Comparison of Plastome SNPs/INDELs among different Wheat (Triticumsp.) Cultivars

Abstract

ABSTRACT: Wheat is the most important cereal crop in the world as compared to other grain crops in terms of acreage and productivity. Based on next-generation sequencing data, we sequenced and assembled chloroplastid (cp) genomes of nine Egyptian wheat cultivars in which eight of them are hexaploid (Triticum sp, 2n=6x) and one is tetraploid (T. turgidum subsp. durum, 2n=4x). Sequencing reads were first filtered in which all sequencing reads that mapped to mitochondrial (mt) genome were removed. Preliminary results indicated no intra-cultivar heteroplasmy for the different cultivars. Size of the resulted chloroplast wheat genome across different cultivars is 133,812 bp, which is less than the cp genome of “Chinese Spring” cultivar partially due to the presence of three large sequences in the later genome belonging to rice cp genome. Three new non-coding tRNA gene sequences were also found and function of one conserved ORF namely ycf5 is shown. The protein-coding genes represent 67.26% of the total plastid genes. In the non-coding regions, a number of 5 tandem and 31 long repeats were found. Codon usage in the wheat cp genome has the same trend as that published for wheat mitochondrial genome. Assembled cp genomes after filtering out the gaps (≥ 5 bp) generated in the nine cultivars were also used for SNPs and INDELs analyses. Across different cultivars, 564 SNPs and 160 INDELs were identified, of which 230 and 4 were in the protein-coding regions, respectively. Five and nine cultivar-specific SNPs and INDELs were found, respectively. One SNP, while none for INDELs, was found in the genic regions unique to one of the two inverted repeats (IRa) in the coding sequence of ndhB gene. Two SNPs were non-synonymous substitutions in the two protein-coding genes rpoA and rpl16, while one was synonymous substitution in the protein coding gene rpl23. Three INDELs exist in rpl2 gene. The first is 12-nucleotide that starts at nucleotide 4 of the gene and encodes for four amino acids. Two other INDELs starts from nucleotide 160 of the gene and are 19-nt apart. These two INDELs resulted in a frameshift of six amino acids, with a glycine amino acid in the middle that remained unchanged, then the default frame was restored. Results of dendrogram aligned with known relationships among cultivars. In conclusion, SNPs and INDELs analyses of wheat plastome were successfully used for detecting polymorphism among wheat cultivars.