De novo assembly for Dicty has always been a big challenge, but maybe the newer long read implementations in either Nanopore or PacBio SMRT are immune enough to the homopolymeric repeats to handle it. I don’t think we ever established a project for a high quality AX2 reference, though one would be very useful. There are significant enough genomic differences between the different archival strains of domesticated Dicty that some amount of confirmatory finishing may be necessary. 

> On May 6, 2022, at 8:58 AM, Levin, Tera <[log in to unmask]> wrote:
> 
> ***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.
> Dear Thierry,
> We have been sequencing some strains of D. discoideum near relatives and making nice hybrid nanopore/illumina assemblies lately. If it would be helpful, we’d be happy to collaborate with you or someone else on an Ax2 genome- send us your reads and we could run it through our pipeline.
> 
> I’d imagine that the Ax2 sequences should be close enough to the Ax4 genome that you could do most of your analyses without a full de novo assembly. Still, let me know if you would be interested,
> Tera
> 
> Get Outlook for iOS
> From: DICTY <[log in to unmask]> on behalf of Thierry Soldati <[log in to unmask]>
> Sent: Friday, May 6, 2022 2:25:38 AM
> To: [log in to unmask] <[log in to unmask]>
> Subject: [DICTY] Full Ax2 genome sequences ?!
>  
> Dear Colleagues and amoeba-lovers,
> 
> We want to implement Oxford nanopore sequencing (https://urldefense.com/v3/__https://nanoporetech.com__;!!Dq0X2DkFhyF93HkjWTBQKhk!AE7ieFa6-5nYjA0bSQiTnQuY18CahuTGObhAt5c4zwl__nzsQLBl7KktsBovk_I6gtpMVF4oZW7xnA$ ) to fully sequence both complicated vector constructions and Dicty genomes from KO/KI/CRISPR mutants that are hard to validate by conventional means, such as genomic PCR.
> 
> For this, as we are working with Ax2 (both Gerisch and Ka), we really miss a reference genome.
> 
> Would anybody have fully sequenced and assembled Ax2 genome(s)?
> 
> Maybe the topic would be interesting for the community to discuss in Sterling?
> With best regards,
> 
> Thierry
> 
> ================================================
> Prof. Thierry Soldati
> Department of Biochemistry
> Faculty of Science
> University of Geneva
> 30 quai Ernest Ansermet, Sciences II
> CH-1211-Genève-4, Switzerland
> 
> Tel: +41-22-379-6496
> email: [log in to unmask]
> https://urldefense.com/v3/__https://www.unige.ch/sciences/biochimie/labs/thierry-soldati/research/__;!!Dq0X2DkFhyF93HkjWTBQKhk!AE7ieFa6-5nYjA0bSQiTnQuY18CahuTGObhAt5c4zwl__nzsQLBl7KktsBovk_I6gtpMVF7QmVID_A$ 
> @SoldatiLab
> ================================================
>