Expressed sequence tags

Microsatellite markers derived from Japanese scallop (Mizuhopecten yessoensis) expressed sequence tags

Y. F. Li, Gao, X. G., Liu, W. D., Tian, Y., Gao, L., Li, S. L., and He, C. B., “Microsatellite markers derived from Japanese scallop (Mizuhopecten yessoensis) expressed sequence tags”, vol. 13. pp. 1989-1992, 2014.

Japanese scallop (Mizuhopecten yessoensis) is a cold-water shellfish, and a species of economic importance in China. In this study, we developed and evaluated simple sequence repeat (SSR) markers from the expressed sequence tags (ESTs) of M. yessoensis. The characteristics of 12 EST-SSR loci were investigated in 30 individual scallops, and the result revealed that the number of alleles per locus ranged from 2-4, with an observed heterozygosity ranging from 0.0333-0.7692, and an expected heterozygosity ranging from 0.0333-0.6312.

Identification and characterization of differentially expressed genes during incompatible interaction between the foliar rust Melampsora larici-populina and poplar

Z. J. Chen, Cao, Z. M., and Yu, Z. D., “Identification and characterization of differentially expressed genes during incompatible interaction between the foliar rust Melampsora larici-populina and poplar”, vol. 13, pp. 2082-2093, 2014.

Poplars are extensively cultivated worldwide, and their susceptibility to the foliar rust fungus leads to considerable damages in plantations. To better understand the molecular basis of poplar responses to the foliar rust, suppression subtractive hybridization was used to identify the potential important or novel genes involved in the Populus szechuanica infection by Melampsora larici-populina. A total of 515 expressed sequence tags (ESTs) with high quality were obtained and clustered into 66 contigs and 75 singletons to give a set of 141 uniESTs.

Differential expression of resistance to powdery mildew at the early stage of development in wheat line N0308

M. A. Alam, Hongpo, W., Hong, Z., and Ji, W. Q., “Differential expression of resistance to powdery mildew at the early stage of development in wheat line N0308”, vol. 13, pp. 4289-4301, 2014.

Powdery mildew, caused by Blumeria graminis f. sp tritici (Bgt) is one of the devastating diseases of wheat and causes yield losses in temperate wheat growing regions. A wheat line, N0308 with resistance to powdery mildew was used in this study. A suppression subtractive hybridization cDNA library was constructed from the wheat leaves inoculated by Bgt at the two-leaf stage.

Genome-wide identification and phylogenetic analysis of the AP2/ERF gene superfamily in sweet orange (Citrus sinensis)

T. M. Ito, Polido, P. B., Rampim, M. C., Kaschuk, G., and Souza, S. G. H., “Genome-wide identification and phylogenetic analysis of the AP2/ERF gene superfamily in sweet orange (Citrus sinensis)”, vol. 13, pp. 7839-7851, 2014.

Sweet orange (Citrus sinensis) plays an important role in the economy of more than 140 countries, but it is grown in areas with intermittent stressful soil and climatic conditions. The stress tolerance could be addressed by manipulating the ethylene response factor (ERF) transcription factors because they orchestrate plant responses to environmental stress. We performed an in silico study on the ERFs in the expressed sequence tag database of C. sinensis to identify potential genes that regulate plant responses to stress.

New polymorphic microsatellite markers for the Korean manila clam (Ruditapes philippinarum) and their application to wild populations

E. M. Kim, An, H. S., Kang, J. H., An, C. M., Dong, C. M., Hong, Y. K., and Park, J. Y., “New polymorphic microsatellite markers for the Korean manila clam (Ruditapes philippinarum) and their application to wild populations”, vol. 13, pp. 8163-8173, 2014.

Manila clam (Ruditapes philippinarum) is a valuable and intensively exploited shellfish species in Korea. Despite its importance, information on its genetic background is scarce. For the genetic characterization of R. philippinarum, expressed sequence tag-derived microsatellite markers were developed using next-generation sequencing. A total of 5879 tandem repeats containing di- to hexanucleotide repeat motifs were obtained from 236,746 reads (mean = 413 bp).

