Denovo identification of Centromere and Telomere

[Jassipox]

Dear Member,


I am looking for any denovo tool or any idea to locate the centromere and telomere position in the chromosome of plant genome .

Although I have tried the blast for telomere but get few related information but for centromere still looking for any proper solution.


Any related suggestion is welcome!!


Thank you in advance!


Pawan

[PhaseGenomics]

Hi Pawan,

There is a precedent for using Hi-C data to identify centromere locations (Accurate identification of centromere locations in yeast genomes using Hi-C)

This should be possible in plants as well - please PM me if you'd like to discuss further.

[JTH-Genome]

Hi Pawan,

I also would highly recommend Phase Genomics' HiC approach to getting telomere and centromere information. Blasting for it may be tricky since those portions generally don't assemble well. That's changing. Adam Phillippy's lab and others are beginning to get resolutions in these regions.

https://www.nature.com/articles/nbt.4060%20.

https://www.slideshare.net/AdamPhillippy/telomeretotelomere-assembly-of-a-complete-human-x-chromosome