[Xenopus] Xenbase Newsletter Autumn|Fall 2024

Wed Sep 25 12:24:40 EDT 2024

Xenbase Newsletter Autumn|Fall 2024 [text version]

Open PDF to see figures/tables

NEW TOOL Xenbase Simple Synteny Search: 16,000 Xenopus synteny maps!
Synteny, the conserved order of genes on a chromosome, carries valuable information for comparative genomics, phylogenetics and informs gene nomenclature. We have generated new synteny maps comparing X. tropicalis, X. laevis L and X. laevis S sub-genomes, Human, mouse and chick. The maps are based on explicit orthology assertions, combined with symbol matching. Each map shows the gene of interest at center, in yellow, flanked by 5 upstream and 5 downstream gene models. Orthologs/paralogs are shown in same color, connecting matched gene symbols by same-colored lines.
Try it here: https://www.xenbase.org/xenbase/static/gene/synteny.jsp   Just enter a gene symbol, hit search.  It’s not perfect, and LOC genes are currently excluded from the serch, though they do show up in the maps. We are working to expand coverage- the next version will integrate reciprocal BLAST and InParanoid to resolve orthology for more genes.

Test it out and tell us if you find any bugs: Xenbase at cchmc.org<mailto:Xenbase at cchmc.org>

REGISTER NOW for XRET 20224: Xenopus Resources and Emerging Technologies Meeting @ NXR, Woods Hole MA.    Registration closing soon!!
When: Fri, October 11, 2024 — Mon, October 14, 2024
Register here: https://www.mbl.edu/research/resources-research-facilities/national-xenopus-resource/workshops-and-meetings

WORKSHOP GO Jamboree at XRET: Community Curation for Xenopus genes
In the 2024 Xenopus researcher survey, 63% of people said YES, they would be happy to annotate the genes they work on for GO! A community curation workshop will be held on the last day of the XRET meeting in Woods Holes MA. We will train you to use a simple GO annotation tool (called GOAT) to annotate the genes you know best using GO, from your own papers. Just bring your laptop! GO Xenopus! In preparation, register for an ORCID here<https://info.orcid.org/what-is-orcid/>. No need to register for the workshop itself- everyone is welcome!
When:  Monday 9-10.30am Monday October 14th, 2024, XRET Woods Hole.

NEW ANATOMY RESOURCE Xenopus 3D anatomy atlas module from Jakub Harnos’ Lab (Masaryk University, Czech Republic) now on Xenbase.

High-quality X-ray microtomography images cover the lifespan of the African Clawed Frog in unprecedented detail were recently published in Gigascience (doi: 10.1093/gigascience/giae037) and shared with Xenbase, to share with you! All of the microCT data files from this open access resource can be downloaded from Xenbase server. Access the Xenopus 3D atlas files here: https://bigfrog2.xenbase.org/pub/xenbase/images/Laznovsky_3D_Atlas/

NEW XENOPUS BOOK Xenopus Normal Table Redux.
Edited by Peter Vize. Illustrated by Natalya Zahn. A reworked version of Nieuwkoop & Faber’s classic text, the new Xenopus Normal Table Redux merges the beauty, art and science of Natalya Zahn’s extraordinary nature illustrations with the wisdom and richness of the 1956 N&F text, supplemented by new stages (e.g., oogenesis, metamorphs), views, internal and external staging details, and molecular markers. The volume itself is also a work of art! Limited to just 100 copies, it is hand sewn and bound by artist and lecturer Adj. Prof. Sydney Vize (yes, Peter’s daughter!), in a flat large format (12x9.5inches/ 30.5x24cm; 14pt font) that lays flat when opened. It is produced in 4 colors on luxurious egg-shell textured 80lb Neenah paper and will be priced at $300 USD. First copies will be available in October. To reserve your copy, please contact Peter Vize directly: pvize at ucalgary.ca<mailto:pvize at ucalgary.ca>

LAST CHANCE!  The 2024 Xenbase -Xenopus Research community survey.
Thank you to everyone who has replied to our survey questions- you’ve given us lots of great feedback and new ideas… but we’d like to hear from even more people.  The survey is closing soon, so if you can spare us a few minutes, please take it today:  https://forms.gle/5WFANQTKA6TuSyg67

LATEST v10 Xenopus Genome Files for Download
In collaboration with of colleague Taejoon Kwon (UNIST, Rep. Korea), Xenbase has made new downloadable files which you can use for high-throughput data analysis (RNA-Seq and ChIP-Seq) and gene list for GO enrichment. These ‘clean’ files and the most up-to-date gene reports available.
We highly recommend you use v10 Xenopus genome and proteome files for data analysis!

