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Comparative karyotype analysis in chickpea (Cicer arietinum L.) using oligo painting FISH

Citation

Hribova, Eva (2021), Comparative karyotype analysis in chickpea (Cicer arietinum L.) using oligo painting FISH, Dryad, Dataset, https://doi.org/10.5061/dryad.66t1g1k32

Abstract

Chickpea (Cicer arietinum L.) is one of the main sources of plant proteins in the Indian subcontinent and West Asia, where two different morphotypes, desi and kabuli, are grown. Despite the progress in genome mapping and sequencing, the knowledge of chickpea genome at chromosomal level, including the long-range molecular chromosome organization is limited. Earlier cytogenetic studies in chickpea suffered from limited number of cytogenetic landmarks and did not permit to identify individual chromosomes in the metaphase spreads or to anchor pseudomolecules to chromosomes in situ. In this study, we developed a system for fast molecular karyotyping for both morphotypes of cultivated chickpea. We demonstrate that even draft genome sequences are adequate to develop oligo-FISH barcodes for identification of chromosomes and comparative analysis among closely related chickpea genotypes. Our results show the potential of oligo-FISH barcoding for identification of structural changes in chromosomes, which accompanied genome diversification among chickpea cultivars. Moreover, oligo-FISH barcoding in chickpea pointed out some problematic, most probably wrongly assembled regions of the pseudomolecules of both, kabuli and desi reference genomes. Thus, oligo painting appears as a powerful tool not only for comparative karyotyping, but also for validation of genome assemblies.

Methods

Four BAC clones (05E03, 10I13, 11K07 and 14M02) which gave chromosome specific cytogenetic position in desi accession WR315 (Zatloukalová et al. 2011) were sequenced using Illumina. Sequencing libraries were prepared from 2 µg of fragmented DNA using TruSeq® DNA PCR-free kit (Illumina) and sequenced on the MiSeq Illumina platform with reads length 2 × 300 bp to achieve minimal sequence depth of 100×. Illumina sequences were processed using homemade perl script combining the assembly processes using MaSuRCA (Zimin et al. 2013) and identification of vector sequences flanking the chickpea assembles contigs/scaffolds.

Funding

European Regional Development Fund, Award: CZ.02.1.01/0.0/0.0/16_019/0000827