initial commit Aphis_hillerislambersi

[MartinPippel]

Assembly review request

• ToLID: ihAphHill11
• Species: Aphis hillerislambersi
• Project: ERGA-BGE
• Affiliation: SciLifeLab

[erga-ear-bot]

Hi @MartinPippel, thanks for sending the EAR of Aphis hillerislambersi.
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.

[MartinPippel]

quick addition: synteny plots with GCA_976991415.1_ihAphHede1.hap1:
ihAphHill11.ref.karyotype.pdf
ihAphHill11.ref.pdf

[erga-ear-bot]

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

[MartinPippel]

@additive3, @diegomics, @tbrown91 I got pinged?

[diegomics]

Ok I'll take this one

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2026-02-02 17:01

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
jesgomez      | Jessica Gomez Garrido | CNAG        | 16            | 2026-02-02  | Y      | 0           | 1026          | 1076          
EmilieTeo     | Emilie Teodori        | Genoscope   | 16            | 2026-02-02  | Y      | 1           | 1041          | 1071          
joannacollins | Jo Collins            | Sanger      | 7             | 2026-01-16  | Y      | 1           | 1027          | 1057          
DomAbsolon    | Dom Absolon           | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1026          | 1056          
bistace       | Benjamin Istace       | Genoscope   | 12            | 2026-01-21  | Y      | 2           | 1046          | 1056          
auryjm        | Jean-Marc Aury        | Genoscope   | 14            | 2026-01-27  | Y      | 2           | 1043          | 1053          
ldemirdj      | Lola Demirdjian       | Genoscope   | 14            | 2026-01-29  | Y      | 2           | 1043          | 1053          
additive3     | Jo Wood               | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1026          | 1051          
CaroB-M       | Caroline Menguy       | Genoscope   | 18            | 2026-02-02  | Y      | 2           | 1040          | 1050          
msozzoni      | Marcella Sozzoni      | UNIFI       | 0             | NA          | Y      | 3           | 1007          | 1047          
talioto       | Tyler Alioto          | CNAG        | 9             | 2026-01-09  | Y      | 2           | 1032          | 1042          
tbrown91      | Tom Brown             | IZW         | 12            | 2026-01-22  | Y      | 0           | 995           | 1040          
gitcruz       | Fernando Cruz         | CNAG        | 14            | 2026-01-14  | Y      | 2           | 1029          | 1039          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 2           | 1027          | 1037          
SarahPelan    | Sarah Pelan           | Sanger      | 7             | 2025-12-19  | Y      | 2           | 1027          | 1037          

Selected reviewer: Jessica Gomez Garrido (jesgomez)
The decision was based on:
- different institution ('CNAG')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1076)

[erga-ear-bot]

Hi @jesgomez, do you agree to review this assembly?
Please reply to this message only with Yes or No by 06-Feb-2026 at 22:00 CET

[jesgomez]

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.

[jesgomez]

Hi @MartinPippel, thanks for the detailed explanation of the assembly process. Good job doing the manual curation without runninig yahs to bypass the fact of having low quality Hi-C data but still making good use of it.

I only have a few suggestions:
ptg000016_l1 seems a haplotig of SUPER_2
ptg000027_l1 maybe could be unloc or haplotigged to SUPER_2 (despite corresponding to the repetitive end of the chromosomes and it having some signal trough several chromosomes, seems to have a more specific tail to SUPER_2.)
ptg000093_l1 could be unloc to super_X
ptg000011_l1 could be unloced to SUPER_X

Let me know if you agree with these changes. For the rest, I'd say the assembly looks fine. Congratulations!

[diegomics]

I agree, nicely done. Please check the unlocs. Also double check SUPER_1 @ 61,901
I think we can sign off this one after that ;)

[MartinPippel]

Hej @jesgomez, hej @diegomics,

thanks for all your comments - I agree. Haven't looked that closely at the final map and was a bit worried to remove even more.

• I will mark 27l and 16l as haplotigs -> they really show a nice duplication pattern of the start and end of SUPER_2 with corresponding coverage drop
• i will mark 11l and 93l as unlocalized of SUPER_X
• @diegomics: I would try to keep the repeat pattern in SUPER_1 48M vs 61M. I know it looks odd, I also discussed this species in the curation slack channel. I checked the alignment pile in IGV and there is definitely a heterozygous signal. Its a 16Kb gap and 60% of the reads brake but 40% align 'un-soft-clipped' into the gap and there 3 spanning reads too.

Will recreate the EAR today.

[erga-ear-bot]

Attention @jesgomez, the EAR PDF was updated.