1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Genome analysis of Cardamine hirsuta using whole genome sequensing approach
Paper ID : 1071-ICB10
Authors:
Mahmood Ghorbani Marghashi *1, Hedayat Bagheri2
1ملایر-دانشگاه ملایر-دانشکده کشاورزی-گروه باغبانی
2دانشگاه بوعلی سینا-دانشکده کشاورزی-گروه بیوتکنولوژی
Abstract:
Recently, Cardamine hirsuta has emerged as an exclusively powerful genetic system for comparative studies of development. C. hirsuta is a small plant in the cruciferous family, which is a very close relative of Arabidopsis thaliana and has many desirable characteristics as a model species [1, 2]. The C. hirsuta genome is estimated to be 1.5 times that of A. thaliana, with eight chromosomes. Also the constructed high-quality reference genome of the C. hirsuta strain ‘Oxford’ provided a powerful platform for molecular studies [3].
Genomic DNA of Mashhad ecotype was extracted using CTAB method. 30 microliters of high quality DNA at a concentration of 20 ng /μL were sent to Novogene for genomic sequencing. Sequencing was performed by HiSeq X Ten using the Pair end method. The obtained sequence was sorted using IGV software and reference genome and then analyzed for sequencing quality using Fastqc software [4].
Using Smudgeplot and Genome Scope software, the polyploidy level and homozygosity of the sequenced genome of Mashhad were determined. Genomescope uses k-mer frequencies generated from raw read data to estimate the genome size, the abundance of repetitive elements and rate of heterozygosity, and Smudgeplot to visualize and estimate the ploidy and genome structure of a genome by analyzing heterozygous k-mer pairs [5, 6, 7].
Using the Genome Scope program and kmer16 size, the size of the Mashhad ecotype genome was estimated between 190 to 230 Mb, which was similar to the size of the Oxford genome as the reference genome. Also, the rate of homozygosity was 99.95% and the rate of heterozygosity was 0.05%. Smudgeplot showed that cardamine hirsuta is a diploid plant. Visualization and estimating the ploidy and genome structure of a genome by analyzing heterozygous k-mer pairs is an important assessment prior to genome assembly.
Keywords:
Cardamine hirsuta, GenomeScope, Smudgeplot
Status : Paper Accepted (Poster Presentation)