Novel genes are enriched in normalized cDNA libraries from drought-stressed seedlings of rice (<i>Oryza sativa</i> L. subsp. <i>indica </i>cv. Nagina 22)

Reddy, A. R.; Ramakrishna, Wusirika; Akila, Chandra Sekhar; Ithal, Nagabhushana; Babu, P. D.; Bonaldo, Maria F.; Soares, Marcelo B.; Bennetzen, Jeffrey L.

doi:10.1139/g01-114

Cited by 71 publications

(42 citation statements)

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“…An EST project yields close to 100% nuclear gene discovery in its very early stage (although it also uncovers transcribed transposable elements and organellar genes), but it rapidly loses efficiency because of redundant sequencing of the same highly expressed genes. This redundancy problem is significantly decreased, but far from eliminated, in normalized libraries (Soares et al 1994;Reddy et al 2002) or by using different tissue, developmental time, and treatment sources of RNA. HMPR analysis yields all unmethylated genic regions at levels associated with their genomic representation.…”

Section: Discussionmentioning

confidence: 99%

Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries

Emberton¹,

Ma²,

Yuan³

et al. 2005

Genome Res.

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A new technology was developed to assist gene-enrichment sequencing of any complex plant genome, employing maize as the test organism. Hypomethylated partial restriction (HMPR) libraries were constructed by using independent partial digestions with methylation-sensitive restriction enzymes HpaII (5Ј-CCGG-3Ј) and HpyCH4IV (5Ј-ACGT-3Ј). Fragments of 1-4 kb were purified and cloned, followed by sequence analysis of >2000 clones from 10 separate libraries. Organellar clones comprised ∼10% of each library but were useful in showing that no chimeric clones were generated and that digestion efficiencies were 10%-25% in different libraries. Four separate HMPR libraries, analyzed in detail, exhibited very similar degrees of gene enrichment and repeat depletion. Known gene homologies were found in ∼25% of the HMPR clones, compared with <4% in clones from a fully random set of unfiltered maize shotgun sequences. This six-to sevenfold enrichment for genes compares favorably with the best previous gene enrichment techniques in maize, High Cot analysis and methylation filtration. Compared with High Cot and methylation filtration, HMPR is exceptional in depleting retrotransposons' content to the lowest level yet observed (<5%, compared with >70% for unfiltered maize sequences) and in providing an unmatched enrichment for the "unknown" sequences that contain promoters, introns, and other gene-adjacent regions.[The sequence data from this study have been submitted to GenBank under accession nos. CW539179-CW542054.]Although flowering plant genomes vary enormously in nuclear DNA content, from the <150 Mb of a handful of species to the ∼140,000 Mb of Fritillaria assyriaca, most contain between 1000 and 8000 Mb per haploid genome (with a median of ∼3000 Mb) scattered across anywhere from two to >300 chromosomes (Kenton et al. 1993;Leitch et al. 2005). Gene content is much more constant, for instance varying less than twofold between the large genome of barley (Hordeum vulgare, ∼4900 Mb) and the smaller genome of rice (Oryza sativa, ∼440 Mb) (Van Deynze et al. 1998). Some publications (Goff et al. 2002;Yu et al. 2002;Feng et al. 2003; Rice Chromosome 10 Sequencing Consortium 2003;Sasaki et al. 2002) have concluded that rice might have about twice as many genes as does Arabidopsis thaliana (120-150 Mb), but other studies have indicated that most of these "extra" rice genes are artifacts of annotation, leading to the current conclusion that rice and Arabidopsis contain very similar gene numbers (Bennetzen 2002b;Bennetzen et al. 2004;Jabbari et al. 2004;. Moreover, the average size of genes does not vary >50% between the small genome of Arabidopsis and large genome species such as barley or cotton (Dubcovsky et al. 2001;Wendel et al. 2002). Hence, the space occupied by genes within a plant nuclear genome, the "gene space," is not nearly so variable as is the overall DNA content of the genome.In the maize (Zea mays) genome, ∼2400 Mb of DNA is distributed across the 10 chromosomes in a haploid nucleus. A precise gene number is not known f...

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Section: Discussionmentioning

confidence: 99%

Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries

Emberton¹,

Ma²,

Yuan³

et al. 2005

Genome Res.

