High-throughput sequencing

Identification of highly expressed host microRNAs that respond to white spot syndrome virus infection in the Pacific white shrimp Litopenaeus vannamei (Penaeidae)

D. G. Zeng, Chen, X. L., Xie, D. X., Zhao, Y. Z., Yang, Q., Wang, H., Li, Y. M., and Chen, X. H., Identification of highly expressed host microRNAs that respond to white spot syndrome virus infection in the Pacific white shrimp Litopenaeus vannamei (Penaeidae), vol. 14, pp. 4818-4828, 2015.

MicroRNAs (miRNAs) are known to play an important role in regulating both adaptive and innate immunity. Pacific white shrimp (Litopenaeus vannamei) is the most widely farmed crustacean species in the world. However, little is known about the role miRNAs play in shrimp immunity. To understand the impact of viral infection on miRNA expression in shrimp, we used high-throughput sequencing technology to sequence two small RNA libraries prepared from L. vannamei under normal and white spot syndrome virus (WSSV) challenged conditions.

A new reliable reference gene UBA52 for quantitative real-time polymerase chain reaction studies in pyloric cecal tissues of the starfish Asterias rubens

A. F. Sadritdinova, Dmitriev, A. A., Snezhkina, A. V., Belenikin, M. S., Krasnov, G. S., Manylov, O. G., Kudryavtsev, A. A., Melnikova, N. V., Speranskaya, A. S., Darii, M. V., Lakunina, V. A., Uroshlev, L. A., Smurov, A. O., Stepanov, O. A., and Kudryavtseva, A. V., A new reliable reference gene UBA52 for quantitative real-time polymerase chain reaction studies in pyloric cecal tissues of the starfish Asterias rubens, vol. 13, pp. 3972-3980, 2014.

The starfish Asterias rubens is one of the most abundant echinoderm species in the White, Barents, North, and Baltic Seas. This species is an important component of marine ecosystems and a model object for certain biological studies, in particular those requiring quantitative estimation of gene expression. As a rule, expression at the transcriptional level is estimated by real-time qPCR using the ΔΔCt method, which allows the comparison of the copy number of target gene transcripts in samples with unknown mRNA/cDNA concentration.

Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum)

M. Nicolaï, Pisani, C., Bouchet, J. - P., Vuylsteke, M., and Palloix, A., Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum), vol. 11. pp. 2295-2300, 2012.

Genetic markers based on single nucleotide polymorphisms (SNPs) are in increasing demand for genome mapping and fingerprinting of breeding populations in crop plants. Recent advances in high-throughput sequencing provide the opportunity for whole-genome resequencing and identification of allelic variants by mapping the reads to a reference genome. However, for many species, such as pepper (Capsicum annuum), a reference genome sequence is not yet available. To this end, we sequenced the C. annuum cv.

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