Transcriptome

De novo assembly and characterization of farmed blue fox (Alopex lagopus) global transcriptome using Illumina paired-end sequencing

P. C. Guo, Yan, S. Q., Si, S., Bai, C. Y., Zhao, Y., Zhang, Y., Yao, J. Y., Li, Y. M., Guo, P. C., Yan, S. Q., Si, S., Bai, C. Y., Zhao, Y., Zhang, Y., Yao, J. Y., Li, Y. M., Guo, P. C., Yan, S. Q., Si, S., Bai, C. Y., Zhao, Y., Zhang, Y., Yao, J. Y., and Li, Y. M., De novo assembly and characterization of farmed blue fox (Alopex lagopus) global transcriptome using Illumina paired-end sequencing, vol. 15, p. -, 2016.

The blue fox (Alopex lagopus), a coat-color variant of the Arctic fox, is a domesticated fur-bearing mammal. In the present study, transcriptome data generated from a pool of nine different tissues were obtained with Illumina HiSeq2500 paired-end sequencing technology. After filtering from raw reads, 32,358,290 clean reads were assembled into 161,269 transcripts and 97,252 unigenes by the Trinity fragment assembly software.

Transcriptome analysis and anthocyanin-related genes in red leaf lettuce

Y. Z. Zhang, Xu, S. Z., Cheng, Y. W., Ya, H. Y., Han, J. M., Zhang, Y. Z., Xu, S. Z., Cheng, Y. W., Ya, H. Y., Han, J. M., Zhang, Y. Z., Xu, S. Z., Cheng, Y. W., Ya, H. Y., and Han, J. M., Transcriptome analysis and anthocyanin-related genes in red leaf lettuce, vol. 15, p. -, 2016.

This study aimed to analyze the transcriptome profile of red lettuce and identify the genes involved in anthocyanin accumulation. Red leaf lettuce is a popular vegetable and popular due to its high anthocyanin content. However, there is limited information available about the genes involved in anthocyanin biosynthesis in this species. In this study, transcriptomes of 15-day-old seedlings and 40-day-old red lettuce leaves were analyzed using an Illuminia HiseqTM 2500 platform.

Gene expression profiles in the pituitary glands of Sichuan White geese during prelaying and laying periods

G. L. Gao, Zhao, X. Z., Li, Q., Su, J., and Wang, Q. G., Gene expression profiles in the pituitary glands of Sichuan White geese during prelaying and laying periods, vol. 14, pp. 12636-12645, 2015.

To better understand the molecular mechanism(s) underlying egg-laying in Sichuan white geese, the profiles of genes in the pituitary gland were investigated during the prelaying and laying periods. Total RNA was extracted from the pituitary glands of geese during prelaying or laying periods and cDNA was generated. After sequencing and annotation, 54 upregulated and 84 downregulated genes were obtained from gene libraries.

Comparative transcriptome analysis of Nile tilapia (Oreochromis niloticus) in response to alkalinity stress

Y. Zhao, Wang, J., Thammaratsuntorn, J., Wu, J. W., Wei, J. H., Wang, Y., Xu, J. W., and Zhao, J. L., Comparative transcriptome analysis of Nile tilapia (Oreochromis niloticus) in response to alkalinity stress, vol. 14, pp. 17916-17926, 2015.

To identify genes of potential importance to alkalinity tolerance, RNA sequencing (RNA-Seq) was performed to survey gill transcriptome profiles from freshwater (FW) and alkaline water (AW) exposed Nile tilapia (Oreochromis niloticus). A total of 22,724,036 (AW)/16,461,040 (FW) single-end reads were generated in which 20,304,348 (AW)/14,681,290 (FW) reads (90.0/89.72%) were aligned to the reference genome. Differential expression analysis revealed 302 up-regulated and 193 down-regulated genes between AW- and FW-exposed fish.

