Add Lyristes plebejus

[CaroB-M]

Assembly review request

• ToLID: ihLyrPleb1
• Species: Lyristes plebejus
• Project: ERGA-BGE
• Affiliation: Genoscope

[erga-ear-bot]

Hi @CaroB-M, thanks for sending the EAR of Lyristes plebejus.
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: 2026-01-12 10:08

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
DomAbsolon    | Dom Absolon           | Sanger      | 8             | 2025-11-04  | Y      | 0           | 1022          | 1072          
talioto       | Tyler Alioto          | CNAG        | 9             | 2026-01-09  | Y      | 1           | 1030          | 1060          
jesgomez      | Jessica Gomez Garrido | CNAG        | 14            | 2025-12-19  | Y      | 1           | 1026          | 1056          
joannacollins | Jo Collins            | Sanger      | 6             | 2025-10-10  | Y      | 1           | 1024          | 1054          
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1023          | 1053          
SarahPelan    | Sarah Pelan           | Sanger      | 7             | 2025-12-19  | Y      | 1           | 1023          | 1053          
additive3     | Jo Wood               | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1022          | 1047          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
gitcruz       | Fernando Cruz         | CNAG        | 13            | 2025-11-17  | Y      | 2           | 1028          | 1038          
MartinPippel  | Martin Pippel         | SciLifeLab  | 2             | 2025-10-06  | Y      | 2           | 1025          | 1035          
gbdias        | Guilherme Dias        | SciLifeLab  | 4             | 2025-11-19  | Y      | 2           | 1023          | 1033          
tbrown91      | Tom Brown             | IZW         | 11            | 2025-07-29  | Y      | 1           | 996           | 1021          

Selected reviewer: Dom Absolon (DomAbsolon)
The decision was based on:
- different institution ('Sanger')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1072)

[erga-ear-bot]

Hi @DomAbsolon, do you agree to review this assembly?
Please reply to this message only with Yes or No by 16-Jan-2026 at 15:07 CET

[erga-ear-bot]

@DomAbsolon Time is out! I will look for the next reviewer on the list :)

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2026-01-16 21:21

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
gitcruz       | Fernando Cruz         | CNAG        | 14            | 2026-01-14  | Y      | 1           | 1027          | 1057          
jesgomez      | Jessica Gomez Garrido | CNAG        | 14            | 2025-12-19  | Y      | 1           | 1026          | 1056          
gbdias        | Guilherme Dias        | SciLifeLab  | 5             | 2026-01-14  | Y      | 1           | 1023          | 1053          
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1023          | 1053          
joannacollins | Jo Collins            | Sanger      | 7             | 2026-01-16  | Y      | 1           | 1023          | 1053          
DomAbsolon    | Dom Absolon           | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1022          | 1052          
additive3     | Jo Wood               | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1022          | 1047          
talioto       | Tyler Alioto          | CNAG        | 9             | 2026-01-09  | Y      | 2           | 1030          | 1040          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
MartinPippel  | Martin Pippel         | SciLifeLab  | 2             | 2025-10-06  | Y      | 2           | 1026          | 1036          
SarahPelan    | Sarah Pelan           | Sanger      | 7             | 2025-12-19  | Y      | 2           | 1023          | 1033          
tbrown91      | Tom Brown             | IZW         | 11            | 2025-07-29  | Y      | 1           | 996           | 1021          

Selected reviewer: Fernando Cruz (gitcruz)
The decision was based on:
- different institution ('CNAG')
- active ('Y')
- working on 1 PR(s) currently
- highest adjusted calling score in this particular selection (1057)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

[erga-ear-bot]

Hi @gitcruz, do you agree to review this assembly?
Please reply to this message only with Yes or No by 23-Jan-2026 at 02:20 CET

[gitcruz]

Yes El vie, 16 ene 2026, 22:22, erga-ear-bot[bot] ***@***.***> escribió:

…

*erga-ear-bot[bot]* left a comment (ERGA-consortium/EARs#318) <#318 (comment)> Hi @gitcruz <https://github.com/gitcruz>, do you agree to review this assembly? Please reply to this message only with *Yes* or *No* by 23-Jan-2026 at 02:20 CET — Reply to this email directly, view it on GitHub <#318 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB34KVK74AW4WAGFVOOTNHL4HFJAZAVCNFSM6AAAAACRMXN7CCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTONRRHA2TIOBTGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[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.

