Add Pseudanchomenus aptinoides

[SMangenot]

Assembly review request

• ToLID: icPseApti1
• Species: Pseudanchomenus aptinoides
• Project: ERGA-BGE
• Affiliation: Genoscope

[erga-ear-bot]

Hi @SMangenot, thanks for sending the EAR of Pseudanchomenus aptinoides.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

[erga-ear-bot]

Hi @tbrown91, do you agree to supervise this assembly?
Please reply to this message only with OK to give acknowledge.

[tbrown91]

ok

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2026-02-11 10:17

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
joannacollins | Jo Collins            | Sanger      | 7             | 2026-01-16  | Y      | 1           | 1030          | 1060          
DomAbsolon    | Dom Absolon           | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1029          | 1059          
MartinPippel  | Martin Pippel         | SciLifeLab  | 4             | 2026-01-30  | Y      | 1           | 1026          | 1056          
jesgomez      | Jessica Gomez Garrido | CNAG        | 17            | 2026-02-09  | Y      | 1           | 1026          | 1056          
gbdias        | Guilherme Dias        | SciLifeLab  | 6             | 2026-01-23  | Y      | 1           | 1024          | 1054          
additive3     | Jo Wood               | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1029          | 1054          
talioto       | Tyler Alioto          | CNAG        | 9             | 2026-01-09  | Y      | 2           | 1033          | 1043          
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 2           | 1030          | 1040          
SarahPelan    | Sarah Pelan           | Sanger      | 7             | 2025-12-19  | Y      | 2           | 1030          | 1040          
tbrown91      | Tom Brown             | IZW         | 12            | 2026-01-22  | Y      | 0           | 995           | 1040          
gitcruz       | Fernando Cruz         | CNAG        | 14            | 2026-01-14  | Y      | 2           | 1030          | 1040          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
msozzoni      | Marcella Sozzoni      | UNIFI       | 1             | 2026-02-05  | Y      | 2           | 1007          | 1017          

Selected reviewer: Jo Collins (joannacollins)
The decision was based on:
- different institution ('Sanger')
- active ('Y')
- working on 1 PR(s) currently
- highest adjusted calling score in this particular selection (1060)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

[erga-ear-bot]

Hi @JoannaCollins, do you agree to review this assembly?
Please reply to this message only with Yes or No by 17-Feb-2026 at 15:16 CET

[tbrown91]

Hey @SMangenot this one is really challenging. I've had a go at trying to incorporate what I can. There are a few unlocs I moved as well. See what you think. Hopefully some fresh eyes of another reviewer will also help
icPseApti1_hr.pretext.map.savestate_1_tom.gz

[JoannaCollins]

yes

[erga-ear-bot]

Thanks for agreeing!
I appointed you as the EAR reviewer.
I will track this as one of your Working PRs until you finish this review.
Please check the Wiki if you need to refresh something. (and remember that you must download the EAR PDF to be able to click on the link to the contact map file!)
Contact the PR assignee for any issues.

[ldemirdj]

Hi, any update on this ? Thanks @JoannaCollins :)

[JoannaCollins]

Hi @ldemirdj

I took a couple of days leave so only just getting to it now.

[JoannaCollins]

Hi @SMangenot

I have taken a look at the assembly and agree with @tbrown91 that this very challenging data to work with. I have made some changes, and also tried to add some more of the unassigned data to the exisiting chromosomes. I have attached my save state for you to take a look.

I am unable to find a published karyotype for this species but i am concerned there may be joins between some of these chromosomes that are not evident due to the poor quality of the data. We frequently see examples in coleoptera where chromosomes are hard to pull together due to the vast quantity of hetrochromatic sequence that sits between the chromosome arms, this results in the HIC signal between the more euchromatic regions being very weak. One thing that we have found that can help to see the relationship between chromosome arms is to use a normal resoultion map (default map quality 0) also a normal map using map quality 10. So I think it would be really useful if you were able to remake your map with the aforementioned parameters so we could take a look and see if that helps to confirm the assemble of the chromosomes.

Please let me know if you have any questions.

icPseApti1_hr.pretext.map.savestate_1_jcc.txt

Thanks very much, Jo

[erga-ear-bot]

Ping @tbrown91,
One week without any movements on this PR!

[tbrown91]

@auryjm is anyone able to pick this up on your end?

[erga-ear-bot]

Attention @JoannaCollins, the EAR PDF was updated.

