Add Messor wasmanni

[SMangenot]

Assembly review request

• ToLID: iyMesWasm6
• Species: Messor wasmanni
• Project: ERGA-BGE
• Affiliation: Genoscope

[erga-ear-bot]

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

[erga-ear-bot]

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

[diegomics]

ok

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2025-10-07 13:25

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
talioto       | Tyler Alioto          | CNAG        | 7             | 2025-09-26  | Y      | 1           | 1024          | 1054          
jesgomez      | Jessica Gomez Garrido | CNAG        | 9             | 2025-09-17  | Y      | 1           | 1023          | 1053          
gitcruz       | Fernando Cruz         | CNAG        | 12            | 2025-10-06  | Y      | 1           | 1020          | 1050          
joannacollins | Jo Collins            | Sanger      | 5             | 2025-03-25  | Y      | 1           | 1019          | 1049          
DomAbsolon    | Dom Absolon           | Sanger      | 5             | 2025-09-04  | Y      | 1           | 1019          | 1049          
SarahPelan    | Sarah Pelan           | Sanger      | 6             | 2025-09-16  | Y      | 1           | 1018          | 1048          
tommathers    | Tom Mathers           | Sanger      | 6             | 2025-09-19  | Y      | 1           | 1018          | 1048          
epaule        | Michael Paulini       | Sanger      | 6             | 2025-09-22  | Y      | 1           | 1018          | 1048          
additive3     | Jo Wood               | Sanger      | 6             | 2025-09-18  | Y      | 1           | 1018          | 1043          
gbdias        | Guilherme Dias        | SciLifeLab  | 1             | 2025-09-26  | Y      | 1           | 1008          | 1038          
MartinPippel  | Martin Pippel         | SciLifeLab  | 2             | 2025-10-06  | Y      | 1           | 1007          | 1037          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 988           | 983           
tbrown91      | Tom Brown             | IZW         | 11            | 2025-07-29  | Y      | 1           | 991           | 966           

Selected reviewer: Tyler Alioto (talioto)
The decision was based on:
- different institution ('CNAG')
- active ('Y')
- working on 1 PR(s) currently
- highest adjusted calling score in this particular selection (1054)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

[erga-ear-bot]

Hi @talioto, do you agree to review this assembly?
Please reply to this message only with Yes or No by 13-Oct-2025 at 19:25 CET

[talioto]

Yes

…

On Oct 7, 2025, at 3:26 PM, erga-ear-bot[bot] ***@***.***> wrote: erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#249) <#249 (comment)> Hi @talioto <https://github.com/talioto>, do you agree to review this assembly? Please reply to this message only with Yes or No by 13-Oct-2025 at 19:25 CET — Reply to this email directly, view it on GitHub <#249 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAI5CMMH73VLMIPXDNMUEXT3WO5O3AVCNFSM6AAAAACIP5Q2BGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTGNZWHA4DSNRQHA>. You are receiving this because you were mentioned.

[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.

[talioto]

SUPER_1_unloc_1: I'm not sure how specific it is to SUPER_1. would be good to check map with higher mq threshold. I'm ok if you leave it, though.
SUPER_7:10.4 Mb internal telomere (check sequence to see if real).
Discontinuity in contact density.
Try SUPER_7:10.4-15.5 (end), invert and place at beginning of SUPER_7. Leave telomere at end of new scaffold. I think it looks better like this.
scaffold_57 unloc to SUPER_7
SUPER_19:1-240kb break and put in chaff. not specific enough.

See my savestate.

[diegomics]

Hi Sophie, I did y quick pass and agree with Tyler's points.
From a quick look, please also check what do you think about the following:
scaffold_59 to unloc of SUPER_2
scaffold_60 to unloc of SUPER_1
scaffold_69 to unloc of SUPER_1
scaffold_73 to unloc of SUPER_15

[erga-ear-bot]

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

[erga-ear-bot]

Attention @talioto, the EAR PDF was updated.

[SMangenot]

Corrections based on your feedback

[talioto]

looking good. does anyone else have more comments? I'm pretty good with it.

[diegomics]

Thanks @talioto, please approve if nothing else from your side. I'll take a last look tomorrow and merge :)

[talioto]

my only concerns are that it's at the limit of EBP contiguity threshold and sex chroms not identified, but other than that, it's quite good.

[diegomics]

All good from my side. I agree, Tyler, it's just below the threshold, but honestly, I think the only way to improve it is by starting the assembly all over again. Maybe tweaking hifiasm a little or trying Flye. @SMangenot, can you expand a little more about the assembly process here in the chat? Did you try something to decrease the fragmentation? I see the hifiasm version is 0.19.5. I don't think that 0.25 will improve a lot but may be worth a try in the future, you can update the approved EAR later (you guys updated a few approved EARs already). Or maybe try Flye increasing the read error rate to increase contiguity? Anyway, please expand a little bit so the full story stays tracked here so we can approve this ;)

[additive3]

Regarding sex chromosomes, hymenoptera typically utilise haplodiploidy where females are diploid and males haploid. There is a sex determining locus (single or multi) but it isn't widely characterised outside of A. melifera.

[erga-ear-bot]

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

[talioto]

SUPER_1: 6.9-7.9 Mb: I don't like that this has contact with subtelomeric sequence on all the other chromosomes and this discontinuity in contact signal at the end of this segment. It suggests the super could be split here, but the other contacts still seem to support keeping in the same super. I am of two minds on this. I think we should leave it the way it is a assume that there was a chromosome fusion event relatively recently.
SUPER_12: 0-1.43 Mb: invert so telomere is at beginning and less off-diagonal signal.
SUPER_14: end: not sure of contig order. I made some changes. See if you like.
See my savestate

[erga-ear-bot]

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

[erga-ear-bot]

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

[diegomics]

hi @SMangenot have you had time to update this?

[SMangenot]

Hello everyone,
Sorry for the delay.
I hope to be able to post a new update before the end of this week.

[erga-ear-bot]

Attention @talioto, the EAR PDF was updated.

[erga-ear-bot]

Attention @talioto, the EAR PDF was updated.

[SMangenot]

I agree with you that it's at the limit of EBP contiguity threshold but we cannot spend any more time on this genome at the moment without a guarantee of results.
Below is the process for analyzing this genome
Assembly of PacBio readsets with Hifiasm (Hifiasm/0.24.0-r703) : 770 contigs/N50 924 285 pb/Cumulative size 334 225 297 pb
Decontamination : 755 contigs/N50 924 285 pb/Assembly cumulative size 334 067 185 pb
Assembly Haplotypic Duplication Purge(purge_dups/1.2.5) : 621 contigs/N50 948 625pb/Assembly cumulative size 327 604 377 pb
Genome Contigs Scaffolding (yahs/1.2.2) : 109 scaffolds/N50 13 841 405pb/ Assembly cumulative size 327 658 177 pb

[diegomics]

Hi @talioto is there anything else on your side with this one?

[erga-ear-bot]

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

[erga-ear-bot]

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

[erga-ear-bot]

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