @atlasea.bsky.social | @biogeneurope.bsky.social | @ergabiodiv.bsky.social | @vertebrategenomes.bsky.social | @invertebrates.bsky.social | @projectpsyche.bsky.social |
| @bat1kgenomes.bsky.social |
@kurakulabmsm.bsky.social | @atlasea.bsky.social | @biogeneurope.bsky.social | @ergabiodiv.bsky.social | @vertebrategenomes.bsky.social | @invertebrates.bsky.social | @projectpsyche.bsky.social |
September 4, 2025 at 4:26 PM
Thanks to our whole EBP community for making this milestone possible.
| @bat1kgenomes.bsky.social |
@kurakulabmsm.bsky.social | @atlasea.bsky.social | @biogeneurope.bsky.social | @ergabiodiv.bsky.social | @vertebrategenomes.bsky.social | @invertebrates.bsky.social | @projectpsyche.bsky.social |
| @bat1kgenomes.bsky.social |
@kurakulabmsm.bsky.social | @atlasea.bsky.social | @biogeneurope.bsky.social | @ergabiodiv.bsky.social | @vertebrategenomes.bsky.social | @invertebrates.bsky.social | @projectpsyche.bsky.social |
Due to a power outage caused by a lightning strike on Sep 5th, the web servers operated by us, incl. #aLeaves (but excl. #gVolante), are currently down.
More information could be posted at the top of this 'annex' page (which is still alive) if the down time lasts long.
github.com/Squalomix/me...
More information could be posted at the top of this 'annex' page (which is still alive) if the down time lasts long.
github.com/Squalomix/me...
GitHub - Squalomix/medaka-annex: Listing of omics data resources for medaka fishes coordinated by Medaka Informatics Team of Japan's National BioResource Project (NBRP), namely Kuraku Lab at National ...
Listing of omics data resources for medaka fishes coordinated by Medaka Informatics Team of Japan's National BioResource Project (NBRP), namely Kuraku Lab at National Institute of Genetics in M...
github.com
September 6, 2025 at 12:47 AM
Due to a power outage caused by a lightning strike on Sep 5th, the web servers operated by us, incl. #aLeaves (but excl. #gVolante), are currently down.
More information could be posted at the top of this 'annex' page (which is still alive) if the down time lasts long.
github.com/Squalomix/me...
More information could be posted at the top of this 'annex' page (which is still alive) if the down time lasts long.
github.com/Squalomix/me...
Travelling back from Intl Basking Shark Conf in Galway, Ireland. It's so important for those studying the species that travels across oceans to connect globally. Huge thanks to everyone who worked hard to make the conf happen.
Love to visit 🇮🇪 again!!
#Squalomix
Love to visit 🇮🇪 again!!
#Squalomix
August 31, 2025 at 5:38 PM
Travelling back from Intl Basking Shark Conf in Galway, Ireland. It's so important for those studying the species that travels across oceans to connect globally. Huge thanks to everyone who worked hard to make the conf happen.
Love to visit 🇮🇪 again!!
#Squalomix
Love to visit 🇮🇪 again!!
#Squalomix
Reposted by Tree-thinkers Lab✨分子生命史研究室
Today we’re introducing a major update to the family seed alignments, protein features, and relationship data visualizations on the Dfam website. In addition, we are adding two new datasets: ULTRA reported tandem repeats, and self-alignments.
Dfam Family Visualization Improvements
Today we’re introducing a major update to how TE family seed alignments, protein features, and relationship data are visualized on the Dfam website. Previously, these datasets were presented separa…
xfam.wordpress.com
August 6, 2025 at 8:56 PM
Today we’re introducing a major update to the family seed alignments, protein features, and relationship data visualizations on the Dfam website. In addition, we are adding two new datasets: ULTRA reported tandem repeats, and self-alignments.
