Assembly and analysis of the chloroplast genome of the North American hybrid grape ‘Norton’
Keywords:grapevine, chloroplast, genome, variant, indel, SNP
'Norton' is a hybrid grape cultivar of North American Vitis aestivalis. In this report, the whole chloroplast (cp) genome was assembled and analyzed. Total length of the 'Norton' cp genome is 160,913 bp in comparison to 160,928 bp of the cp genome of V. vinifera 'Maxxa'. The sequence is highly conserved between the two cp genomes, with a sequence identity of 99 % and identical haplotypes for the three best-studied cpSSR markers (cpSSR3, cpSSR5 and cpSSR10). A total of 73 indels and 147 single nucleotide polymorphisms (SNPs) were found between the two genomes. Amino acid changes were identified in 10 coding regions. Six DNA fragments with predicted changes between the two cp genomes were amplified from 'Norton' and wild V. aestivalis by polymerase chain reaction (PCR). The sequencing of these DNA fragments verified assembled sequences except for one region that has low coverage in the assembly. Comparison of indels and SNPs in the verified regions indicated that 'Norton' cp genome contains signature variants that are found only in the cp genome of wild V. aestivalis. These sequence variants can be used as genetic markers for distinguishing grape cultivars and in breeding new cultivars.
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