Journal of

Plant Biotechnology

Schematic map of overall features of the S. cardiophyllum chloroplast genome. From the center, the first track shows the dispersed repeats, which consist of direct and palindromic repeats, connected with red and green arcs. The second track shows the long tandem repeats as short blue bars. The third track shows the short tandem repeats or microsatellite sequences as short bars with different colors. The colors, the type of repeat they represent, and the description of the repeat types are as follows. Black: complex repeat; Green: repeat unit size = 1; Yellow: repeat unit size = 2. The small single-copy (SSC), inverted repeat (IRa and IRb), and large single-copy (LSC) regions are shown on the fourth track. The GC content is plotted on the fifth track. The genes are shown on the sixth track. The optional codon usage bias is displayed in the parenthesis after the gene name. Genes are color-coded based on their functional classification. The transcription directions for the inner and outer genes are clockwise and anticlockwise, respectively. The functional classification of the genes is shown in the bottom left corner.|@|~(^,^)~|@|Schematic map of the cis- (A) and trans- (B) splicing genes in the S. cardiophyllum chloroplast genome. The 13 cis-splicing genes are arranged from top to bottom based on their order on the chloroplast genome. The gene names are shown on the left, and the gene structures are on the right. The exons are shown in black; the introns are shown in white. The arrow indicates the sense direction of the gene. Lengths of exons and introns are not drawn to scale. The trans-splicing gene rps12 in the chloroplast genome has three unique exons. Two of them are duplicated as they are located in the IR regions.|@|~(^,^)~|@|Maximum likelihood phylogenetic tree of S. cardiophyllum with 32 species belonging to the Solanaceae family based on the chloroplast protein-coding sequences. Numbers in the nodes are the bootstrap values from 1,000 replicates. The data are partially adopted from Park (2021a)|@|~(^,^)~|@|Multiple sequence alignments of the intergenic or intragenic regions containing SNPs used to develop the PCR-based markers. The chloroplast genome sequences of S. cardiophyllum (SC1_9: MK690622), S. jamesii (SJ8: MK690624), S. bulbocastanum (Sblb: DQ347958), S. berthaultii (Sber: KY419708), S. tuberosum (Stub: KM489056), S. verrucosum (SV1_4: MK690625), S. hougasii (SH2 _10: MF471372), S. hjertingii (SH1_16: MK690623), and S. commersonii (Scmr: KM489054) were used and listed from top to bottom in each region of the SNPs. The regions of the SNPs detected on S. cardiophyllum chloroplast genome are in bold font, highlighted and underlined|@|~(^,^)~|@|PCR-based markers for the discrimination of S. cardiophyllum from other Solanum species. A: SC1-9_SNP2. B: SC1-9_SNP6. C: SC1-9_SNP9. D: SC1-9_SNP10. The markers SC1-9_SNP6, SC1-9_SNP9, and SC1-9_SNP10 are positively specific to S. cardiophyllum, and the marker SC1-9_SNP2 is negatively specific to S. cardiophyllum. SC1-9 and SC1-3 indicate two different lines of S. cardiophyllum (PI341233). SN is S. nigrum collected in Gyeongsan, South Korea. M, DS, DJ, SM, SH1, SJ, SV1, SI, SM1, SP, SK, SC4, SV2, SA, SS, SH2, and SB2 indicate a size marker ladder, potato varieties ‘Daeseo’, ‘Daeji’, ‘Sumi’, S. hjertingii (PI1 86559), S. jamesii (PI578326), S. verrucosum (PI160228), S. iopetalum (PI230459), S. mochiquense (PI338616), S. pinnatisectum (PI190115), S. kurtzianum (PI578236), S. S. candolleanum (PI210035), S. vernei (PI230468), S. acaule (PI310970), S. stoloniferum (PI160224), S. hougasii (PI161174), and S. brevicaule (PI205394), respectively. Yellow and red arrows indicate negative and positive bands on S. cardiophyllum, respectively

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