Development of 12 Microsatellite Markers in Dorcus titanus castanicolor (Motschulsky, 1861) (Lucanidae, Coleoptera) from Korea Using Next-Generation Sequencing
Abstract
:1. Introduction
2. Results and Discussion
2.1. Next-Generation Sequencing and Microsatellite Loci Identification
2.2. Microsatellite Marker Assessment
2.3. Genetic Diversity of the Korean Dorcus titanus castanicolor Population
3. Materials and Methods
3.1. Sample Collection and Genomic DNA Extraction
3.2. Next-Generation Sequencing, Microsatellite Loci Identification, Marker Selection, and Genotyping
3.3. Data Analysis
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Number of Contigs (>1000 bp) | Total Bases | Maximum Length | N50 Length | Average Contig Length | GC Content |
---|---|---|---|---|---|
124,291 | 339,287,381 | 103,231 | 3258 | 2729 | 33.98% |
MSL | Forward Sequence | Reverse Sequence | RM | SS | MN | NAn |
---|---|---|---|---|---|---|
31,870 | CGACACTCACACGCAATAAATAG | GCCATTCCATCGGTGAATTTTTA | (CGTT)6 | 214 bp | DT01 | KX268665 |
13,508 | TGAAGTTTCAGAAGGAGTTTGGA | CAATCAACTCCGGATAGAGTGAA | (ACAT)6 | 264 bp | DT02 | KX268666 |
78,687 | AGAACGCGTGAACTTGTTTATTT | TTGTCACGTTCTAAAGCGTTTTT | (AAG)8 | 244 bp | DT03 | KX268667 |
9989 | CCCCACGAACAATAAATCAGAAC | TACTTCCGCTTACAGCAGTAAAT | (CGT)8 | 202 bp | DT05 | KX268668 |
9645 | TTATGACGAACTTGTTTTGGCAG | TGTGGAATTTTGTTTCGGATGTT | (AC)12 | 298 bp | DT06 | KX268669 |
8497 | GTCATCTTACTAGAGGTTGGTCG | CAACACTTCTTCTAATGCACTCG | (AAG)17 | 205 bp | DT08 | KX268670 |
15,216 | ATTACGTAGACATGGCTTAAGCA | TCCTCATGCCAAATATGATCCAA | (AACT)10 | 245 bp | DT11 | KX268671 |
29,993 | TAATGACGCCATTCACACATTTC | GGTCTTTAAACAGTCTGCCAAAA | (GT)20 | 239 bp | DT12 | KX268672 |
12,743 | ACTTGACTGTCACATACACACAT | TTGTATGTCTGGCTTTGGTTACT | (CT)19 | 212 bp | DT13 | KX268673 |
30,799 | AAGACGATCGGCAATTTCAAAAT | TAGACCAGAGTCCTTCATTACCA | (AG)17 | 209 bp | DT15 | KX268675 |
24,714 | GAGCACCTAGATAATCAACCCAA | GATTTGGTTTCTTGCATTGTCCT | (AAG)11 | 230 bp | DT17 | KX268676 |
3144 | TCATTTGGACGTAGCAAATGTTC | TGCATGTTGAAAGGTACCAAGTA | (AAC)10 | 260 bp | DT24 | KX675371 |
3488 | TAATCCTTGCATGCAGCCTAATA | AGTTTGTGTTTGTGATGAAGTGG | (AGC)10 | 298 bp | DT25 | KX675372 |
74,360 | GTTATGGTGTGAGCTGGAATTTC | ATTTACATCAAGATTCGCCGTTG | (GTT)10 | 271 bp | DT26 | KX675373 |
557 | AACAAATAACGTGTTGGAGTTCG | AGTAGATGAGAACTGTGTTTGGG | (ACAT)7 | 284 bp | DT27 | KX675374 |
4515 | TCCACGTTATCTTTCAAAACACG | TTCAAGTTTGGGTGAAACAATCG | (CT)14 | 226 bp | DT28 | KX675375 |
2260 | AACATGACCCACTAAGGTATCAA | CTAACAAGAAGTACCACCACCAT | (GCT)9 | 300 bp | DT32 | KX675376 |