[erga-ear-bot]

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

[CaroB-M]

Hello @gitcruz and @tbrown91
Have you had a chance to look at this assembly?
Best,
Caroline

[tbrown91]

Hi @CaroB-M

This is looking really nice for a big genome. The only obvious thing I would change is:
haplotig in scaffold_4:108-111Mb

The X chromosome is a little more difficult. I can see for example what looks like missing sequence at ~154Mb and 179Mb. I don't think these are retained haplotypic sequences.

[gitcruz]

Hi @CaroB-M,

I finally took crack on it. Excellent big genome. As @tbrown91 my only worries concern the X chromosome. Personally, I find hard to order and orient all the "blocks" in this chromosome and I am missing the telomere extension (did you try to generate it?).

WRT Tom's comment about the haplotigs, I was looking at the coverage in those regions. It's actually very high, rather than half coverage: so for me either are real tandem duplicates or they come from the Y chromosome...could that be the case?

Coming back to the whole X, I would group the regions that contact more clearly and have similar coverage together and tag the rest as unloc...as I said, no clue on the orientation:

Please let me know what you think.

Minor comment: the TAPAs plot is from the rpecurated assembly right? reading the notes I understood that the reviewed assembly was contaminated.

Question: Is "Context" a contaminant removal tool or a strategy? If it is a tool, could you post the link here?

Thanks.
Fernando

[gitcruz]

Hi @CaroB-M and @tbrown91,

Another thought after the morning coffee: why don't you produce a map for just the X chromosome?

This will drop the resolution from 68K/texel to 10-15K/texel for a 1Gb chromosome. With more resolution meaybe we could tease out haplotigs from tandem repeats and be more sure of the orientation zooming in the boundaries of the different sections.

I know that we are bit short of time because of the deadlines but if you still have the bams it should be relatively quick using PretextMap and the FilterInclude option: https://github.com/sanger-tol/PretextMap?tab=readme-ov-file#new-option-version-01

What do you two think?

Cheers,
Fernando
WRT to the telomere sequence I was consulting Telobase and the most frequent motif for Hemiptera is TTAGG

[CaroB-M]

Hello @gitcruz
thanks a lot for the review.
Concerning Context, this is a tool developped internally, including TAPAS, that we use to assign a taxonomic rank to each contig/scaffold. We first do a gene prediction with metagen (https://metagene.nig.ac.jp/). When we have all gene predictions, we assign a taxonomic rank to them by doing a mapping against NR. Then, we assign a taxonomic rank to each contig/scaffold by using its gene predictions taxonomic assignments and we apply a weighted-LCA to find the taxonomic rank that will be given to the contig/scaffold.
We are currently working on a version that could be distributed.
The TAPAS plot in the EAR is based on the pre curated assembly.
For the X chromosome, I agree that the organization is uncertain. Unfortunately, I didn't keep the bam file, but I just restarted the mapping.

[gitcruz]

Thanks @CaroB-M

Hope you get the mappings done fast so we can look at the X in more detail. The rest of the assembly, looks excellent to me.

Best,
Fernando

[CaroB-M]

Hi @gitcruz
here is the link for the map https://www.genoscope.cns.fr/lbgb/bge/Lyristes_plebejus_X_HighRes.track.map
I'm not sure we can improve the organisation of the X chromosome.
I'll let you take a look!
Thanks

[gitcruz]

Hi @CaroB-M

I finally have a look at the map. It does not look that bad but I'd like you to add the coverage extension. Do you still have the bam of Hifi mapped against the whole assembly?

It will really help to distinguish some false duplications

Thanks
Fernando

[tbrown91]

@CaroB-M are you able to get the coverage track on this map? It's really difficult to tell real duplication/repeat arrays from potential retained haplotypes.

I do appreciate the work done and think it is looking much better

[CaroB-M]

Hello @tbrown91 and @gitcruz , I have added the coverage track to the map. You can use the same link to download it
https://www.genoscope.cns.fr/lbgb/bge/Lyristes_plebejus_X_HighRes.track.map
Best
Caroline

[tbrown91]

Thanks @CaroB-M Given this, I am leaning towards believing that most of these duplications/repeats are genuine.

