Integration of Expressed Sequence Tag Data Flanking Predicted RNA Secondary Structures Facilitates Novel Non-Coding RNA Discovery

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

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Screening and analysis of differentially expressed genes from an alien addition line of wheat Thinopyrum intermedium induced by barley yellow dwarf virus infection

Genome ◽

10.1139/g04-070 ◽

2004 ◽

Vol 47 (6) ◽

pp. 1114-1121 ◽

Cited By ~ 8

Author(s):

Shu-Mei Jiang ◽

Long Zhang ◽

Jun Hu ◽

Rui Shi ◽

Guang-He Zhou ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Expressed Sequence Tag ◽

Barley Yellow Dwarf Virus ◽

Differentially Expressed ◽

Addition Line ◽

Alien Chromosome ◽

Thinopyrum Intermedium ◽

Barley Yellow Dwarf ◽

Yellow Dwarf Virus ◽

Expressed Sequence

The alien addition line TAI-27 contains a pair of chromosomes of Thinopyrum intermedium that carry resistance against barley yellow dwarf virus (BYDV). A subtractive library was constructed using the leaves of TAI-27, which were infected by Schizaphis graminum carrying the GAV strain of BYDV, and the control at the three-leaf stage. Nine differentially expressed genes were identified from 100 randomly picked clones and sequenced. Two of the nine clones were highly homologous with known genes. Of the remaining seven cDNA clones, five clones matched with known expressed sequence tag (EST) sequences from wheat and (or) barley whereas the other two clones were unknown. Five of the nine differentially expressed sequences (WTJ9, WTJ11, WTJ15, WTJ19, and WTJ32) were highly homologous (identities >94%) with ESTs from wheat or barley challenged with pathogens. These five sequences and another one (WTJ18) were also highly homologous (identities >86%) with abiotic stress induced ESTs in wheat or barley. Reverse Northern hybridization showed that seven of the nine differentially expressed cDNA sequences hybridized with cDNA of T. intermedium infected by BYDV. Three of these also hybridized with cDNA of line 3B-2 (a parent of TAI-27) infected by BYDV. The alien chromosome in TAI-27 was microdissected. The second round linker adaptor mediated PCR products of the alien chromosomal DNA were labeled with digoxygenin and used as the probe to hybridize with the nine differentially expressed genes. The analysis showed that seven differentially expressed genes were homologous with the alien chromosome of TAI-27. These seven differentially expressed sequences could be used as ESTs of the alien chromosome of TAI-27. This research laid the foundation for screening and cloning of new specific functional genes conferring resistance to BYDV and probably other pathogens.Key words: suppression subtractive hybridization (SSH), expressed sequence tag (EST), linker adaptor mediated polymerase chain reaction (LA-PCR), chromosome microdissection.

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Evolution of ITS Ribosomal RNA Secondary Structures in Fungal and Algal Symbionts of Selected Species of Cladonia sect. Cladonia (Cladoniaceae, Ascomycotina)

Journal of Molecular Evolution ◽

10.1007/s00239-006-0115-x ◽

2007 ◽

Vol 64 (5) ◽

pp. 528-542 ◽

Cited By ~ 31

Author(s):

Sara Beiggi ◽

Michele D. Piercey-Normore

Keyword(s):

Ribosomal Rna ◽

Secondary Structures ◽

Rna Secondary Structures ◽

Algal Symbionts

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Mutually exclusive RNA secondary structures regulate translation initiation of DinQ in Escherichia coli

RNA ◽

10.1261/rna.058461.116 ◽

2016 ◽

Vol 22 (11) ◽

pp. 1739-1749 ◽

Cited By ~ 10

Author(s):

Knut I. Kristiansen ◽

Ragnhild Weel-Sneve ◽

James A. Booth ◽

Magnar Bjørås

Keyword(s):

Escherichia Coli ◽

Translation Initiation ◽

Secondary Structures ◽

Rna Secondary Structures

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Characterization of expressed sequence tag-derived simple sequence repeat markers for 17 Linum species

Botany ◽

10.1139/b10-019 ◽

2010 ◽

Vol 88 (5) ◽

pp. 537-543 ◽

Cited By ~ 11

Author(s):

Yong-Bi Fu ◽

Gregory W. Peterson

Keyword(s):

Simple Sequence Repeat ◽

Expressed Sequence Tag ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Linum Usitatissimum L ◽

Evolutionary Studies ◽

Expressed Sequence ◽

Simple Sequence ◽

Cultivated Flax

One major challenge in genetic and evolutionary studies of wild flax species is the lack of informative molecular markers. A set of 100 informative expressed sequence tag-derived simple sequence repeat (EST-SSR) primer pairs developed in cultivated flax ( Linum usitatissimum L.) were characterized on 35 Linum accessions representing 17 Linum species for their transferability to other Linum species. Ninety-nine primer pairs displayed scorable polymorphisms across 35 Linum samples and generated 627 bands likely from 121 loci. About 50% of the detected bands occurred only in three or fewer samples. A total of 393 bands, likely from 116 loci, were detected by 97 primer pairs in Linum bienne Mill. samples, but only up to 60 bands, likely from up to 39 loci, were revealed by 6 to 37 primer pairs in the samples of the other 15 Linum species. The L. bienne samples displayed 23.7% more EST-SSR variation than the L. usitatissimum samples. These characterized EST-SSR markers should be useful for future genetic diversity and evolutionary studies of Linum species, particularly for the progenitor of cultivated flax.

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