Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Integrating Genetic and Chromosome Maps of Allium Cepa: From Markers Visualization to Genome Assembly Verification

Aleksey Ermolaev
ORCID logo ,
Natalia Kudryavtseva
ORCID logo ,
Anton Pivovarov
,
Ilya Kirov
ORCID logo ,
Gennady Karlov
,
Ludmila Khrustaleva
* ORCID logo
Version 1 : Received: 11 August 2022 / Approved: 12 August 2022 / Online: 12 August 2022 (12:54:02 CEST)

A peer-reviewed article of this Preprint also exists.

Ermolaev, A.; Kudryavtseva, N.; Pivovarov, A.; Kirov, I.; Karlov, G.; Khrustaleva, L. Integrating Genetic and Chromosome Maps of Allium cepa: From Markers Visualization to Genome Assembly Verification. Int. J. Mol. Sci. 2022, 23, 10486. Ermolaev, A.; Kudryavtseva, N.; Pivovarov, A.; Kirov, I.; Karlov, G.; Khrustaleva, L. Integrating Genetic and Chromosome Maps of Allium cepa: From Markers Visualization to Genome Assembly Verification. Int. J. Mol. Sci. 2022, 23, 10486.

Abstract

The ability to directly look into genome sequences has opened great opportunities in plant breeding. Yet, the assembly of full-length chromosomes remains one of the most difficult problems in modern genomics. Genetic maps are commonly used in de novo genome assembly and are constructed on the basis of a statistical analysis of the number of recombination rather than physical distance in base pairs. This may affect the accuracy of the ordering and orientation of scaffolds within the chromosome, especially in the region of recombination suppression. Here we report the use of Tyr-FISH for validation of genetic and pseudochromosome maps. For probe design we developed a pipeline that is based on selection of a unique sequence with minimal potential fluorescent background arising from non-specific in situ hybridization. In total of 24 unique genes were located on physical chromosomes 2 and 6. The order of markers has been corrected by integration genetic and cytogenetic maps. Tyr-FISH mapping showed that the order of 23.1% (chromosome 2) and 27.3% (chromosome 6) of the tested genes differed between physical chromosomes and pseudochromosomes. Also the position of the mlh1 gene, which was not on the genetic map, was defined on physical chromosome 2. The results suggest the possibility of Tyr-FISH mapping of any gene that may not be neither on the genetic map nor in the assembly. Hence, Tyr-FISH provides valuable information for the improvement of the genome assembly.

Keywords

Tyr-FISH; integration genetic; cytogenetic and pseudochromosome maps; transcript based markers; genome assembly; bioinformatics; Allium cepa

Subject

Biology and Life Sciences, Biochemistry and Molecular Biology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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