Add Cotoneaster nebrodensis

[auryjm]

Assembly review request

• ToLID: drCotNebr1
• Species: Cotoneaster nebrodensis
• Project: ERGA-BGE
• Affiliation: Genoscope

[erga-ear-bot]

Hi @auryjm, thanks for sending the EAR of Cotoneaster nebrodensis.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

[erga-ear-bot]

Hi @additive3, do you agree to supervise this assembly?
Please reply to this message only with OK to give acknowledge.

[additive3]

OK From: "erga-ear-bot[bot]" ***@***.***> Reply to: ERGA-consortium/EARs ***@***.***> Date: Tuesday, 9 December 2025 at 10:53 To: ERGA-consortium/EARs ***@***.***> Cc: Jo Wood ***@***.***>, Mention ***@***.***> Subject: Re: [ERGA-consortium/EARs] Add Cotoneaster nebrodensis (PR #300) [EXT] erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#300) [github. com] Hi @additive3 [github. com], do you agree to supervise [github. com] this assembly? Please reply to this message only with OK to give acknowledge. — Reply to this email [Image removed by sender.]erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#300) [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_300-23issuecomment-2D3618033810&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=gh65eXP55ma8-gkinD3SQdMmthts8nCE_FQn6MDwVMiy_jOG_yHygzSLejdHefsw&s=bCxY8bX8sCx0r-xff48RVopJT4c3dsS3eZwqn59nxRU&e=> Hi @additive3 [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_additive3&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=gh65eXP55ma8-gkinD3SQdMmthts8nCE_FQn6MDwVMiy_jOG_yHygzSLejdHefsw&s=FC7NKrgcrsNgYMkAvBuz1b8xI1IW11Gqc4CKX9-8YDo&e=>, do you agree to supervise [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_wiki_Assignees-2Dsection&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=gh65eXP55ma8-gkinD3SQdMmthts8nCE_FQn6MDwVMiy_jOG_yHygzSLejdHefsw&s=09cEBn-V3WEc58cTz78NLZJAR4-P4Pcqwca8LzKMVRo&e=> this assembly? Please reply to this message only with OK to give acknowledge. — Reply to this email directly, view it on GitHub [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_300-23issuecomment-2D3618033810&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=gh65eXP55ma8-gkinD3SQdMmthts8nCE_FQn6MDwVMiy_jOG_yHygzSLejdHefsw&s=bCxY8bX8sCx0r-xff48RVopJT4c3dsS3eZwqn59nxRU&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AEFJV4KS4X4WYL7LHRO34ND4A2SY5AVCNFSM6AAAAACOFY2IKOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTMMJYGAZTGOBRGA&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=gh65eXP55ma8-gkinD3SQdMmthts8nCE_FQn6MDwVMiy_jOG_yHygzSLejdHefsw&s=k2B3aN_qg07AKWgDPCLlLlbLM1wawA1wvfjSh_6n49I&e=>. You are receiving this because you were mentioned.Message ID: ***@***.***>

…

---------------------------------------------------------------------- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA.

[diegomics]

bot behave... Actually, I think we broke it by messing the supervisor selection system :P
I will talk with @arash77 to introduce something for this cases, maybe we can have a magic word or something

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2025-12-16 11:51

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1023          | 1053          
gbdias        | Guilherme Dias        | SciLifeLab  | 4             | 2025-11-19  | Y      | 1           | 1022          | 1052          
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        | 8             | 2025-10-21  | Y      | 2           | 1030          | 1040          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
gitcruz       | Fernando Cruz         | CNAG        | 13            | 2025-11-17  | Y      | 2           | 1026          | 1036          
jesgomez      | Jessica Gomez Garrido | CNAG        | 13            | 2025-12-04  | Y      | 2           | 1026          | 1036          
MartinPippel  | Martin Pippel         | SciLifeLab  | 2             | 2025-10-06  | Y      | 2           | 1024          | 1034          
SarahPelan    | Sarah Pelan           | Sanger      | 6             | 2025-09-16  | Y      | 2           | 1024          | 1034          
joannacollins | Jo Collins            | Sanger      | 6             | 2025-10-10  | Y      | 2           | 1024          | 1034          
tbrown91      | Tom Brown             | IZW         | 11            | 2025-07-29  | Y      | 1           | 996           | 1021          

Selected reviewer: Tom Mathers (tommathers)
The decision was based on:
- different institution ('Sanger')
- active ('Y')
- working on 1 PR(s) currently
- highest adjusted calling score in this particular selection (1053)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

[erga-ear-bot]

Hi @tommathers, do you agree to review this assembly?
Please reply to this message only with Yes or No by 22-Dec-2025 at 16:49 CET

[tommathers]

