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Identification of sense and antisense transcripts regulated by drought in sugarcane.

Lembke CG, Nishiyama MY, Sato PM, de Andrade RF, Souza GM - Plant Mol. Biol. (2012)

Bottom Line: We validated the results obtained using quantitative real-time PCR (qPCR).Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs).The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Transdução de Sinal, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil.

ABSTRACT
Sugarcane is an important sugar and energy crop that can be used efficiently for biofuels production. The development of sugarcane cultivars tolerant to drought could allow for the expansion of plantations to sub-prime regions. Knowledge on the mechanisms underlying drought responses and its relationship with carbon partition would greatly help to define routes to increase yield. In this work we studied sugarcane responses to drought using a custom designed oligonucleotide array with 21,901 different probes. The oligoarrays were designed to contain probes that detect transcription in both sense and antisense orientation. We validated the results obtained using quantitative real-time PCR (qPCR). A total of 987 genes were differentially expressed in at least one sample of sugarcane plants submitted to drought for 24, 72 and 120 h. Among them, 928 were sense transcripts and 59 were antisense transcripts. Genes related to Carbohydrate Metabolism, RNA Metabolism and Signal Transduction were selected for gene expression validation by qPCR that indicated a validation percentage of 90%. From the probes presented on the array, 75% of the sense probes and 11.9% of the antisense probes have signal above background and can be classified as expressed sequences. Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs). The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts.

Show MeSH
The Probe Design Pipeline was composed of five main steps: 1 Selection of most representative SAS, 2 Identification of Orientation, coding and non-coding SAS and Selection by Functional Category, 3 Design of all available sense and antisense probes for selected SAS, 4 Exclusion of probes that do not agree with the criteria and 5 Probe Blast alignment against Sugarcane EST database to identify the unique probes
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Fig1: The Probe Design Pipeline was composed of five main steps: 1 Selection of most representative SAS, 2 Identification of Orientation, coding and non-coding SAS and Selection by Functional Category, 3 Design of all available sense and antisense probes for selected SAS, 4 Exclusion of probes that do not agree with the criteria and 5 Probe Blast alignment against Sugarcane EST database to identify the unique probes

Mentions: This 44 K microarray consists of sense and antisense probes designed from potential genes using an in house pipeline (Fig. 1) based on the 43,141 Sugarcane Assembled Sequences (SAS) from the Sugarcane EST Project (SUCEST) (Vettore et al. 2003). The features are distributed in a 4 × 44 K array format and are composed of 45,220 total features, corresponding to 1,217 Agilent Controls and 43,803 probes representing SAS. The probes are represented in duplicate on the array, so each array has 21,901 different probes.Fig. 1


Identification of sense and antisense transcripts regulated by drought in sugarcane.

Lembke CG, Nishiyama MY, Sato PM, de Andrade RF, Souza GM - Plant Mol. Biol. (2012)

The Probe Design Pipeline was composed of five main steps: 1 Selection of most representative SAS, 2 Identification of Orientation, coding and non-coding SAS and Selection by Functional Category, 3 Design of all available sense and antisense probes for selected SAS, 4 Exclusion of probes that do not agree with the criteria and 5 Probe Blast alignment against Sugarcane EST database to identify the unique probes
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3369129&req=5

Fig1: The Probe Design Pipeline was composed of five main steps: 1 Selection of most representative SAS, 2 Identification of Orientation, coding and non-coding SAS and Selection by Functional Category, 3 Design of all available sense and antisense probes for selected SAS, 4 Exclusion of probes that do not agree with the criteria and 5 Probe Blast alignment against Sugarcane EST database to identify the unique probes
Mentions: This 44 K microarray consists of sense and antisense probes designed from potential genes using an in house pipeline (Fig. 1) based on the 43,141 Sugarcane Assembled Sequences (SAS) from the Sugarcane EST Project (SUCEST) (Vettore et al. 2003). The features are distributed in a 4 × 44 K array format and are composed of 45,220 total features, corresponding to 1,217 Agilent Controls and 43,803 probes representing SAS. The probes are represented in duplicate on the array, so each array has 21,901 different probes.Fig. 1

Bottom Line: We validated the results obtained using quantitative real-time PCR (qPCR).Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs).The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Transdução de Sinal, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil.

ABSTRACT
Sugarcane is an important sugar and energy crop that can be used efficiently for biofuels production. The development of sugarcane cultivars tolerant to drought could allow for the expansion of plantations to sub-prime regions. Knowledge on the mechanisms underlying drought responses and its relationship with carbon partition would greatly help to define routes to increase yield. In this work we studied sugarcane responses to drought using a custom designed oligonucleotide array with 21,901 different probes. The oligoarrays were designed to contain probes that detect transcription in both sense and antisense orientation. We validated the results obtained using quantitative real-time PCR (qPCR). A total of 987 genes were differentially expressed in at least one sample of sugarcane plants submitted to drought for 24, 72 and 120 h. Among them, 928 were sense transcripts and 59 were antisense transcripts. Genes related to Carbohydrate Metabolism, RNA Metabolism and Signal Transduction were selected for gene expression validation by qPCR that indicated a validation percentage of 90%. From the probes presented on the array, 75% of the sense probes and 11.9% of the antisense probes have signal above background and can be classified as expressed sequences. Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs). The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts.

Show MeSH