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“…Transient gene induction was also found following abiotic stress treatment, such as cold, osmotic, or drought (Bray, 2002;Reddy et al, 2002), and by addition of the phytohormone ABA (AtGenExpress; Lin et al, 2003). Another link with plant hormones is also suggested by remorin AtREM1.3 (Alliotte et al, 1989), which was copurified with the cytokinin-induced response regulator AtARR4 (Yamada et al, 1998).…”

Section: The Remorin Family Consists Of Six Different Groupsmentioning

confidence: 99%

Genome-Wide Annotation of Remorins, a Plant-Specific Protein Family: Evolutionary and Functional Perspectives

et al. 2007

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“…Yamaguchi-Shinozaki and Shinozaki, 1993a; Siddiqui et al, 1998;Thomashow, 1999;Finkelstein et al, 2002;Soulages et al, 2003). In addition to the dehydration-associated genes, there were also examples of genes associated with stomatal distribution and regulation (Berger and Altmann, 2000) and signal transduction pathways induced by hypobaria that included kinases and kinase-related proteins (Guo et al, 2002;Yoshida et al, 2002), calcium-binding proteins (Takahashi et al, 2000;Sadiqov et al, 2002) and a cytochrome p450 (Reddy et al, 2002).…”

Section: Differential Expression Of Genes On the Arraymentioning

confidence: 99%

Hypobaric Biology: Arabidopsis Gene Expression at Low Atmospheric Pressure

et al. 2004

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(M.P.P.) As a step in developing an understanding of plant adaptation to low atmospheric pressures, we have identified genes central to the initial response of Arabidopsis to hypobaria. Exposure of plants to an atmosphere of 10 kPa compared with the sea-level pressure of 101 kPa resulted in the significant differential expression of more than 200 genes between the two treatments. Less than one-half of the genes induced by hypobaria are similarly affected by hypoxia, suggesting that response to hypobaria is unique and is more complex than an adaptation to the reduced partial pressure of oxygen inherent to hypobaric environments. In addition, the suites of genes induced by hypobaria confirm that water movement is a paramount issue at low atmospheric pressures, because many of gene products intersect abscisic acid-related, drought-induced pathways. A motivational constituent of these experiments is the need to address the National Aeronautics and Space Administration's plans to include plants as integral components of advanced life support systems. The design of bioregenerative life support systems seeks to maximize productivity within structures engineered to minimize mass and resource consumption. Currently, there are severe limitations to producing Earth-orbital, lunar, or Martian plant growth facilities that contain Earth-normal atmospheric pressures within light, transparent structures. However, some engineering limitations can be offset by growing plants in reduced atmospheric pressures. Characterization of the hypobaric response can therefore provide data to guide systems engineering development for bioregenerative life support, as well as lead to fundamental insights into aspects of desiccation metabolism and the means by which plants monitor water relations.Interest in the exploration of environments beyond Earth's atmosphere has brought unique challenges to bear on the understanding of the biological systems that will inhabit those environments. Among these challenges are alterations in atmospheric pressure, which are known to have effects on plant physiology and development (Mansell et al., 1968; Gale, 1973; Andre and Richaux, 1986;McKay and Toon, 1991; Andre and Massimino, 1992;Wheeler, 2000; He et al., 2003). Concepts for greenhouses on Mars, on the moon, and in Earth orbit incorporate low atmospheric pressures to address engineering and systems limitations (Boston, 1981; Drysdale, 2001).Historically, low-pressure environments have been used throughout the U.S. human space exploration programs to reduce the masses of structural and consumable components of space vehicles. Such reductions have resulted in increased mission lengths and/or increased masses of launched payloads. For example, the Mercury, Gemini, and Apollo environments were designed to operate at 34 kPa with a pure oxygen environment to simplify support of humans in space (Baker, 1981;Martin and McCormick, 1992). Skylab was also operated at 34 kPa (with a 70% O 2 /30% N 2 gas mixture), and that pressure was further reduced during period...

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Novel genes are enriched in normalized cDNA libraries from drought-stressed seedlings of rice (Oryza sativa L. subsp. indica cv. Nagina 22)

Cited by 71 publications

References 34 publications

Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries

Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries

Genome-Wide Annotation of Remorins, a Plant-Specific Protein Family: Evolutionary and Functional Perspectives

Hypobaric Biology: Arabidopsis Gene Expression at Low Atmospheric Pressure

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