Various Schizo ortholog related

[ValWood]

1. We need to update the pombe japonicus ortholog table to represent Li-lins SOGs.
   This uses better ortholog detection methods, and a more complete japonicus assembly

2. A list of pombe genes (using SOGS) that are absent in japonicus and versatilis

3. A list of genes conserved in versitilus and japonicus but absent from pombe

Data check the new list should include these missing pairs (plus others, these are the ones @snezhkaoliferenko spotted
SPAC11D3.14c SZJAPO_01995
SPAC11D3.14c SZJAPO_01995
SPBC23G7.16 SZJAPO_07212

[kimrutherford]

We need to update the pombe japonicus ortholog table to represent Li-lins SOGs. This uses better ortholog detection methods, and a more complete japonicus assembly

Would it be worth including more of the SOG results for the current gene in the orthologs section? Are any other species studied enough to add?

[ValWood]

The main issue will be that some of the S. japonicus ORFS are not in JaponicusDB.
We should probably switch to @lilindu 's assembly which is more complete.

@lilindu where is the best place to get the new annotated assembly ?

I think we can hold off adding other orthologs as they are immediately available in the SOGS, and we would link them to the SGA pages anyway...

[lilindu]

Val and Kim,

Our S. japonicus genome assembly has been published (https://pubmed.ncbi.nlm.nih.gov/38450805/) and is accessible at NCBI (https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_032883015.1/). But this NCBI version is without gene annotation.

We are not ready to release the annotation yet, as, on one hand, Guo-Song Jia (@guosongjia) in my lab is still actively polishing it, and on the other hand, we hope that the improved gene annotations will be one of the selling points of a manuscript we are preparing. We plan to release the annotation once we post the manuscript on bioRxiv, hopefully within this year.

[ValWood]

thanks Li-Lin, we will wait.

Kim for now you could prepare the lists we need from SOGs, but we won't update PomBase yet.

[kimrutherford]

Kim for now you could prepare the lists we need from SOGs, but we won't update PomBase yet.

As a first step, I've added the SOG table to SVN:
pombe-embl/orthologs/sog_gene_table-2026-05-19.tsv

[kimrutherford]

A list of pombe genes (using SOGS) that are absent in japonicus and versatilis

There are 228 SOGs where there is no japonicus and versatilis gene but there is a pombe gene or genes, and a gene present in one or more of cryophilus, octosporus, lindneri or osmophilus:

genes_in_pombe_not_japonicus.tsv

(247 pombe genes in total)

A list of genes conserved in versitilus and japonicus but absent from pombe

There are 16 genes in this set. 2 aren't in JaponicusDB:

• SJAG_07121 / SZJAPO_07121
• SJAG_07127 / SZJAPO_07127

The other 14:
https://www.japonicusdb.org/results/from/id/feb636ea-2bbb-43ed-95a2-8d5be8fa09f0

• SJAG_02961
• SJAG_03665
• SJAG_01741
• SJAG_01968
• SJAG_00713
• SJAG_00097
• SJAG_02143
• SJAG_02179
• SJAG_00450
• SJAG_05920
• SJAG_03675
• SJAG_05344
• SJAG_01594
• SJAG_02710

[ValWood]

First set as a one-per-line list
genes_in_pombe_not_in_japonicus.txt

[ValWood]

I have Unknown identifiers: SPB2025.22_a SPB2025.23_b SPB2025.24_c need to not sure where they come from?

[kimrutherford]

I have Unknown identifiers: SPB2025.22_a SPB2025.23_b SPB2025.24_c need to not sure where they come from?

In the SOG table it looks like:
SPB2025.22|mal1_a, SPB2025.23|mal1_b, SPB2025.24|mal1_c

[ValWood]

@snezhkaoliferenko
This is the list that should probably have japonicus ortholog added

https://www.pombase.org/results/from/id/98aa8a88-b782-45a9-97b7-390228596b16

the list includes the 2 you mentioned

i'll work through these

[ValWood]

hi @guosongjia,

I think SPAC7D4.14c is definitely present in cryophilus (and likely other schizos)
jackhmmr:
S9W246 | Uncharacterized protein | Schizosaccharomyces cryophilus | 7.9e-268

[snezhkaoliferenko]

Thank you guys! Sorry, I was away at the Crick PI retreat which was crazy busy (including brainstorming with Júrg), just got back. I'll look at the lists. Re: the list of present in japonicus+versatilis but absent in other fission yeast species - the one Kim made has those that are absent in pombe but present in other species, including japonicus and versatilis. Would it be possible to have those which are present JUST in japonicus and versatilis? Sorry to trouble you! Thank you again! Sx

…

________________________________ From: Val Wood ***@***.***> Sent: 19 May 2026 14:17 To: pombase/website ***@***.***> Cc: Snezhana Oliferenko ***@***.***>; Mention ***@***.***> Subject: Re: [pombase/website] Various Schizo ortholog related (Issue #2500) [https://avatars.githubusercontent.com/u/7359272?s=20&v=4]ValWood left a comment (pombase/website#2500)<#2500 (comment)> @snezhkaoliferenko<https://github.com/snezhkaoliferenko> This is the list that should probably have japonicus ortholog added https://www.pombase.org/results/from/id/98aa8a88-b782-45a9-97b7-390228596b16 the list includes the 2 you mentioned i'll work through these — Reply to this email directly, view it on GitHub<#2500 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AUYNMT56WH4DID756G4IOED43RNFJAVCNFSM6AAAAACZBGSGSGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DIOBYGEZDENRXG4>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[kimrutherford]

Would it be possible to have those which are present JUST in japonicus and versatilis

There are 354 japonicus genes present only in japonicus and versatilis. From 240 SOGs:
sog_japonicus+versatilis_only.tsv

Please let me know if you'd like that in a different format.

232 of those genes are in JaponicusDB (if SZJAPO_01362 is the same as SJAG_01362 etc.):
https://www.japonicusdb.org/results/from/id/8d7ab741-ea74-406e-aa37-f76c91f28fc8

33 of those 232 have orthologs in JaponicusDB so maybe SZJAPO_01362 isn't the same as SJAG_01362 etc.?:
https://www.japonicusdb.org/results/from/id/70094c75-8dff-45cc-b98d-86d5a1197ce0

91 aren't in JaponicusDB: missing.txt

There are also 9 SOGs that are japonicus only (so not even in versatilis):
sog_japonicus_only.tsv

And 7 that are only in versatilis:
sog_versatilis_only.tsv