scholarly journals Identification of Differentially Expressed Genes in Axillary Tillers of Perennial Ryegrass

2009 ◽  
Vol 63 (1-2) ◽  
pp. 25-28
Author(s):  
Gintaras Brazauskas ◽  
Izolda Pašakinskienė
Keyword(s):  
Differentially Expressed Genes ◽  
Perennial Ryegrass ◽  
Expressed Sequence Tags ◽  
Sequence Similarity ◽  
Differentially Expressed ◽  
Sequence Length ◽  
Auxin Response ◽  
Suppression Subtractive Hybridisation ◽  
Subtractive Hybridisation ◽  
Expressed Sequence

Identification of Differentially Expressed Genes in Axillary Tillers of Perennial Ryegrass A PCR-based suppression subtractive hybridisation (SSH) technique was used to identify differentially expressed genes in the primary and axillary tillers of a perennial ryegrass (Lolium perenne L.) mutant with enhanced axillary tillering. A total of 310 expressed sequence tags (ESTs) were obtained representing 249 non-redundant sequences. The average EST sequence length was 249 nt and varied from 30 to 508 nt. Putative function was assigned to 152 ESTs by comparing sequences with publicly available databases of NCBI. The remaining 97 ESTs had no sequence similarity matches to any of the known databases. Several ESTs were selected as potential candidates for the control of axillary tiller formation. RUB1 conjugating enzyme and BIG protein were shown to play role in auxin response regulation, SHOOT1 protein was associated with fasciation mutation in soybean (Glycine max L.), and brassinosteroid LRR receptor kinase with brassinosteroid signalling.

scholarly journals Analysis of expressed sequence tags derived from the endophytic fungus Neotyphodium lolii grown in vitro and in association with its host plant perennial ryegrass

2007 ◽  
Vol 13 ◽  
pp. 501-504
Author(s):  
R. Johnson ◽  
A. Khan ◽  
C. Voisey ◽  
S. Bassett ◽  
C. Gaborit ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Virulence Genes ◽  
In Planta ◽  
Suppression Subtractive Hybridisation ◽  
The Public ◽  
Neotyphodium Lolii ◽  
Subtractive Hybridisation ◽  
Plant Genes ◽  
Expressed Sequence

As a first step towards a functional genomics approach to gain a greater understanding of this important symbiosis, we have generated, sequenced and analysed two EST libraries from cultures of N. lolii and six in planta subtracted EST libraries enriched for differentially expressed genes. A total of 12871 ESTs were sequenced which, after filtering for quality, clustered into 1066 contigs and 3230 singletons to give a set of 4296 unique sequences or unigenes. BLASTX analysis revealed that 60% of fungal sequences derived from cultures were of unknown function with a sub-set of these corresponding to orphans. For the in planta-derived ESTs, most of the sequences with homologs in the public databases (98%) were of ryegrass origin. Comparisons made against fully sequenced genomes revealed that most fungal ESTs were homologous to genes present in both pathogenic and non-pathogenic ascomycete filamentous fungi, whereas the subtracted libraries comprised mostly plant genes. A range of sequences having significant homology to demonstrated pathogenicity/virulence genes in other fungal pathosystems were also identified, as well as some ESTs with proven roles in endophyte secondary metabolism. Keywords: ESTs, cDNA, Neotyphodium lolii, Lolium perenne, symbiosis, mutualism, suppression subtractive hybridisation

scholarly journals An Empirical Bayesian Method for Detecting Differentially Expressed Genes Using EST Data

2008 ◽  
Vol 2008 ◽  
pp. 1-4 ◽  
Author(s):  
Na You ◽  
Junmei Liu ◽  
Chang Xuan Mao
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Expressed Sequence Tags ◽  
Bayesian Method ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Gene Expression Patterns ◽  
Empirical Bayesian ◽  
Empirical Bayesian Method ◽  
Expressed Sequence

Detection of differentially expressed genes from expressed sequence tags (ESTs) data has received much attention. An empirical Bayesian method is introduced in which gene expression patterns are estimated and used to define detection statistics. Significantly differentially expressed genes can be declared given detection statistics. Simulation is done to evaluate the performance of proposed method. Two real applications are studied.

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

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1114-1121 ◽  
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.

scholarly journals Suppressed expression of genes involved in transcription and translation in in vitro compared with in vivo cultured bovine embryos

Reproduction ◽  
2006 ◽  
Vol 131 (4) ◽  
pp. 651-660 ◽  
Author(s):  
D Corcoran ◽  
T Fair ◽  
S Park ◽  
D Rizos ◽  
O V Patel ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Differentially Expressed ◽  
Bovine Embryos ◽  
Quantitative Real Time Pcr ◽  
Expression Of Genes ◽  
Mrna Transcripts ◽  
Induced Changes ◽  
Expressed Sequence

In vivo-derived bovine embryos are of higher quality than those derivedin vitro. Many of the differences in quality can be related to culture environment-induced changes in mRNA abundance. The aim of this study was to identify a range of mRNA transcripts that are differentially expressed between bovine blastocysts derived fromin vitroversusin vivoculture. Microarray (BOTL5) comparison betweenin vivo- andin vitro-cultured bovine blastocysts identified 384 genes and expressed sequence tags (ESTs) that were differentially expressed; 85% of these were down-regulated inin vitrocultured blastocysts, showing a much reduced overall level of mRNA expression inin vitro- compared within vivo-cultured blastocysts. Relative expression of 16 out of 23 (70%) differentially expressed genes (according toPvalue) were verified in new pools ofin vivo- andin vitro-cultured blastocysts, using quantitative real-time PCR. Most (10 out of 16) are involved in transcription and translation events, suggesting that the reason whyin vitro-derived embryos are of inferior quality compared within vivo-derived embryos is due to a deficiency of the machinery associated with transcription and translation.

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