The analysis of repetitive sequences in Nigella sativa and N. damascena plants

Background and Aim: The Nigella genus belongs to Ranunculaceae family and consists of about ۲۰ species. Nigella sativa (۲n = ۲x = ۱۲) and Nigella damascena (۲n = ۲x = ۱۲) are two important species with large genomes. DNA repetitive sequences (i.e., transposons and satellite sequences) comprise ۲۵-۸۵% of plant genome. The study of the nature and distribution of repetitive sequences reveals valuable information about their evolution in different plant species. Some types of repetitive sequences are conserved among species, and some others show more variations. This study investigated the distribution of repetitive sequences in N. sativa and N. damascena by sequencing of the whole genome and k-mer analysis of sequences.Methods: Sat-۱ and Sat-۲ primers were designed by Primer۳, and sequences were amplified by PCR methods. The PCR products were labeled by Nick-translation kit. The genomic DNA was sequenced by paired-ends methods with coverage ۰.۱X (Illumina HiSeq ۲۵۰۰, NovoGene Co). The repetitive sequences identification was done by RepeatExplorer pipeline. The consensus monomers of satellite and dispersed repetitive sequences were identified by TAREAN. The FISH method with Sat-۱ and Sat-۲ probes was applied to locate the satellite repetitive sequences.Results: The results revealed that highly-repetitive sequences comprised ۵۴% of N. sativa genome. Retro-transposable elements were the major part of repetitive sequences, and retro-transposable type LTR comprised ۴۱% of repetitive sequences. Satellite repetitive sequences had a low frequency in Nigella genome, in which only two satellite repetitive sequences with half a percent of the genome were identified. The FISH revealed that repetitive sequences Sat-۱ and Sat-۲ were centromeric sequences in N. sativa, while they were not seen in N. damascena genome. Conclusion: The studied species had the same karyotype profile in terms of chromosomes shape and size, but their repetitive sequences revealed variation and evolution. The N. sativa chromosomes were distinguished by probes Sat-۱ and Sat-۲, ۵S rDNA and ۴۵S rDNA, and N. damascena chromosomes were identified by probes ۵S rDNA and ۴۵S rDNA.

کلیدواژه ها:

Whole genome sequencing ، Fluorescent in situ hybridization ، Karyotype ، repetitive sequences ، Nigella spp.