@gitcruz see what you think

[gitcruz]

I actually think that most of them are artifacts of the contigging (specially those appearing in adjacent contigs). Often the show coverage peaks around them and If I'm right is due to the fact that they share the same secondary alignments. My interpretation is that they have been contigged twice. Also there are some contigs with a repeat structure that contacts strongly in more than one place ***@***.***,605-387,516) that I think should be unplaced. I'd like to prune the map a bit and share a savestate with you two. Please give me some time, I'll try to share a savestate asap. Cheers.

…

On Thu, 12 Feb 2026 at 15:59, Tom Brown ***@***.***> wrote: *tbrown91* left a comment (ERGA-consortium/EARs#318) <#318 (comment)> Thanks @CaroB-M <https://github.com/CaroB-M> Given this, I am leaning towards believing that most of these duplications/repeats are genuine. @gitcruz <https://github.com/gitcruz> see what you think — Reply to this email directly, view it on GitHub <#318 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB34KVN4BNOJ3B7Q3PQ2SWT4LSINDAVCNFSM6AAAAACRMXN7CCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTQOJRGQ2TANJWGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[gitcruz]

Hello again,

I have been trying to clean up a bit the map, but whenever I try to break a contig PretextViewAI v1.0.5 crashes. I triead to clear the cache and started all over, but same problem. It seems to be an issue with single large chromosomes' maps...Tyler had lot of problems with wpGesJame1 too.

Anyway, you can have a look at savestate_3, just moved that contig as unloc, and after that the map looks good to me there. As that contig contacts other repeat, I doubt it really fits in.

My following edit was intended to be this one, I think the sequence after gap@123,013Kb is a FalseDuplicate that was contigged twice:

IMO these are repeat structures that have been alternatively assembled in different contigs, and should be removed.

If you @CaroB-M want to try, let me know if PretextView works for you and which version you use.

Otherwise, If we are uncapable to clean it from "FalseDuplicates" I'll aprove it as at least the overall order seems more or less right.

Anyway let me know what you guys think.

Cheers,
Fernando

[CaroB-M]

Hello @gitcruz
can you give me access to the savestate_3 ?
Thanks

[gitcruz]

oops sorry, i put them in the wrong folder. Could you try here and let me know if it works?
ihLyrPleb1_EAR review

[CaroB-M]

Hello @gitcruz
I have downloaded your savestate 👍 and I have the same issue with PretextView
I will transfer your change to the complete map and regenerate a new EAR
Best

[gitcruz]

Hi @CaroB-M Hold your horses, no need to regenerate a new EAR. Just produce the new fasta and upload it to ENA. I think that there are many false dups in this chromosome, but we cannot remove them with PretextViewAI 1.0.5 I'll follow up with this issue in github. So I will approve immediately, and If @tbrown91 can merge it that would be lovely. Great job @CaroB-M sorry for delaying this so much. Just thought we could improve the X chromosome a bit. Have a nice weekend Fernando

…

On Fri, 13 Feb 2026 at 11:10, CaroB-M ***@***.***> wrote: *CaroB-M* left a comment (ERGA-consortium/EARs#318) <#318 (comment)> Hello @gitcruz <https://github.com/gitcruz> I have downloaded your savestate 👍 and I have the same issue with PretextView I will transfer your change to the complete map and regenerate a new EAR Best — Reply to this email directly, view it on GitHub <#318 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB34KVLM4YAAJTKAW7SMGID4LWPI5AVCNFSM6AAAAACRMXN7CCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTQOJWGI3DENZWHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[erga-ear-bot]

Thanks @gitcruz for the review.
I will add a new reviewed species for you to the table when @tbrown91 merges the PR ;)

Congrats on the assembly @CaroB-M!
Please make sure that the fasta file to upload to ENA is generated based on the final reviewed version of the assembly.

After @tbrown91 confirmation, you can start with the assembly submission to save time.
The PR will be merged only when the final version of the EAR pdf is available.

[CaroB-M]

Thanks @gitcruz

[tbrown91]

Thanks both