Reposted by Tree-thinkers Lab✨分子生命史研究室
「野生生物を虐げる不法ペット貿易」
自然界から生物が姿を消しているのは，生息地の喪失よりも野生動物のペット取引によるところが大きいかもしれない。
別冊日経サイエンス274『鳥の惑星 飛翔, 渡り, さえずりを科学する』
www.nikkei-science.com/sci_book/bes...
自然界から生物が姿を消しているのは，生息地の喪失よりも野生動物のペット取引によるところが大きいかもしれない。
別冊日経サイエンス274『鳥の惑星 飛翔, 渡り, さえずりを科学する』
www.nikkei-science.com/sci_book/bes...
鳥の惑星 飛翔, 渡り, さえずりを科学する｜日経サイエンス
まえがき 第1章 鳥の飛翔と渡り 羽毛の進化 自然が育んだ鳥の機能美 M. B. ハビブ 渡り鳥の量子コンパス 高精度ナビの仕組み P. J. ホア／ H. モウリットセン 動物たちの磁気感覚 出村政彬 第2章 鳥 … 続きを読む →
www.nikkei-science.com
August 26, 2025 at 1:40 PM
「野生生物を虐げる不法ペット貿易」
自然界から生物が姿を消しているのは，生息地の喪失よりも野生動物のペット取引によるところが大きいかもしれない。
別冊日経サイエンス274『鳥の惑星 飛翔, 渡り, さえずりを科学する』
www.nikkei-science.com/sci_book/bes...
自然界から生物が姿を消しているのは，生息地の喪失よりも野生動物のペット取引によるところが大きいかもしれない。
別冊日経サイエンス274『鳥の惑星 飛翔, 渡り, さえずりを科学する』
www.nikkei-science.com/sci_book/bes...
Confirmed the ties between consortia @ergabiodiv.bsky.social and #Squalomix by visiting at the ERGA booth with @rmwaterhouse.bsky.social at #ESEB2025
August 18, 2025 at 1:12 PM
Confirmed the ties between consortia @ergabiodiv.bsky.social and #Squalomix by visiting at the ERGA booth with @rmwaterhouse.bsky.social at #ESEB2025
New chapter of sex determination, with sharks and rays!
Our study, utilizing embryonic samples from cooperative aquariums, revealed the ancient sex chromosome origin and unique sex determination potentials.
Published today in PNAS
www.pnas.org/doi/full/10....
#Squalomix
Our study, utilizing embryonic samples from cooperative aquariums, revealed the ancient sex chromosome origin and unique sex determination potentials.
Published today in PNAS
www.pnas.org/doi/full/10....
#Squalomix
July 23, 2025 at 5:07 AM
New chapter of sex determination, with sharks and rays!
Our study, utilizing embryonic samples from cooperative aquariums, revealed the ancient sex chromosome origin and unique sex determination potentials.
Published today in PNAS
www.pnas.org/doi/full/10....
#Squalomix
Our study, utilizing embryonic samples from cooperative aquariums, revealed the ancient sex chromosome origin and unique sex determination potentials.
Published today in PNAS
www.pnas.org/doi/full/10....
#Squalomix
Reposted by Tree-thinkers Lab✨分子生命史研究室
\ ⏰まだまだ参加募集中 /
三島市内小学生のみなさま、遺伝研でお待ちしています！！
三島市内小学生のみなさま、遺伝研でお待ちしています！！
【イベント】遺伝学普及会では、7/23（水）三島市内小学生（4〜6年生）対象に「子ども遺伝学講座」を開催いたします。近藤滋先生（遺伝研 所長）が「生物が『変身』する方法」をお話しします。夏休みに楽しく学べる“ふしぎ”を体験しませんか？
📅締切：7/13（土）
🔗詳細： www.nig.ac.jp/nig/ja/2025/...
📅締切：7/13（土）
🔗詳細： www.nig.ac.jp/nig/ja/2025/...
