Add Hypericum elodes #216

ldemirdj · 2025-09-02T16:19:18Z

Assembly review request

ToLID: ddHypElod1
Species: Hypericum elodes
Project: ERGA-BGE
Affiliation: Genoscope

erga-ear-bot · 2025-09-02T16:19:51Z

Hi @ldemirdj, thanks for sending the EAR of Hypericum elodes.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

erga-ear-bot · 2025-09-02T16:19:55Z

Hi @tbrown91, do you agree to supervise this assembly?
Please reply to this message only with OK to give acknowledge.

tbrown91 · 2025-09-03T12:45:13Z

ok

erga-ear-bot · 2025-09-03T12:45:52Z

*****
EAR Reviewer Selection Process
Date: 2025-09-03 12:45

All Eligible Candidates:

Github ID | Full Name             | Institution | Total Reviews | Last Review | Active | Busy | Calling Score | Adjusted Score
------------------------------------------------------------------------------------------------------------------------------
jesgomez  | Jessica Gomez Garrido | CNAG        | 7             | 2025-08-07  | Y      | N    | 1021          | 1071          

Selected reviewer: Jessica Gomez Garrido (jesgomez)
The decision was based on:
- different institution ('CNAG')
- active ('Y')
- not busy ('N')
- highest adjusted calling score in this particular selection (1071)

erga-ear-bot · 2025-09-03T12:45:54Z

Hi @jesgomez, do you agree to review this assembly?
Please reply to this message only with Yes or No by 09-Sep-2025 at 18:45 CET

jesgomez · 2025-09-05T10:52:07Z

Yes

erga-ear-bot · 2025-09-05T10:52:48Z

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.

tbrown91 · 2025-09-05T12:06:51Z

Hi @ldemirdj

Let's do what we can to make this as good as it can without Hi-C. There are quite a few chromosome-level assemblies from
Hypericum, although with differing numbers of chromosomes. I wonder if a simple mapping between the assemblies could highlight any remaining haplotigs. The duplication rate appears to be quite high, so it would be nice to get rid of some if possible

Hypericum genomes

auryjm · 2025-09-05T12:35:35Z

Hi @tbrown91 and @ldemirdj,

I’m pasting below an exchange we had with the sample ambassador about the Hypericum genome assembly:
"[...] several Hypericum assemblies are already available, with assembly sizes ranging from 338 Mb to 1,541 Mb. This variation might be due to different ploidy levels. Similarly, the number of chromosomes in this genus appears to vary significantly, from 9 to 20 => https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=55962&assembly_level=2:3
Given these observations, I would expect that the assembly size is correct, potentially due to a different ploidy level similar to that observed in H. androsaemum, H. pulchrum, H. hircinum, and H. hirsutum.[...]"

Please note that, for example, Hypericum perforatum also shows a high rate of duplicated BUSCOs, which may indicate polyploidization events. Be careful when removing suggested allelic contigs or regions, as they might actually correspond to polyploidization events!

Jean-Marc

diegomics · 2025-09-05T12:41:14Z

Hi all, I just remember that you may find interesing to try Inspector here since Hi-C data is not available, just a comment :)

tbrown91 · 2025-09-05T13:31:41Z

Thanks @auryjm

I will give my "philosophical" opinion, and then others can let me know what they think.

If the species is genuinely tetraploid, we should try to either include the contigs from the 2X set of the chromosomes, or reduce it to 1X representation of each chromosome. You will probably have a better idea of whether it is auto-/allo-tetraploid and what is feasible from genomescope and smudgeplots, but looking at the spectra it almost looks like it would better to put back sequences, to account for the missing kmers under what I'm assuming is the homozygous peak.

Are you able to pair the sequences you already have, via something like Dgenies, to get an idea of how many "copies" of the genome are currently included? I note the coverage is also on the lower end for such an assembly, but I would like us to push for as good, or as "complete" as possible.

Before I forget as well, were you able to identify mito and chloroplast sequences? I love OatK for this.

auryjm · 2025-09-05T14:37:09Z

Thank you @tbrown91 ,

I believe it is important to submit a 1n genome, but we cannot exclude the possibility that in the 1n genome all chromosomes are duplicated. If you then look at the 2n genome, you should observe four copies of each region.

For example, Brassica napus contains two genomes, A (B. rapa) and C (B. oleracea). The 1n genome to be submitted is the one composed of 10 A chromosomes and 9 C chromosomes and obvisouly BUSCOs duplicated score is high but this is expected.
It is sometimes not very easy to distinguish between polyploidy and alleles! I remember that for Androsace I did it based on Smudgeplot and SNP detection.

We will have a look, as another plant genome for BGE is in the same situation, except that for that one we do have Hi-C data.

erga-ear-bot · 2025-09-12T21:15:08Z