16,503 | ACGCTACTGGCAATCAAATAAAC | GCACCCACAAACAACATACATAA | (ACT)9 | 284 bp | DT33 | KX675377 |
426 | GCACGTCACGACTATTTTGATTT | TAACTCGTTAATGAACATGTGCG | (AC)13 | 210 bp | DT35 | KX675378 |
MSL | DT1 | DT2 | DT3 | DT5 | DT6 | DT8 | DT11 | DT12 | DT13 | DT15 |
NP | no | no | no | no | no | no | no | no | no | no |
NFreq | −0.1909 | −0.1408 | −0.3352 | −0.3970 | −0.1199 | −0.0986 | −0.1269 | −0.0874 | −0.2445 | −0.0930 |
MSL | DT17 | DT24 | DT25 | DT26 | DT27 | DT28 | DT32 | DT33 | DT35 | – |
NP | no | no | no | no | no | no | no | no | no | – |
NFreq | −0.1109 | 0.0250 | −0.0022 | −0.6180 | −0.0642 | −0.0800 | 0.0171 | −0.0144 | −0.1185 | – |
MSL | MAF | Gn | SS | An | He | Ho | PIC | HWE |
---|---|---|---|---|---|---|---|---|
DT1 | 0.8182 | 3 | 22 | 3 | 0.3140 | 0.3636 | 0.2918 | 1.0000 |
DT2 | 0.6591 | 5 | 22 | 6 | 0.5103 | 0.6364 | 0.4619 | 0.1100 |
DT6 | 0.3409 | 9 | 22 | 6 | 0.7789 | 0.9545 | 0.7466 | 0.0120 |
DT12 | 0.3409 | 10 | 22 | 6 | 0.7397 | 0.8636 | 0.6968 | 0.5770 |
DT13 | 0.3864 | 7 | 22 | 6 | 0.7118 | 1.0000 | 0.6647 | 0.0190 |
DT15 | 0.3636 | 9 | 22 | 7 | 0.7717 | 0.9091 | 0.7404 | 0.0510 |
DT17 | 0.4091 | 8 | 22 | 9 | 0.7603 | 0.8636 | 0.7330 | 0.0010 |
DT24 | 0.6818 | 5 | 22 | 4 | 0.4917 | 0.5000 | 0.4507 | 0.1530 |
DT25 | 0.4318 | 11 | 22 | 6 | 0.7293 | 0.7273 | 0.6939 | 0.4650 |
DT27 | 0.4545 | 6 | 22 | 4 | 0.6353 | 0.6818 | 0.5632 | 0.0060 |
DT28 | 0.3182 | 10 | 22 | 6 | 0.7531 | 0.8636 | 0.7109 | 0.5390 |
DT32 | 0.7045 | 4 | 22 | 3 | 0.4287 | 0.4091 | 0.3543 | 1.0000 |
DT33 | 0.4773 | 9 | 22 | 6 | 0.6901 | 0.6818 | 0.6499 | 0.4200 |
Mean | 0.4913 | 7.3846 | 22 | 5.5385 | 0.6396 | 0.7273 | 0.5968 | – |
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Kang, T.H.; Han, S.H.; Park, S.J. Development of 12 Microsatellite Markers in Dorcus titanus castanicolor (Motschulsky, 1861) (Lucanidae, Coleoptera) from Korea Using Next-Generation Sequencing. Int. J. Mol. Sci. 2016, 17, 1621. https://doi.org/10.3390/ijms17101621
Kang TH, Han SH, Park SJ. Development of 12 Microsatellite Markers in Dorcus titanus castanicolor (Motschulsky, 1861) (Lucanidae, Coleoptera) from Korea Using Next-Generation Sequencing. International Journal of Molecular Sciences. 2016; 17(10):1621. https://doi.org/10.3390/ijms17101621
Chicago/Turabian StyleKang, Tae Hwa, Sang Hoon Han, and Sun Jae Park. 2016. "Development of 12 Microsatellite Markers in Dorcus titanus castanicolor (Motschulsky, 1861) (Lucanidae, Coleoptera) from Korea Using Next-Generation Sequencing" International Journal of Molecular Sciences 17, no. 10: 1621. https://doi.org/10.3390/ijms17101621