Genome analysis of Cardamine hirsuta using whole genome sequensing approach

Recently, Cardamine hirsuta has emerged as an exclusively powerful genetic system for comparative studiesof development. C. hirsuta is a small plant in the cruciferous family, which is a very close relative ofArabidopsis thaliana and has many desirable characteristics as a model species. The C. hirsuta genome isestimated to be ۱.۵ times that of A. thaliana, with eight chromosomes. Also the constructed high-qualityreference genome of the C. hirsuta strain ‘Oxford’ provided a powerful platform for molecular studies.Genomic DNA of Mashhad ecotype was extracted using CTAB method. ۳۰ microliters of high quality DNAat a concentration of ۲۰ ng /μL were sent to Novogene for genomic sequencing. Sequencing was performedby HiSeq X Ten using the Pair end method. The obtained sequence was sorted using IGV software andreference genome and then analyzed for sequencing quality using Fastqc software.Using Smudgeplot and Genome Scope software, the polyploidy level and homozygosity of the sequencedgenome of Mashhad were determined. Genomescope uses k-mer frequencies generated from raw read datato estimate the genome size, the abundance of repetitive elements and rate of heterozygosity, and Smudgeplotto visualize and estimate the ploidy and genome structure of a genome by analyzing heterozygous k-merpairs.Using the Genome Scope program and kmer۱۶ size, the size of the Mashhad ecotype genome was estimatedbetween ۱۹۰ to ۲۳۰ Mb, which was similar to the size of the Oxford genome as the reference genome. Also,the rate of homozygosity was ۹۹.۹۵% and the rate of heterozygosity was ۰.۰۵%. Smudgeplot showed thatcardamine hirsuta is a diploid plant. Visualization and estimating the ploidy and genome structure of agenome by analyzing heterozygous k-mer pairs is an important assessment prior to genome assembly.

کلیدواژه ها:

Cardamine hirsuta ، GenomeScope ، Smudgeplot