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Reposted by Tree-thinkers Lab✨分子生命史研究室

Earth BioGenome Project 🌍 @ebpgenome.bsky.social · Sep 4

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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · Sep 6

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...

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

Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · Aug 31

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

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Dfam Database of Transposable Elements @dfam.bsky.social · Aug 6

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

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Reposted by Tree-thinkers Lab✨分子生命史研究室

日経サイエンス @nikkei-science.com · Aug 26

「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...

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

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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · Aug 18

Confirmed the ties between consortia @ergabiodiv.bsky.social and #Squalomix by visiting at the ERGA booth with @rmwaterhouse.bsky.social at #ESEB2025

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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · Jul 23

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

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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · Jul 10

www.science.org/content/arti...

Mutation behind night blindness in humans helps whale sharks see in the dark

Alterations in vision gene allow massive fish to detect blue light in inky depths

www.science.org

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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · Jul 10

www.haaretz.com/science-and-...

Obesity genes evolved 450 million years ago, shark study reveals

***

www.haaretz.com

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Reposted by Tree-thinkers Lab✨分子生命史研究室

国立遺伝学研究所 @nigidenken.bsky.social · Jul 4

\　⏰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！！

国立遺伝学研究所 @nigidenken.bsky.social · Jun 25

【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/...

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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · Jul 1

Very curious to follow up how the taxa of our interests, particularly Chondrichthyes 🦈, of course, are catalogued under this 'Tree of Sex Consortium' relaunched.

Tree of Sex @treeofsex.bsky.social · May 12

Officially (re-)annoucing the Tree of Sex! Read all about it in JEB below!

Aurora Ruiz-Herrera @aruizherrera.bsky.social · May 12

🔖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

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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · Jun 14

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。

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ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · May 14

#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

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Reposted by Tree-thinkers Lab✨分子生命史研究室

ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · Jun 12

#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

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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · Jun 13

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

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Irish Basking Shark Group @irishbaskingshark.bsky.social · May 23

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...

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Reposted by Tree-thinkers Lab✨分子生命史研究室

Shawn Burgess @burgesslab.bsky.social · Apr 8

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...

Danio rerio genome assembly GRCz12tu

- Danio rerio

www.ncbi.nlm.nih.gov

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Reposted by Tree-thinkers Lab✨分子生命史研究室

Earth BioGenome Project 🌍 @ebpgenome.bsky.social · May 22

(3/4) 🌍 The EBP dream-team are sequencing genomes 🧬 to accelerate #research, improve protections, and identify the species that make up critical ecosystems.
🧬Dive into these genomes with @kurakulabmsm.bsky.social, @ergabiodiv.bsky.social, @vertebrategenomes.bsky.social, and many more 🌏

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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · Dec 3

We are based at National Institute of Genetics in Mishima, Japan, close to Suruga Bay >2500m deep & Mt. Fuji >3700m high.

#Squalomix #MedakaBase

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bioRxiv Genomics @biorxiv-genomic.bsky.social · May 16

Empowering medaka fish biology with versatile genomic resources in MedakaBase https://www.biorxiv.org/content/10.1101/2025.05.13.653297v1

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Reposted by Tree-thinkers Lab✨分子生命史研究室

RepeatMasker Project @repeatmasker.bsky.social · May 5

RepeatMasker 4.1.9 released. This release includes fixes for ProcessRepeats (speed issues, and divide-by-zero), a
fix for clade-level pHMM (nhmmer) searches, and some minor utility/documentation updates. See the www.repeatmasker.org for more release details.

RepeatMasker Home Page

www.repeatmasker.org

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Reposted by Tree-thinkers Lab✨分子生命史研究室

Trends in Genetics @cp-trendsgenetics.bsky.social · May 5

“Intragenomic mutational heterogeneity: structural and functional insights from gene evolution”

by Yuichiro Hara & Shigehiro Kuraku (@kurakulabmsm.bsky.social)

FREE access till June 24th at this link:
authors.elsevier.com/a/1l2K3cQbJF...

Figure 1. Genomic and epigenetic features contributing to and resulting from the intragenomic heterogeneity of mutations.
The genomic regions shown in red and cyan indicate the genomic compartments with the intragenomic heterogeneity.

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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · Apr 24

www.treethinkers.info/post/%E6%96%...

新年度近況いろいろ

3月は中旬に札幌での日本生態学会、そして下旬に相模原の北里大での日本水産学会に参加しました。前者には毎回参加しているわけではありませんが、今回は日本の希少生物のゲノム情報の集積状況について紹介しました（発表スライド; さらに参考、以前の記事）。後者の会では発表はありませんでしたが、最新の話題を追うとともに進行中の共同研究やこれから着手する連携研究についての相談も兼ねて参加しました。4月に入り、学振...

www.treethinkers.info

Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · Apr 15

Our research on sharks and rays conducted in National Institute of Genetics, Japan, at the foot of Mt Fuji has just been introduced at #PacBioPRISM.

#Squalomix

Lab HP www.nig.ac.jp/nig/research...

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Zebrafish Rock! @zebrafishrock.bsky.social · Apr 14

Learn about the internationally-diverse Phng Lab @riken-bdr.bsky.social 🇲🇾 🇦🇺 🇯🇵 🇨🇳 🇺🇦 🇲🇲 🇮🇳 🐟 #zebrafish @phnglab.bsky.social

the Node @the-node.bsky.social · Apr 14

Lab Meeting with the Phng Lab

Meet the lab of @phnglab.bsky.social, based @riken-bdr.bsky.social, Kobe, Japan. The lab is interested in vascular #morphogenesis, in particular, endothelial cell mechanobiology in #zebrafish 🐟

Find out more about the lab and what it's like working at RIKEN BDR:

Lab Meeting with the Phng Lab - the Node

Meet the Phng Lab, based at the RIKEN Center for Biosystems Dynamics Research, Japan. The lab is interested in vascular morphogenesis and, in particular, endothelial cell mechanobiology.

thenode.biologists.com

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