Next-generation sequencing

Development of novel microsatellite markers for conservation genetic studies of Vulpes vulpes (Canidae) by using next-generation sequencing method

J. - N. Yu, Chung, C. - U., Oh, K. H., Lee, B. - K., and Lim, C. E., “Development of novel microsatellite markers for conservation genetic studies of Vulpes vulpes (Canidae) by using next-generation sequencing method”, vol. 14. pp. 3980-3983, 2015.

The red fox, Vulpes vulpes (Canidae), is the most widely distributed terrestrial carnivore worldwide, but this species is classified as endangered in Korea. In this study, we developed 25 polymorphic microsatellite markers that included 3-13 (mean = 6.32) alleles per locus using 22 red fox individuals. The most polymorphic locus was FR(59)TG (13 alleles) and the least polymorphic loci were FR(70)TG and FR(182)AG (3 alleles each).

Next-generation sequencing identification and characterization of microsatellite markers in Aconitum austrokoreense Koidz., an endemic and endangered medicinal plant of Korea

Y. - E. Yun, Yu, J. - N., Nam, G. H., Ryu, S. - A., Kim, S., Oh, K., and Lim, C. E., “Next-generation sequencing identification and characterization of microsatellite markers in Aconitum austrokoreense Koidz., an endemic and endangered medicinal plant of Korea”, vol. 14, pp. 4812-4817, 2015.

We used next-generation sequencing to develop 9 novel microsatellite markers in Aconitum austrokoreense, an endemic and endangered medicinal plant in Korea. Owing to its very limited distribution, over-harvesting for traditional medicinal purposes, and habitat loss, the natural populations are dramatically declining in Korea. All novel microsatellite markers were successfully genotyped using 64 samples from two populations (Mt. Choejeong, Gyeongsangbuk-do and Ungseokbong, Gyeongsangnam-do) of Gyeongsang Province.

Updates and perspectives on the utilization of molecular makers of complex traits in rice

G. Li, Kwon, S. W., and Park, Y. J., “Updates and perspectives on the utilization of molecular makers of complex traits in rice”, vol. 11, pp. 4157-4168, 2012.

After complete sequencing of its genome and annotation of the majority of its ~32,000 genes, rice genome has become the model genome among the cereal genomes, and the focus has shifted from structural to functional genomics and application of genomic-derived information in rice breeding. During the past 2 decades, intensive worldwide efforts have led to significant improvements in rice.

Benchmark comparison of ab initio microRNA identification methods and software

L. L. Hu, Huang, Y., Wang, Q. C., Zou, Q., and Jiang, Y., “Benchmark comparison of ab initio microRNA identification methods and software”, vol. 11, pp. 4525-4538, 2012.

MicroRNAs (miRNAs) are short, non-coding RNA molecules that play an important role in the world of genes, especially in regulating the gene expression of target messenger RNAs through cleavage or translational repression of messenger RNA. Ab initio methods have become popular in computational miRNA detection. Most software tools are designed to distinguish miRNA precursors from pseudo-hairpins, but a few can mine miRNA from genome or expressed sequence tag sequences. We prepared novel testing datasets to measure and compare the performance of various software tools.

New polymorphic microsatellite loci of threadsail filefish, Stephanolepis cirrhifer (Teleostei, Monacanthidae), from Korean waters

C. - M. An, An, H. S., Lee, J. W., and Hong, S. W., “New polymorphic microsatellite loci of threadsail filefish, Stephanolepis cirrhifer (Teleostei, Monacanthidae), from Korean waters”, vol. 12, pp. 1679-1690, 2013.

The threadsail filefish, Stephanolepis cirrhifer (Monacanthidae), is found mainly in the western Pacific. It is intensively caught in Korea and is a highly appreciated seafood delicacy. Consequently, the natural population of this species has drastically decreased, despite introductions from hatcheries. To provide information necessary for its conservation and management, we developed 24 polymorphic microsatellite markers using a combination of a total enriched genomic library and a small-scale 454 pyrosequencing.

ReSeqTools: an integrated toolkit for large-scale next-generation sequencing based resequencing analysis

W. He, Zhao, S., Liu, X., Dong, S., Lv, J., Liu, D., Wang, J., and Meng, Z., “ReSeqTools: an integrated toolkit for large-scale next-generation sequencing based resequencing analysis”, vol. 12, pp. 6275-6283, 2013.

Large-scale next-generation sequencing (NGS)-based resequencing detects sequence variations, constructs evolutionary histories, and identifies phenotype-related genotypes. However, NGS-based resequencing studies generate extraordinarily large amounts of data, making computations difficult. Effective use and analysis of these data for NGS-based resequencing studies remains a difficult task for individual researchers.

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