[SMangenot]

Hi @JoannaCollins
I am also sending you the normal map using map quality 10
https://www.genoscope.cns.fr/lbgb/bge/icPseApti1_nm.pretext.map

[JoannaCollins]

Hi @SMangenot,

Thank you for sending the updated map :-), and sorry for the delay in getting back to you.

I asked Jo Wood (@additive3 ) to take a look at this one as i was still concerned about chromosome numbers and the data is tricky to interpret. Having assessed this yesterday he suggested that a number of the units currently tagged as chromosomes are likely not chromosomes (chrs 3, 5,10, 17, 21). For 10, 17 and 21 you can see that they all hit heavily to the repetitive scaffolds in the shrapnel this repeat should be unasigned. For chromosomes 3 and 5, these are half cov and Jo suspects these repeats may be Y linked.

In order to try and fully resolve the assembly would it be possible for you to send the precurated combined pri/alt map (both normal mq0 and mq10). If it doesn't already exist it would be really good if you are able to generate this to try and unpick which scaffolds are part of which chromosomes.

Thanks very much

Jo

[auryjm]

Hi @JoannaCollins , @additive3, @SMangenot and @tbrown91 ,

For this tricky assembly, unfortunately we do not have the primary/alternate assemblies, as the scaffolding was performed from the collapsed assembly. I had a look at the map and, apart from chromosomes 3, 5, 10, 17, and 21, which I agree appear to correspond to repetitive regions, the others look good and of sufficient quality.

I propose moving these chromosomes to the shrapnel as unplaced sequences, adding some explanations in the assembly description, and finalizing the assembly so that we can move forward. What do you think?

Jean-Marc

[JoannaCollins]

Hi @auryjm, @SMangenot and @tbrown91 ,

@additive3 and I have had a discussion about this assembly today and both agree that given the quality of the data your proposal to unassign current chrs 3, 5, 10, 17, and 21 and add a comment to the assembly description is the most logical thing to do in this scenario.

Best Wishes

Jo

[erga-ear-bot]

Attention @JoannaCollins, the EAR PDF was updated.

[erga-ear-bot]

Attention @JoannaCollins, the EAR PDF was updated.

[JoannaCollins]

Hi @SMangenot,@auryjm and @tbrown91,

Thanks for uploading the updated map :-).

I have had a look through and there are just a couple of things to correct.

It looks like there my have been a painting/tagging error as in the assembly there is a SUPER_16 and 3 SUPER_16 unlocs but all of these are tiny scaffolds so these need unpainting/tagging. The observed chr number in the assembly report will then also need updating.

I would unassign SUPER_10_unloc_1 as i don't think we can say it defintely belongs with SUPER_10.

The first 2 chromosomes are half coverage, you might want to consider assigning the sex chromosomes if you can find a close releative to align the data to.

Any questions please let me know

Best Wishes

Jo

[erga-ear-bot]

Attention @JoannaCollins, the EAR PDF was updated.

[tbrown91]

@SMangenot The only thing I would say about this one is in relation to @JoannaCollins' about the first two scaffolds. These seem to be very clearly at lower coverage than the rest of the assembly, so I would lean towards tagging them as sex chromosomes.

Other than that, I think we can probably wrap this up. @additive3 please have a look through in case you want to add anything

[JoannaCollins]

Hi @SMangenot,@auryjm and @tbrown91,

Thanks very much for sending on the updated map :-).

Having had a chat with @additive3 we feel its ok not to assign the reamaining half coverage chromosomes if we can't be certain of their assignment.

There are 2 remaining issues to fix and then this can be signed off.

SUPER_10: 22.31-24.47Mb - I think this was previously SUPER_10_unloc_1 which i mentioned should be unassigned (and left in the shrapnel as we can't be sure where it goes) has now been jonied to the end of SUPER_10. This needs removing from the end of this chromosomeas you can see there is telo signal where the join has been made.

SUPER_12: needs breaking @ the gap 7.08Mb as there is telo signal here indicating that SUPER_12 splits into 2 chromosomes. In a previous iteration of the map these were 2 seperate chromosomes so at some point have been joined but the telo evidence does point to them being seperate entities.

I have attached a savestate indicating with waymarkers the regions that should be broken off.

Thanks very much

Jo
icPseApti1_hr.pretext.map.savestate_1_jcc_6.8.26.txt