July 4, 2025 at 7:18 AM
\ ⏰まだまだ参加募集中 /
三島市内小学生のみなさま、遺伝研でお待ちしています！！
三島市内小学生のみなさま、遺伝研でお待ちしています！！
Very curious to follow up how the taxa of our interests, particularly Chondrichthyes 🦈, of course, are catalogued under this 'Tree of Sex Consortium' relaunched.
Officially (re-)annoucing the Tree of Sex! Read all about it in JEB below!
🔖The Tree of Sex consortium: A global initiative for studying the evolution of reproduction in eukaryotes
Advanced article version👇
academic.oup.com/jeb/advance-...
📖 Read more: treeofsex.sanger.ac.uk
Follow us here 👉 @treeofsex.bsky.social
#TreeOfSex #Evolution #Genomics #Biodiversity
Advanced article version👇
academic.oup.com/jeb/advance-...
📖 Read more: treeofsex.sanger.ac.uk
Follow us here 👉 @treeofsex.bsky.social
#TreeOfSex #Evolution #Genomics #Biodiversity
July 1, 2025 at 1:22 PM
Very curious to follow up how the taxa of our interests, particularly Chondrichthyes 🦈, of course, are catalogued under this 'Tree of Sex Consortium' relaunched.
Ready for Satellite Symposium at Okinawa Churaumi Aquarium, our long-term scientific partner,
after fruitful days at #ipfc12 in Taipei 🇹🇼.
先週台北で開かれたアジア・パシフィック魚類会議のサテライト研究会が沖縄美ら海水族館で本日開催されます。当研究室が進めてきた、深海適応の分子メカニズムを含むサメ・エイ類のゲノム進化学研究についてその場で紹介します。
ご興味おありでしたら、 #Squalomix で検索ください。
after fruitful days at #ipfc12 in Taipei 🇹🇼.
先週台北で開かれたアジア・パシフィック魚類会議のサテライト研究会が沖縄美ら海水族館で本日開催されます。当研究室が進めてきた、深海適応の分子メカニズムを含むサメ・エイ類のゲノム進化学研究についてその場で紹介します。
ご興味おありでしたら、 #Squalomix で検索ください。
June 14, 2025 at 11:25 PM
Ready for Satellite Symposium at Okinawa Churaumi Aquarium, our long-term scientific partner,
after fruitful days at #ipfc12 in Taipei 🇹🇼.
先週台北で開かれたアジア・パシフィック魚類会議のサテライト研究会が沖縄美ら海水族館で本日開催されます。当研究室が進めてきた、深海適応の分子メカニズムを含むサメ・エイ類のゲノム進化学研究についてその場で紹介します。
ご興味おありでしたら、 #Squalomix で検索ください。
after fruitful days at #ipfc12 in Taipei 🇹🇼.
先週台北で開かれたアジア・パシフィック魚類会議のサテライト研究会が沖縄美ら海水族館で本日開催されます。当研究室が進めてきた、深海適応の分子メカニズムを含むサメ・エイ類のゲノム進化学研究についてその場で紹介します。
ご興味おありでしたら、 #Squalomix で検索ください。
Reposted by Tree-thinkers Lab✨分子生命史研究室
#ERGAReads | Can #genomic analysis estimate past population size? ⌛️📉
Sequentially Markovian coalescent #SMC methods can lead to misleading estimates. Cross-disciplinary collaboration is needed to interpret them accurately. 🧬
🔗 Read more: www.cell.com/trends/genet... @qmul.ac.uk
Sequentially Markovian coalescent #SMC methods can lead to misleading estimates. Cross-disciplinary collaboration is needed to interpret them accurately. 🧬
🔗 Read more: www.cell.com/trends/genet... @qmul.ac.uk
May 14, 2025 at 7:43 AM
#ERGAReads | Can #genomic analysis estimate past population size? ⌛️📉
Sequentially Markovian coalescent #SMC methods can lead to misleading estimates. Cross-disciplinary collaboration is needed to interpret them accurately. 🧬
🔗 Read more: www.cell.com/trends/genet... @qmul.ac.uk
Sequentially Markovian coalescent #SMC methods can lead to misleading estimates. Cross-disciplinary collaboration is needed to interpret them accurately. 🧬
🔗 Read more: www.cell.com/trends/genet... @qmul.ac.uk
Reposted by Tree-thinkers Lab✨分子生命史研究室
#ERGAReads | This week, we highlight Squalomix, our newest associated partner 🦈🧬 #Squalomix tackles key challenges in #elasmobranch genomics through advanced cytological techniques and high-fidelity long-read sequencing.