Comparative transcriptome analysis of testes and ovaries for the discovery of novel genes from Amur sturgeon (Acipenser schrenckii)

S. B. Jin, Zhang, Y., Dong, X. L., Xi, Q. K., Song, D., Fu, H. T., and Sun, D. J., Comparative transcriptome analysis of testes and ovaries for the discovery of novel genes from Amur sturgeon (Acipenser schrenckii), vol. 14, pp. 18913-18927, 2015.

Sturgeons (Acipenser schrenckii) are of high evolutionary, economic, and conservation value, and caviar isone of the most valuable animal food products in the world. The Illumina HiSeq2000 sequencing platform was used to construct testicular and ovarian transcriptomes to identify genes involved in reproduction and sex determination in A. schrenckii. A total of 122,381 and 114,527 unigenes were obtained in the testicular and ovarian transcriptomes, respectively, with average lengths of 748 and 697 bp.

Transcriptomic analysis of Camellia ptilophylla and identification of genes associated with flavonoid and caffeine biosynthesis

M. M. Li, Xue, J. Y., Wen, Y. L., Guo, H. S., Sun, X. Q., Zhang, Y. M., and Hang, Y. Y., Transcriptomic analysis of Camellia ptilophylla and identification of genes associated with flavonoid and caffeine biosynthesis, vol. 14, pp. 18731-18742, 2015.

Camellia ptilophylla, or cocoa tea, is naturally decaffeinated and its predominant catechins and purine alkaloids are trans-catechins and theobromine Regular tea [Camellia sinensis (L.) O. Ktze.] is evolutionarily close to cocoa tea and produces cis-catechins and caffeine. Here, the transcriptome of C. ptilophylla was sequenced using the 101-bp paired-end technique.

Transcriptomic identification of chemoreceptor genes in the red palm weevil Rhynchophorus ferrugineus

W. Yan, Liu, L., Qin, W. Q., Li, C. X., and Peng, Z. Q., Transcriptomic identification of chemoreceptor genes in the red palm weevil Rhynchophorus ferrugineus, vol. 14, pp. 7469-7480, 2015.

Olfaction is crucial for insects’ survival because it enables them to recognize various environmental information. It is primarily mediated by a large family of chemoreceptors, including olfactory receptors (ORs), gustatory receptors (GRs), and ionotropic receptors (IRs). Here, we assembled the transcriptome of the economically important pest of palms, Rhynchophorus ferrugineus, to reveal its chemoreceptor gene repertoire. About 8.08 Gbp data were generated using a HiSeq platform and their assembly led to a total of 24,439 unigenes.

Leaf transcriptome analysis and development of SSR markers in water chestnut (Eleocharis dulcis)

H. B. Liu, You, Y. N., Zhu, Z. X., Zheng, X. F., Huang, J. B., Hu, Z. L., and Diao, Y., Leaf transcriptome analysis and development of SSR markers in water chestnut (Eleocharis dulcis), vol. 14, pp. 8314-8325, 2015.

Water chestnut (Eleocharis dulcis) is an important aquatic crop in China; however, transcriptomic and genomic data in public databases are limited. To identify genes and development molecular markers, high-throughput transcriptome sequencing was applied to generate transcript sequences from water chestnut leaf. More than 24 million reads were obtained, trimmed, and assembled into 40,796 contigs with an average length of 616.6 bp.

Identification of heat shock proteins via transcriptome profiling of tree peony leaf exposed to high temperature

Y. Z. Zhang, Cheng, Y. W., Ya, H. Y., Han, J. M., and Zheng, L., Identification of heat shock proteins via transcriptome profiling of tree peony leaf exposed to high temperature, vol. 14, pp. 8431-8442, 2015.

The tree peony leaf is an important vegetative organ that is sensitive to abiotic stress and particularly to high temperature. This sensitivity affects plant growth and restricts tree peony distribution. However, the transcriptomic information currently available on the peony leaf in public databases is limited. In this study, we sequenced the transcriptomes of peony leaves subjected to high temperature using the Illumina HiSeq TM 2000 platform. We performed de novo assembly of 93,714 unigenes (average length of 639.7 bp).

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