See PDF for scannable QR codes

Click links below to download specific files.( X. laevis files on left, X. tropicalis on right)

Release notes detailing the sources for the data:

   RELEASE.xenLae10.2024_06<https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenLae10/current/RELEASE.xenLae10.2024_06>                                                            RELEASE.xenTro10.2024_06<https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenTro10/current/RELEASE.xenTro10.2024_06>

GFF3 with all non-coding RNAs removed:

                       xenLae10.xb2024_06.sorted.gff3.gz<https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenLae10/current/xenLae10.xb2024_06.sorted.gff3.gz>                                       xenTro10.xb2024_06.sorted.gff3.gz<https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenTro10/current/xenTro10.xb2024_06.sorted.gff3.gz>

FASTA file for CDS in the GFF3:

                    xenLae10.xb2024_06.sorted.gff3_cds.fa.gz<https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenLae10/current/xenLae10.xb2024_06.sorted.gff3_cds.fa.gz>                                            xenTro10.xb2024_06.sorted.gff3_cds.fa.gz<https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenTro10/current/xenTro10.xb2024_06.sorted.gff3_cds.fa.gz>

FASTA file of protein for CDS in the GFF3:

                    xenLae10.xb2024_06.sorted.gff3_prot.fa.gz<https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenLae10/current/xenLae10.xb2024_06.sorted.gff3_prot.fa.gz>                      xenTro10.xb2024_06.sorted.gff3_prot.fa.gz<https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenTro10/current/xenTro10.xb2024_06.sorted.gff3_prot.fa.gz>

FASTA file of mRNA transcripts in the GFF3:

                    xenLae10.xb2024_06.sorted.gff3_tx.fa.gz<https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenLae10/current/xenLae10.xb2024_06.sorted.gff3_tx.fa.gz>                                                 xenTro10.xb2024_06.sorted.gff3_tx.fa.gz<https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenTro10/current/xenTro10.xb2024_06.sorted.gff3_tx.fa.gz>

GTF version of the GFF file:

    xenLae10.xb2024_06.sorted.gtf.gz<https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenLae10/current/xenLae10.xb2024_06.sorted.gtf.gz>         xenTro10.xb2024_06.sorted.gtf.gz<https://download.xenbase.org/xenbase/Genomics/amphibase/annotation/xenTro10/current/xenTro10.xb2024_06.sorted.gtf.gz>

UPDATE FYI Xenopus v10 gene model annotation improvements by Xenbase.
For X. tropicalis, from Jan23 to Jan24, we increased the number of fully annotated genes by 2,103; and we partially curated more than 7,000 more genes, leaving only 800 unannotated/uncharacterized genes in the v10.1 genome.
For X. laevis, we fully annotated 4,961 genes, and improved names and mappings for 2,568 genes. Our work to further improve X. laevis annotations (naming models, mapping orthologs, associating proteins) is ongoing. The latest genome stats will be released in the winter Xenbase newsletter- stay tuned!

Xenbase has a NEW Xenbase YouTube Channel
Check out new movies about Xenopus frogs on our new YouTube channel:
Latest Videos: https://www.youtube.com/@xenbase_mod2
Xenbase tutorials are on YouTube too:
Xenbase Tutorials: https://www.youtube.com/@XenbaseTips
Please like us and subscribe!
You can view, share, and embed video links for your classes, research talks, or viewing pleasure.
If you do reuse these resources, please give copyright attribution to Xenbase (http://www.xenbase.org/, RRID:SCR_003280). BTW, the old channel still exists, but we will post all new material to the new channel. Access the older videos: https://www.youtube.com/@xenbase_mod1

Community Forums: Join the discussion. Pose a Question. Ask for help.
There are 3 community forums Xenopus people use to reach the community, find a collaborator, request a reagent, and get answers.
Get the details of these Xenopus research community groups here: https://www.xenbase.org/xenbase/static-xenbase/xine/xine.jsp

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Follow us on X (#Xenbase_MOK), Blue Sky (@xenbase.bsky.social), Mastodon (@xenbase_mod
Need Help? Have Questions? Contact us via the Xenbase help desk: Xenbase at cchmc.org<mailto:Xenbase at cchmc.org>

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