no Dr. Thomas Mathers Senior Computer Biologist Genome Reference Informatics Team Tree of Life Wellcome Sanger Institute Hinxton Cambridge CB10 1SA Twitter: @Thomas_Mathers [twitter.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_Thomas-5FMathers-3Flang-3Den-2Dgb&d=DwMGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=tJRHixSYq-VP6FIxTiP35xdkMZl3FaXQVx1qay3XZ-7I4UkhUxDC7h1P98bVhcBb&s=hffLCC65eIfPsnmm3hnO-CV4DYCZYG2ebSippldU3zw&e=> Publications: Google Scholar [scholar.google.co.uk]<https://urldefense.proofpoint.com/v2/url?u=https-3A__scholar.google.co.uk_citations-3Fhl-3Den-26user-3D5XjBm94AAAAJ-26view-5Fop-3Dlist-5Fworks-26sortby-3Dpubdate&d=DwMFAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=KIKynKbLKfS4YVQYVctJHL39ls39CbRogxK7G0OumbwWdwS4Qdlkrg9NnRJHPJGs&s=T2pa4qY1i623xxULQ3x4gTTj4JvNcKbwYHoNm5knTFc&e=> From: "erga-ear-bot[bot]" ***@***.***> Reply to: ERGA-consortium/EARs ***@***.***> Date: Tuesday, 16 December 2025 at 11:51 To: ERGA-consortium/EARs ***@***.***> Cc: Thomas Mathers ***@***.***>, Mention ***@***.***> Subject: Re: [ERGA-consortium/EARs] Add Cotoneaster nebrodensis (PR #300) [EXT] erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#300) [github. com] Hi @tommathers [github. com], do you agree to review this assembly? Please reply to this message only with Yes or No by 22-Dec-2025 at 16: 49 CET — Reply to this email [Image removed by sender.]erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#300) [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_300-23issuecomment-2D3660142777&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=uM3WjhrmM86vIDZPejxvQInGOXnWxDGQJ1pjQ_y_mEMXSSfhIwakP-o_l_i2d4G2&s=hoPtn8W4yMLHCLLZxwFqh1YBckCIT7N0ukClYs9ugug&e=> Hi @tommathers [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_tommathers&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=uM3WjhrmM86vIDZPejxvQInGOXnWxDGQJ1pjQ_y_mEMXSSfhIwakP-o_l_i2d4G2&s=yYS51ig6vzFNLQkSKzI-bvr1Dxljyhei-ne3ilMGreg&e=>, do you agree to review this assembly? Please reply to this message only with Yes or No by 22-Dec-2025 at 16:49 CET — Reply to this email directly, view it on GitHub [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_300-23issuecomment-2D3660142777&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=uM3WjhrmM86vIDZPejxvQInGOXnWxDGQJ1pjQ_y_mEMXSSfhIwakP-o_l_i2d4G2&s=hoPtn8W4yMLHCLLZxwFqh1YBckCIT7N0ukClYs9ugug&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABVP3G5OZ63DUFB4SRW5M3T4B7W4PAVCNFSM6AAAAACOFY2IKOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTMNRQGE2DENZXG4&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=uM3WjhrmM86vIDZPejxvQInGOXnWxDGQJ1pjQ_y_mEMXSSfhIwakP-o_l_i2d4G2&s=TB4HRimSWzrDhR1_HJHx441o9LaF1Gat4TM6wP5qzuQ&e=>. You are receiving this because you were mentioned.Message ID: ***@***.***>

…

---------------------------------------------------------------------- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA.

[erga-ear-bot]

@tommathers Ok thank you, I will look for the next reviewer on the list :)

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2025-12-16 12:16

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
gbdias        | Guilherme Dias        | SciLifeLab  | 4             | 2025-11-19  | Y      | 1           | 1022          | 1052          
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        | 8             | 2025-10-21  | Y      | 2           | 1030          | 1040          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
gitcruz       | Fernando Cruz         | CNAG        | 13            | 2025-11-17  | Y      | 2           | 1026          | 1036          
jesgomez      | Jessica Gomez Garrido | CNAG        | 13            | 2025-12-04  | Y      | 2           | 1026          | 1036          
MartinPippel  | Martin Pippel         | SciLifeLab  | 2             | 2025-10-06  | Y      | 2           | 1024          | 1034          
SarahPelan    | Sarah Pelan           | Sanger      | 6             | 2025-09-16  | Y      | 2           | 1024          | 1034          
joannacollins | Jo Collins            | Sanger      | 6             | 2025-10-10  | Y      | 2           | 1024          | 1034          
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 2           | 1023          | 1033          
tbrown91      | Tom Brown             | IZW         | 11            | 2025-07-29  | Y      | 1           | 996           | 1021          

Selected reviewer: Guilherme Dias (gbdias)
The decision was based on:
- different institution ('SciLifeLab')
- active ('Y')
- working on 1 PR(s) currently
- oldest review and fewest reviews among the finalists (1052)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

[erga-ear-bot]

Hi @gbdias, do you agree to review this assembly?
Please reply to this message only with Yes or No by 22-Dec-2025 at 17:16 CET

[gbdias]

Yes

[diegomics]

@gbdias can you reply yes again?

[gbdias]

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.

[gbdias]

Hi @auryjm

Amazing work. Your Hi-C maps are very clear in the chromosome number, and this assembly for a sister species also supports 17 chromosomes.

The AAABB arrangement also looks very clear in your map.

• I noticed one case of putative inter-chromosomal contacts (screenshot below; I put drCotNebr1_26-30 next to 81-85). In this example perhaps a reciprocal switch would produce a better map. By switch I mean moving the end of scaffold 26 (pos ~28Mb until the end) to the beginning of scaf 85, and moving the beginning of scaf85 (pos 1-5.2Mb; it is flipped in the screenshot) to the end of scaf26.

No more comments from my side. Let me know if you think the screenshot above makes sense. I would be happy to approve the pull request as is too.

[auryjm]

Hi @gbdias ,

Thank you for your feedback!
Regarding the swap between scaf26 and scaf85, I agree that the off-diagonal signals look better after the swap; however, the chromosomes themselves are less concordant than before the swap. In my opinion, this reflects a real translocation between scaf26 and scaf85.

I propose to wait for the opinion of @additive3

Before the swap:

After the swap:

[erga-ear-bot]

Ping @additive3,
One week without any movements on this PR!

[erga-ear-bot]

Ping @additive3,
One week without any movements on this PR!