The complete chloroplast genome sequence of Panax ginseng breeding line 'G07006', showing higher salt tolerance, was confirmed by de novo assembly using whole genome next-generation sequences. The complete chloroplast (CP) genome size is 156,356 bp, including two inverted repeats (IRs) of 52,060 bp,...
The complete chloroplast genome sequence of Panax ginseng breeding line 'G07006', showing higher salt tolerance, was confirmed by de novo assembly using whole genome next-generation sequences. The complete chloroplast (CP) genome size is 156,356 bp, including two inverted repeats (IRs) of 52,060 bp, separated by the large single-copy (LSC 86,174 bp) and the small single-copy (SSC 18,122 bp) regions. One hundred fourteen genes were annotated, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Among them, 18 sites were duplicated in the inverted repeat regions. By comparative analyses of the previously identified CP genome sequences of nine cultivars of P. ginseng and that of G07006, five useful SNPs were defined in this study. Since three of the five SNPs were cultivar-specific to Chunpoong and Sunhyang, they could be easily used for distinguishing from other ginseng accessions. However, on arranging SNPs according to their gene location, the G07006 genotype was 'GTGGA', which was distinct from other accessions. This complete chloroplast DNA sequence could be conducive to discrimination of the line G07006 (salt-tolerant) and further enhancement of the genetic improvement program for this important medicinal plant.
The complete chloroplast genome sequence of Panax ginseng breeding line 'G07006', showing higher salt tolerance, was confirmed by de novo assembly using whole genome next-generation sequences. The complete chloroplast (CP) genome size is 156,356 bp, including two inverted repeats (IRs) of 52,060 bp, separated by the large single-copy (LSC 86,174 bp) and the small single-copy (SSC 18,122 bp) regions. One hundred fourteen genes were annotated, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Among them, 18 sites were duplicated in the inverted repeat regions. By comparative analyses of the previously identified CP genome sequences of nine cultivars of P. ginseng and that of G07006, five useful SNPs were defined in this study. Since three of the five SNPs were cultivar-specific to Chunpoong and Sunhyang, they could be easily used for distinguishing from other ginseng accessions. However, on arranging SNPs according to their gene location, the G07006 genotype was 'GTGGA', which was distinct from other accessions. This complete chloroplast DNA sequence could be conducive to discrimination of the line G07006 (salt-tolerant) and further enhancement of the genetic improvement program for this important medicinal plant.
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문제 정의
(2015) analyzed the CpDNA sequence of nine varieties of ginseng and developed SNP- and indel-based DNA markers that can differentiate between the Chunpoong and Sunhyang varieties. Thus, this study was conducted to develop DNA markers capable of determining distinctness and homogeneity among the salt-resistant varieties of ginseng. For this, the full CpDNA sequence of ‘G07006’, a salt-resistant line, was analyzed using NGS and compared with the recently released CpDNA sequences of nine ginseng varieties (Chunpoong, Yunpoong, Gopoong, Gumpoong, Sunpoong, Sunun, Sunone, Cheongsun and Sunhyang).
제안 방법
In this study, to identify SNP mutations in the CP genome of the decoded G07006 system based on the NCBI DB, CP genome sequences for nine cultivars of P. ginseng were down loaded for comparative analysis (KM067386, KM067387, KM067388, KM067390, KM067391, KM067392, KM067393, KM088019, KM088020). Base sequences were edited using the BioEdit program, saved as no gap, and arranged as Cluster W (ver.
성능/효과
For this, the full CpDNA sequence of ‘G07006’, a salt-resistant line, was analyzed using NGS and compared with the recently released CpDNA sequences of nine ginseng varieties (Chunpoong, Yunpoong, Gopoong, Gumpoong, Sunpoong, Sunun, Sunone, Cheongsun and Sunhyang).
Results showed that 492,591 contigs were within the cpDNA region and the coverage was identified to be 939× (Table 1).
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