icParSeri upload

[msozzoni]

Assembly review request

• ToLID: icParSeri5
• Species: Parapropus sericeus
• Project: ERGA-BGE
• Affiliation: UNIFI

[erga-ear-bot]

Hi @msozzoni, thanks for sending the EAR of Parapropus sericeus.
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: 2026-02-23 08:36

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
CaroB-M       | Caroline Menguy       | Genoscope   | 20            | 2026-02-17  | Y      | 0           | 1042          | 1092          
jesgomez      | Jessica Gomez Garrido | CNAG        | 18            | 2026-02-16  | Y      | 0           | 1034          | 1084          
bistace       | Benjamin Istace       | Genoscope   | 15            | 2026-02-20  | Y      | 1           | 1047          | 1077          
gbdias        | Guilherme Dias        | SciLifeLab  | 7             | 2026-02-11  | Y      | 0           | 1025          | 1075          
auryjm        | Jean-Marc Aury        | Genoscope   | 16            | 2026-02-19  | Y      | 1           | 1045          | 1075          
additive3     | Jo Wood               | Sanger      | 9             | 2026-02-13  | Y      | 0           | 1029          | 1074          
EmilieTeo     | Emilie Teodori        | Genoscope   | 18            | 2026-02-17  | Y      | 1           | 1043          | 1073          
talioto       | Tyler Alioto          | CNAG        | 10            | 2026-02-20  | Y      | 1           | 1041          | 1071          
gitcruz       | Fernando Cruz         | CNAG        | 15            | 2026-02-13  | Y      | 1           | 1038          | 1068          
DomAbsolon    | Dom Absolon           | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1030          | 1060          
SarahPelan    | Sarah Pelan           | Sanger      | 8             | 2026-02-18  | Y      | 1           | 1030          | 1060          
tommathers    | Tom Mathers           | Sanger      | 8             | 2026-02-20  | Y      | 1           | 1030          | 1060          
MartinPippel  | Martin Pippel         | SciLifeLab  | 5             | 2026-02-13  | Y      | 1           | 1027          | 1057          
joannacollins | Jo Collins            | Sanger      | 7             | 2026-01-16  | Y      | 2           | 1031          | 1041          
tbrown91      | Tom Brown             | IZW         | 12            | 2026-01-22  | Y      | 0           | 996           | 1041          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 994           | 1039          

Selected reviewer: Caroline Menguy (CaroB-M)
The decision was based on:
- different institution ('Genoscope')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1092)

[erga-ear-bot]

Hi @CaroB-M, do you agree to review this assembly?
Please reply to this message only with Yes or No by 27-Feb-2026 at 13:36 CET

[CaroB-M]

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.

[CaroB-M]

Hello @msozzoni
There is an issue with the gap track because it shows only one gap. So it is not easy to confirm the organization of the scaffolds.
The unloc of the X chromosome seems to have contacts with several other chromosomes so I would not tag it as unloc.
best
Caroline

[erga-ear-bot]

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

[erga-ear-bot]

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

[msozzoni]

Hi all,

I will produce a new pretext map with the correct gap track
I will post it here once it's ready

I am sorry for the delay

[msozzoni]

Hi all,

Here is the pretext with the correct gap track. I am sorry for the delay.
I will change the X_unloc altogether with the new comment.
Thank you in advance

icParSer5.Hap1.1.pretext

[erga-ear-bot]

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

[erga-ear-bot]

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

[erga-ear-bot]

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

[talioto]

@tbrown91 , please finish or @diegomics , assign a new reviewer.

[auryjm]

Hi @msozzoni ,

Thank you for this new assembly. I have taken over the review, as Caroline has been out of the office for the past few months.

This genome is highly fragmented, with a low contig N50, which makes it difficult to validate the internal chromosomal organization. I think these limitations should be documented in the assembly description accompanying the submission so that users are aware of the assembly context and its remaining uncertainties. I performed a number of inversions and several scaffold relocations that, overall, substantially improved the Hi-C contact map.

My main concern is the chromosome number. You painted 17 autosomes plus the X chromosome, but I believe that several chromosomes should be fused. After reviewing the Hi-C data, I ended up with 12 autosomes plus the X chromosome, which is much more consistent with other Leiodidae species. For example, Graciliella metohijensis has 12 autosomes plus the sex chromosomes.

Please find my saved state attached. I think it would be worthwhile to go through the Hi-C map again after applying these proposed changes, and also to compare the resulting assembly against a closely related reference genome.
icParSer5.Hap1.1.pretext.savestate.txt

One final point: several unloc scaffolds have been moved to different chromosomes. I think they should be renamed before generating the final assembly; otherwise, they will retain the names of their original chromosomes.

[msozzoni]

Hi @auryjm

Thank you for the review. I agree with all the changes you have made and will go through the HiC map again after I apply your changes. I will also add a comment about the low N50 on the final submission as suggested.

I too was concerned about the number of chromosomes, but I was wary about checking with an alignment to a close species, as it was discouraged in another Leiodidae species I have assembled (Anthroherpon ganglbaueri). If you think an alignment or at least a comparison will be helpful, I will perform it and get back to you with the results.