🔗 f1000research.com/articles/11-...
@kurakulabmsm.bsky.social #sharks #rays
🔗 f1000research.com/articles/11-...
@kurakulabmsm.bsky.social #sharks #rays
June 12, 2025 at 7:24 AM
#ERGAReads | This week, we highlight Squalomix, our newest associated partner 🦈🧬 #Squalomix tackles key challenges in #elasmobranch genomics through advanced cytological techniques and high-fidelity long-read sequencing.
🔗 f1000research.com/articles/11-...
@kurakulabmsm.bsky.social #sharks #rays
🔗 f1000research.com/articles/11-...
@kurakulabmsm.bsky.social #sharks #rays
New preprint from #Squalomix
www.biorxiv.org/content/10.1...
Towards bona fide 'whole-genome' analysis encompassing rDNA, tRNA, histones, centromere, elusive HoxC , ... , while featuring genome size change like shown here for the V2R clusters.
@ebpgenome.bsky.social @ergabiodiv.bsky.social
www.biorxiv.org/content/10.1...
Towards bona fide 'whole-genome' analysis encompassing rDNA, tRNA, histones, centromere, elusive HoxC , ... , while featuring genome size change like shown here for the V2R clusters.
@ebpgenome.bsky.social @ergabiodiv.bsky.social
June 13, 2025 at 12:50 AM
New preprint from #Squalomix
www.biorxiv.org/content/10.1...
Towards bona fide 'whole-genome' analysis encompassing rDNA, tRNA, histones, centromere, elusive HoxC , ... , while featuring genome size change like shown here for the V2R clusters.
@ebpgenome.bsky.social @ergabiodiv.bsky.social
www.biorxiv.org/content/10.1...
Towards bona fide 'whole-genome' analysis encompassing rDNA, tRNA, histones, centromere, elusive HoxC , ... , while featuring genome size change like shown here for the V2R clusters.
@ebpgenome.bsky.social @ergabiodiv.bsky.social
Reposted by Tree-thinkers Lab✨分子生命史研究室
We have extended our abstract submission to June 1st! Get conference details here: www.baskingshark.ie/conference2025
and submit your abstract here: docs.google.com/forms/d/e/1F...
and submit your abstract here: docs.google.com/forms/d/e/1F...
May 23, 2025 at 2:15 AM
We have extended our abstract submission to June 1st! Get conference details here: www.baskingshark.ie/conference2025
and submit your abstract here: docs.google.com/forms/d/e/1F...
and submit your abstract here: docs.google.com/forms/d/e/1F...
Reposted by Tree-thinkers Lab✨分子生命史研究室
GRCz12tu is available on Genbank. This will be one of two genomes that will be considered "reference" genomes, there will also be a GRCz12ab assembly coming. It has entered the NCBI annotation pipeline and will also go into the Ensembl annotation pipeline.
www.ncbi.nlm.nih.gov/datasets/gen...
www.ncbi.nlm.nih.gov/datasets/gen...
Danio rerio genome assembly GRCz12tu
- Danio rerio
www.ncbi.nlm.nih.gov
April 8, 2025 at 9:44 PM
GRCz12tu is available on Genbank. This will be one of two genomes that will be considered "reference" genomes, there will also be a GRCz12ab assembly coming. It has entered the NCBI annotation pipeline and will also go into the Ensembl annotation pipeline.
www.ncbi.nlm.nih.gov/datasets/gen...
www.ncbi.nlm.nih.gov/datasets/gen...