Transcript profiling of expressed sequence tags from semimembranosus muscle of commercial and naturalized pig breeds

C. S. Nascimento, Peixoto, J. O., Verardo, L. L., Campos, C. F., Weller, M. M. C., Faria, V. R., Botelho, M. E., Martins, M. F., Machado, M. A., Silva, F. F., Lopes, P. S., and Guimarães, S. E. F., “Transcript profiling of expressed sequence tags from semimembranosus muscle of commercial and naturalized pig breeds”, vol. 11, pp. 3315-3328, 2012.

In general, genetic differences across different breeds of pig lead to variation in mature body size and slaughter age. The Commercial breeds Duroc and Large White and the local Brazilian breed Piau are ostensibly distinct in terms of growth and muscularity, commercial breeds are much leaner while local breeds grow much slower and are fat type pigs. However, the genetic factors that underlie such distinctions remain unclear. We used expressed sequence tags (ESTs) to characterize and compare transcript profiles in the semimembranosus muscle of these pig breeds.

Differentially expressed genes implicated in embryo abortion of mango identified by suppression subtractive hybridization

J. H. He, Ma, F. W., Chen, Y. Y., and Shu, H. R., “Differentially expressed genes implicated in embryo abortion of mango identified by suppression subtractive hybridization”, vol. 11, pp. 3966-3974, 2012.

Embryo abortion in mango severely damages mango production worldwide. The mechanisms by which the mango embryos abort have long been an intriguing question. We used subtractive suppression hybridization to investigate the differentially expressed genes involved in this process. We generated 2 cDNA libraries from normal seed and aborted seed embryos of mango cultivar ‘Jinhuang’. One thousand five hundred and seventy-two high-quality expressed sequence tags (ESTs) were obtained, with 1092 from the normal seed tester library and 480 from the aborted seed tester library.

Paeonia (Paeoniaceae) expressed sequence tag-derived microsatellite markers transferred to Paeonia delavayi

D. X. Wang, Ma, H., Zhang, Y. L., Duan, A. A., Li, W. J., and Li, Z. H., “Paeonia (Paeoniaceae) expressed sequence tag-derived microsatellite markers transferred to Paeonia delavayi”, vol. 12, pp. 1278-1282, 2013.

Paeonia Franchet contains approximately 30 species of perennial herbs and is the only member of the family Paeoniaceae. Paeonia delavayi is an endangered ornamental plant that has a compound flower color and is endemic to southwest China. Its optimal habitats have been fragmented and its population size has greatly decreased as a result of human activities. Using a modified biotin-streptavidin capture method, 51 primer sets were identified in 3 wild populations of P. delavayi in this study.

Development and characterization of novel expressed sequence tag-derived simple sequence repeat markers in Hevea brasiliensis (rubber tree)

Z. W. An, Li, Y. C., Zhai, Q. L., Xie, L. L., Zhao, Y. H., and Huang, H. S., “Development and characterization of novel expressed sequence tag-derived simple sequence repeat markers in Hevea brasiliensis (rubber tree)”, vol. 12, pp. 5905-5910, 2013.

Cultivated clones of Hevea brasiliensis have a narrow genetic base. In order to broaden the genetic base, it is first necessary to investigate the genetic diversity of wild populations. Expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed to investigate the genetic diversity of Hevea populations. Four hundred and thirty microsatellites were identified and 148 primers were designed to amplify the loci. Twenty-nine primer pairs were synthesized and evaluated for their ability to detect genetic polymorphisms among 40 wild accessions of H.

Expressed sequenced tags profiling of resistant and susceptible Gyr x Holstein cattle infested with the tick Rhipicephalus (Boophilus) microplus

C. S. Nascimento, Machado, M. A., Guimarães, S. E. F., Martins, M. F., Peixoto, J. O., Furlong, J., Prata, M. C. A., Verneque, R. S., Teodoro, R. L., and Lopes, P. S., “Expressed sequenced tags profiling of resistant and susceptible Gyr x Holstein cattle infested with the tick Rhipicephalus (Boophilus) microplus”, vol. 10, pp. 3803-3816, 2011.

Tick resistance in cattle is mainly found in zebu (Bos indicus) animals, although it is also present in some taurine (B. taurus) breeds. In order to characterize functional genes involved in tick resistance/susceptibility in cattle, two cDNA libraries were generated using skin tissues of selected Holstein x Gyr animals. A total of 2700 high-quality reads from both resistant and susceptible cDNA were assembled into 458 sequences (contigs) and 834 singletons, with a mean size of 447.7 nucleotides.

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