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Comparative RepeatExplorer analysis of Sorghum purpureosericeum B chromosome positive/negative plant

Citation

Karafiátová, Miroslava et al. (2021), Comparative RepeatExplorer analysis of Sorghum purpureosericeum B chromosome positive/negative plant, Dryad, Dataset, https://doi.org/10.5061/dryad.rxwdbrv5j

Abstract

B chromosomes are supernumerary, dispensable chromosomes, the presence of which has been detected in all major groups of living organisms - animals, plants and fungi. They do not pair with A chromosomes during meiosis and have irregular modes of inheritance. Here, we isolated and sequenced DNA from B positive and B negative nuclei of Sorghum purpureosericeum and performed repeat analysis on Illumina raw sequence data. The sequence reads were analysed using RepeatExplorer pipeline in a comparative fashion. The analysis revealed nine putative B specific clusters, which were further characterized and used in order to develop B chromosome specific markers. This dataset provides access to reads used in the analysis; assembled repetitive clusters; and result of comparative analysis between B positive and B negative samples.

Methods

DNA was collected from Sorghum purpureosericeum plants with and without supernumerary B chromosomes. Libraries for sequencing were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina. Sequence clustering and comparative analysis was performed with aim to identify B chromosome specific repetitive sequences. Illumina sequence reads were analyzed using RepeatExplorer pipeline (Novak et al. 2013, Bioinformatics; Novak et al. 2017, Nucleic Acids Research). 600,000 pair-end reads per sample used in the analysis are available in files Spu_reads_B_negative.fasta and Spu_reads_B_positive.fasta. Sequences of clusters resulting from the analysis are available in file SpuCL_contigs.fasta. Comparative analysis is presented in file SpuCL_comparative_analysis.xlsx. Numbers of reads originating in B positive and B negative sample are presented for each cluster.

Funding

Czech Science Foundation, Award: 18-12338Y

Plants as a tool for sustainable global development, Award: LM2015047