Conference Paper

The next generation of Asytanax mexicanus genome references

Warren, W.C., Koren, S., Meyer, A. and Rohner, N.

Record Number:
4319
Year:
2019
Abstract:
The experimental use of the Astyanax mexicanus (Mexican tetra) is rapidly expanding due to its many troglomorphic trait adaptations. As a computational instrument, the reference genome is a data model that sits at the center of nearly all genome and transcriptome analysis. Our recent Astyanax mexicanus chromosomal assembly, Astyanax mexicanus 2.0, that was constructed from a single female in a lab-reared cross of wild-caught Astyanax mexicanus surface populations from the Rio Sabinas and the Rio Valles surface localities elevates the level of quality for computational measures of various molecular features. However, we are aware of the need for continued improvement of this community resource, in particular, corrections in assembly sequence order and orientation, gaps and base consensus error. Following the recent methodological success of the kmer sorted long-read assembly, TrioCANU, and the recent release of reduced long-read error technology on the Pacific Biosciences platform we plan to create new references of the Pachon surface and cave population using this method. In preliminary experiments, we tested this approach on the asexual Amazon molly genome, Poecilia formosa. In this species, we used the sequences from current populations of the sexual parents, Poecilia mexicana and Poecilia latipinna, that created the original Poecilia formosa over 100,000 years ago to sort the mixed long-reads of the Poecilia formosa genome that resulted in the successful assembly of the parental sequences. Furthermore, this method has the added benefit of identifying the sex chromosomes of many fish species with various sex chromosome systems, XY or ZW. The new surface and cave Astyanax mexicanus references developed from the TrioCANU method will enhance all omics measures.
Times Cited:
1
Conference Name:
Astyanax Interrnational Meeting
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