Development of SSR markers by next-generation sequencing of Korean landraces of chamoe (Cucumis melo var. makuwa)

Park, Inkyu; Kim, Jung-Eun; Lee, Jeongyeo; Kim, Sewon; Cho, Okhee; Yang, Kyungbong; Ahn, Jongmoon; Nahm, Seok-Hyeon; Kim, Hye‐Ran

doi:10.1007/s11033-013-2803-0

Cited by 11 publications

(9 citation statements)

References 30 publications

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“…SSRs, or microsatellites, are repeating sequences of 1–6 nucleotides and are widely distributed in genomes [ 36 ]. They are easily identified in whole genome sequences and are used as molecular markers due to high interspecies polymorphism, locus-specific co-dominance, and high transferability [ 43 ]. We identified 272 and 287 SSRs in the cp genomes of A .…”

Section: Resultsmentioning

confidence: 99%

The complete chloroplast genome sequence of Aconitum coreanum and Aconitum carmichaelii and comparative analysis with other Aconitum species

et al. 2017

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Aconitum species (belonging to the Ranunculaceae) are well known herbaceous medicinal ingredients and have great economic value in Asian countries. However, there are still limited genomic resources available for Aconitum species. In this study, we sequenced the chloroplast (cp) genomes of two Aconitum species, A. coreanum and A. carmichaelii, using the MiSeq platform. The two Aconitum chloroplast genomes were 155,880 and 157,040 bp in length, respectively, and exhibited LSC and SSC regions separated by a pair of inverted repeat regions. Both cp genomes had 38% GC content and contained 131 unique functional genes including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The gene order, content, and orientation of the two Aconitum cp genomes exhibited the general structure of angiosperms, and were similar to those of other Aconitum species. Comparison of the cp genome structure and gene order with that of other Aconitum species revealed general contraction and expansion of the inverted repeat regions and single copy boundary regions. Divergent regions were also identified. In phylogenetic analysis, Aconitum species positon among the Ranunculaceae was determined with other family cp genomes in the Ranunculales. We obtained a barcoding target sequence in a divergent region, ndhC–trnV, and successfully developed a SCAR (sequence characterized amplified region) marker for discrimination of A. coreanum. Our results provide useful genetic information and a specific barcode for discrimination of Aconitum species.

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Section: Resultsmentioning

confidence: 99%

The complete chloroplast genome sequence of Aconitum coreanum and Aconitum carmichaelii and comparative analysis with other Aconitum species

et al. 2017

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“…Aragão et al (2013) found an average of 2.41 alleles per marker for 17 genomic SSR markers in 38 melon accessions representing different botanical groups. Park et al (2013) reported seven genomic SSR markers to identify six oriental melon accessions. These markers only produced a total of 17 alleles with 2 to 3 alleles per marker.…”

Section: Resultsmentioning

confidence: 99%

Development of a Core Set of SSR Markers for Cultivar Identification and Seed Purity Tests in Oriental Melon (Cucumis melo L. var. makuwa)

Nguyen,

Kwon,

Park

et al. 2019

HST

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These authors contributed equally to this work. AbstractOriental melon (Cucumis melo L. var. makuwa), also called 'Korean melon' or 'Chamoe', is widely grown in East Asia, including Korea, Japan, and China. We used 521 simple sequence repeats (SSRs) to develop a core set of SSR markers as an effective tool for cultivar identification and seed purity tests in oriental melon. The polymorphism test using a subset of seven cultivars identified 20 expressed sequence tag SSR (EST-SSR) and 23 genomic SSR markers that showed high levels of polymorphism and simple segregation patterns. These SSR markers were used for DNA fingerprinting in additional 46 commercial cultivars. The average number of alleles per marker was 2.95 and 4.61 for the EST-SSR and genomic SSR markers in the 53 cultivars, respectively. For polymorphic information content (PIC), we found 0.411 to 0.816 with an average of 0.536 for the EST-SSR markers and 0.453 to 0.862 with an average of 0.568 for the genomic SSR markers. The unweighted pair group mean algorithm (UPGMA) dendrograms with the three sets of SSR markers (20 EST-SSR, 23 genomic SSR, and all 43 SSR markers) revealed that the 53 cultivars were separated into 4 to 5 major clusters. Furthermore, the set of all SSR markers was more effective at identifying the 53 cultivars relative to the other two marker sets. Therefore, the 43 SSR markers as a core set will be a valuable tool for several applications, including cultivar identification and seed purity tests in oriental melon.

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“…SSRs or microsatellites are tandem repeat sequences consisting of 1-6 nt sequence motifs in prokaryotic and eukaryotic genomes [22,23]. We detected 183 and 178 SSRs in F. ussuriensis and F. cirrhosa cp genomes, respectively.…”

Section: Repeat Analysis In Two Fritillaria Chloroplast Genomesmentioning

confidence: 91%

The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species

Park¹,

Kim²,

Yeo³

et al. 2017

Preprint

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Abstract:The genus Fritillaria belongs to the widely distributed family Liliaceae. The bulbs of Fritillaria ussuriensis and Fritillaria cirrhosa are valuable herbaceous medicinal ingredients. However, they are still used indiscriminately in herbal medicine. Identification and molecular phylogenic analysis of Fritillaria species is therefore required. Here, we report the complete chloroplast (cp) genome sequences of F. ussuriensis and F. cirrhosa. The two Fritillaria cp genomes were 151,524 and 151,083 bp in length, respectively, including a pair of inverted repeat regions (52,678 and 52,156 bp) separated by a large single copy region (81,732 and 81,390 bp) and small single copy region (17,114 and 17,537 bp). A total of 111 genes in F. ussuriensis and 112 in F. cirrhosa comprised 77 proteincoding genes in F. ussuriensis and 78 in F. cirrhosa, 30 tRNA genes, and four rRNA genes. The gene order, content, and orientation of the two Fritillaria cp genomes exhibited the general structure of flowering plants, and were similar to those of other Fritillaria species. Comparison of the six Fritillaria species' cp genomes indicated seven highly divergent regions in intergenic spacers and in the matK, rpoC1, rpoC2, ycf1, ycf2, ndhD, and ndhF coding regions. We established the position of the six species through phylogenic analysis. The complete chloroplast genome sequences of two Fritillaria species will be useful genomics resources for identification of Fritillaria species and for studying the phylogenetic relationship among Fritillaria species within the Liliaceae family.

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Development of SSR markers by next-generation sequencing of Korean landraces of chamoe (Cucumis melo var. makuwa)

Cited by 11 publications

References 30 publications

The complete chloroplast genome sequence of Aconitum coreanum and Aconitum carmichaelii and comparative analysis with other Aconitum species

The complete chloroplast genome sequence of Aconitum coreanum and Aconitum carmichaelii and comparative analysis with other Aconitum species

Development of a Core Set of SSR Markers for Cultivar Identification and Seed Purity Tests in Oriental Melon (Cucumis melo L. var. makuwa)

The Complete Chloroplast Genome Sequences of<em> Fritillaria ussuriensis</em> Maxim. and <em>Fritillaria cirrhosa</em> D. Don, and Comparative Analysis with Other<em> Fritillaria</em> Species

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