Next-generation sequencing

Multi-threading the generation of Burrows-Wheeler Alignment

H. Jo and Jo, H., “Multi-threading the generation of Burrows-Wheeler Alignment”, vol. 15, p. -, 2016.

Along with recent progress in next-generation sequencing technology, it has become easier to process larger amounts of genome sequencing data at a lower cost. The most time-consuming step of next-generation sequencing data analysis involves the mapping of read data into a reference genome. Although the Burrows-Wheeler Alignment (BWA) tool is one of the most widely used open-source software tools for aligning read sequences, it still has a limitation in that it does not fully support a multi-thread mechanism during the alignment generation step.

Development of microsatellite markers in Hagenia abyssinica (Bruce) J.F. Gmel, an endangered tropical tree of eastern Africa, using next-generation sequencing

A. W. Gichira, Long, Z. C., Hu, G. W., Gituru, R. W., Wang, Q. F., Chen, J. M., Gichira, A. W., Long, Z. C., Hu, G. W., Gituru, R. W., Wang, Q. F., and Chen, J. M., “Development of microsatellite markers in Hagenia abyssinica (Bruce) J.F. Gmel, an endangered tropical tree of eastern Africa, using next-generation sequencing”, vol. 15, p. -, 2016.

Hagenia abyssinica (Bruce) J.F. Gmel is an endangered tree species endemic to the high mountains of tropical Africa. We used Illumina paired-end technology to sequence its nuclear genome, aiming at creating the first genomic data library and developing the first set of genomic microsatellites. Seventeen microsatellite markers were validated in 24 individuals. The average number of alleles per locus was 7.6, while the observed and expected heterozygosities ranged from 0.000 to 0.958 and from 0.354 to 0.883, respectively.

Whole-transcriptome sequencing of Pinellia ternata using the Illumina platform

X. Huang, Jing, Y., Liu, D. J., Yang, B. Y., Chen, H., Li, M., Huang, X., Jing, Y., Liu, D. J., Yang, B. Y., Chen, H., and Li, M., “Whole-transcriptome sequencing of Pinellia ternata using the Illumina platform”, vol. 15, p. -, 2016.

Pinelliae rhizoma is the dried tuber of Pinellia ternata (Thunb.) Breit., and has been used for thousands of years as a traditional Chinese medicine. However, its genomic background is little known. With the development of high-throughput genomic sequencing, it is now easy and cheap to obtain genomic information. In this study, 193,032,910 high-quality clean reads were generated using the Illumina Hiseq 2000 platform. A total of 53,544 unigenes were identified from the contigs assembled.

Development and characterization of microsatellite loci in Brasenia schreberi (Cabombaceae) based on the next-generation sequencing

H. Liu, Long, Z. C., Li, L. N., Wang, Q. F., Chen, J. M., Liao, K., Liu, H., Long, Z. C., Li, L. N., Wang, Q. F., Chen, J. M., Liao, K., Liu, H., Long, Z. C., Li, L. N., Wang, Q. F., Chen, J. M., and Liao, K., “Development and characterization of microsatellite loci in Brasenia schreberi (Cabombaceae) based on the next-generation sequencing”, vol. 15, p. -, 2016.

To understand genetic variability of the endangered aquatic herb Brasenia schreberi (Cabombaceae), we describe 31 microsatellite markers obtained using next-generation sequencing. A total of 24 individuals from the population of Jackson Lake, USA, were genotyped for each marker. Twenty-eight markers were polymorphic. The number of alleles per locus ranged from 1 to 9; the observed and expected heterozygosities ranged from 0 to 1 and from 0 to 0.751, respectively. These markers should be useful tools for genetic variation and conservation studies of B.

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