Sorghum Expressed Sequence Tags Identify Signature Genes for Drought, Pathogenesis, and Skotomorphogenesis from a Milestone Set of 16,801 Unique Transcripts

Abstract

Improved knowledge of the sorghum transcriptome will enhance basic understanding of how plants respond to stresses and serve as a source of genes of value to agriculture. Toward this goal, Sorghum bicolor L. Moench cDNA libraries were prepared from light-and dark-grown seedlings, drought-stressed plants, Colletotrichum-infected seedlings and plants, ovaries, embryos, and immature panicles. Other libraries were prepared with meristems from Sorghum propinquum (Kunth) Hitchc. that had been photoperiodically induced to flower, and with rhizomes from S. propinquum and johnsongrass (Sorghum halepense L. Pers.). A total of 117,682 expressed sequence tags (ESTs) were obtained representing both 3# and 5# sequences from about half that number of cDNA clones. A total of 16,801 unique transcripts, representing tentative UniScripts (TUs), were identified from 55,783 3# ESTs. Of these TUs, 9,032 are represented by two or more ESTs. Collectively, these libraries were predicted to contain a total of approximately 31,000 TUs. Individual libraries, however, were predicted to contain no more than about 6,000 to 9,000, with the exception of light-grown seedlings, which yielded an estimate of close to 13,000. In addition, each library exhibits about the same level of complexity with respect to both the number of TUs preferentially expressed in that library and the frequency with which two or more ESTs is found in only that library. These results indicate that the sorghum genome is expressed in highly selective fashion in the individual organs and in response to the environmental conditions surveyed here. Close to 2,000 differentially expressed TUs were identified among the cDNA libraries examined, of which 775 were differentially expressed at a confidence level of 98%. From these 775 TUs, signature genes were identified defining drought, Colletotrichum infection, skotomorphogenesis (etiolation), ovary, immature panicle, and embryo.

Isolation and characterization of expressed sequence tags (ESTs) from subtracted cDNA libraries of Pennisetum glaucum seedlings

“…For example, 178,000 cDNAs (ESTs) that were randomly sequenced from 61 different cDNA libraries made from different tissues, biotic-and abioticstress challenged and different developmental stages of Arabidopsis identified only 16,115 distinct genes (see Rudd 2003). Similar results were observed in maize (Fernandes et al 2002), sorghum (Pratt et al 2005) and wheat (Houde et al 2006).…”

Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table grape (Muscat Hamburg) and discovery of new candidate genes with potential roles in berry development

“…The authors estimated that their unigene set might have covered upwards of 67% of the grape transcriptome, assuming that the grapevine genome contains ∼ 38,000 genes (da Silva et al, 2005); however, this number of unique sequences derived via computational clustering and assembly of ESTs likely represents an overestimate of the grape genes identified, since the ESTs analyzed represent cDNAs sequenced from both 5′ and 3′ ends. A higher false positive (and false negative) rate was previously observed with 5′ EST clustering (Pratt et al, 2005;Park et al, 2006). For example, using the information available for the Arabidopsis genome, Wang et al (2004) demonstrated that the rate of incorrectly separating ESTs from the same gene into two or more clusters is 30% with 5′ ESTs and 3% with 3′ ESTs.…”

Construction of a full-length cDNA library and preliminary analysis of expressed sequence tags from lymphocytes of half-pipe snowboarding athletes

“…In the present study, we obtained unamplified titers of 1.28 x 10 6 pfu/mL and 1.70 x 10 10 pfu/mL, and inserts between 100 and 1100; 91.2% of the recombinant cDNA library indicated that good quality can provide a basis for the in-depth study of the transcriptional levels of athletes. Another study demonstrated expressed sequence tags (EST) analysis for the study of functional genomics in terms of nucleotide sequences greater than 300 bp that represent information (Pratt et al, 2005). A total of 406 clones were sequenced after the removal of randomly selected sequences of less than 300 bp, leaving 360 sequences of lengths ranging from 300 to 1100, with an average length of 606 bp, which further indicates that the library was well constructed.…”