Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA

Bennetzen, Jeffrey L.; Schrick, Kathrin; Springer, Patricia S.; Brown, Willis E.; SanMiguel, Phillip

doi:10.1139/g94-081

Cited by 176 publications

(137 citation statements)

References 47 publications

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“…Two different wash conditions, a low stringency ‫ן1(‬ SSC at 65°C) and a high stringency ‫ן1.0(‬ SSC at 65°C) were compared to determine how much of the difference in signal was attributable to sequence divergence (Table 5). Relative abundances of the different families are in fairly good accordance with the abundance estimates derived from Table 2, and with those described more generally in similar dot-blot experiments (Bennetzen et al 1994). The copy number of most of these elements doubles under low stringency hybridizations ‫ן1(‬ SSC; Table 5), possibly indicating the presence of extended and overlapping divergent families of retroelements and explaining at least partly the fact that estimates based on hybridization tend to be higher than those based on sequence analysis (Table 1).…”

Section: Maize Repetitive Elementssupporting

confidence: 88%

“…Repetitive DNA in plants is often methylated, whereas single or low-copy sequences such as genes are usually hypomethylated (Bennetzen et al 1994). Rabinowicz et al (1999) demonstrated that many repeated DNA sequences in maize can be excluded from small-insert DNA libraries using bacterial restriction-modification systems to select against methylated DNA sequences.…”

Section: Hypomethylated Regions Contain Few Members Of Abundant Retromentioning

confidence: 99%

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Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome

Meyers

Tingey²,

Morgante³

2001

Genome Res.

376

313

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Long terminal repeat (LTR) retrotransposons have been shown to make up much of the maize genome. Although these elements are known to be prevalent in plant genomes of a middle-to-large size, little information is available on the relative proportions composed by specific families of elements in a single genome. We sequenced a library of randomly sheared genomic DNA from maize to characterize this genome. BLAST analysis of these sequences demonstrated that the maize genome is composed of diverse sequences that represent numerous families of retrotransposons. The largest families contain the previously described elements Huck, Ji, and Opie. Approximately 5% of the sequences are predicted to encode proteins. The genomic abundance of 16 families of elements was estimated by hybridization to an array of 10,752 maize bacterial artificial chromosome (BAC) clones. Comparisons of the number of elements present on individual BACs indicated that retrotransposons are in general randomly distributed across the maize genome. A second library was constructed that was selected to contain sequences hypomethylated in the maize genome. Sequence analysis of this library indicated that retroelements abundant in the genome are poorly represented in hypomethylated regions. Fifty-six retroelement sequences corresponding to the integrase and reverse transcriptase domains were isolated from ∼407,000 maize expressed sequence tags (ESTs). Phylogenetic analysis of these and the genomic retroelement sequences indicated that elements most abundant in the genome are less abundant at the transcript level than are more rare retrotransposons. Additional phylogenies also demonstrated that rice and maize retrotransposon families are frequently more closely related to each other than to families within the same species. An analysis of the GC content of the maize genomic library and that of maize ESTs did not support recently published data that the gene space in maize is found within a narrow GC range, but does indicate that genic sequences have a higher GC content than intergenic sequences (52% vs. 47% GC).

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Section: Maize Repetitive Elementssupporting

confidence: 88%

Section: Hypomethylated Regions Contain Few Members Of Abundant Retromentioning

confidence: 99%

Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome

Meyers

Tingey²,

Morgante³

2001

Genome Res.

376

313

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“…Seventeen clones carrying maize repetitive nucleotide sequences (30) were kindly provided by J. Bennetzen (Purdue University, West Lafayette, IN). A clone containing the maize 185-bp knob repeat (36) was provided by W. Peacock (Commonwealth Scientific and Industrial Research Organization, Canberra, Australia).…”

Section: Methodsmentioning

confidence: 99%

“…The success of isolating maize DNA from oat-maize chromosome-addition lines depends on how many maize-specific (relative to oat) high-copy-number dispersed nucleotide sequences are found in the maize genome. Genome analysis in grasses, including maize and oat, reveals that a major portion of genomic DNA consists of families of repetitive sequences dispersed throughout the genome (26,29,30). According to DNA-DNA renaturation data in maize (28), unique sequences of average length 2,100 bp are interspersed with mid-repetitive sequences.…”

mentioning

confidence: 99%

Oat–maize chromosome addition lines: A new system for mapping the maize genome

Ananiev

Riera‐Lizarazu

Rines

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

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Novel plants with individual maize chromosomes added to a complete oat genome have been recovered via embryo rescue from oat (Avena sativa L., 2n ‫؍‬ 6x ‫؍‬ 42) ؋ maize (Zea mays L., 2n ‫؍‬ 20) crosses. An oat-maize disomic addition line possessing 21 pairs of oat chromosomes and one maize chromosome 9 pair was used to construct a cosmid library. A multiprobe (mixture of labeled fragments used as a probe) of highly repetitive maize-specific sequences was used to selectively isolate cosmid clones containing maize genomic DNA. Hybridization of individual maize cosmid clones or their subcloned fragments to maize and oat genomic DNA revealed that most high, middle, or low copy number DNA sequences are maize-specific. Such DNA markers allow the identification of maize genomic DNA in an oat genomic background. Chimeric cosmid clones were not found; apparently, significant exchanges of genetic material had not occurred between the maize-addition chromosome and the oat genome in these novel plants or in the cloning process. About 95% of clones selected at random from a maize genomic cosmid library could be detected by the multiprobe. The ability to selectively detect maize sequences in an oat background enables us to consider oat as a host for the cloning of specific maize chromosomes or maize chromosome segments. Introgressing maize chromosome segments into the oat genome via irradiation should allow the construction of a library of overlapping fragments for each maize chromosome to be used for developing a physical map of the maize genome.

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“…MF has already been applied successfully in maize (Zea mays), sorghum (Sorghum bicolor), and cowpea (Vigna unguiculata; Rabinowicz et al, 1999;Palmer et al, 2003;Whitelaw et al, 2003;Chen et al, 2007). The development of MF followed studies of genome architecture that revealed that repetitive elements tend to form clusters within plant genomes that become heavily methylated (hypermethylated), leaving stretches of less-methylated (hypomethylated), low-copy gene-rich space scattered in islands throughout the genome (Bennetzen et al, 1994;Bedell et al, 2005).…”

mentioning

confidence: 99%

Tobacco Transcription Factors: Novel Insights into Transcriptional Regulation in the Solanaceae

Rushton

Bokowiec²,

Han³

et al. 2008

Plant Physiology

240

179

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Tobacco (Nicotiana tabacum) is a member of the Solanaceae, one of the agronomically most important groups of flowering plants. We have performed an in silico analysis of 1.15 million gene-space sequence reads from the tobacco nuclear genome and report the detailed analysis of more than 2,500 tobacco transcription factors (TFs). The tobacco genome contains at least one member of each of the 64 well-characterized TF families identified in sequenced vascular plant genomes, indicating that evolution of the Solanaceae was not associated with the gain or loss of TF families. However, we found notable differences between tobacco and non-Solanaceae species in TF family size and evidence for both tobacco-and Solanaceae-specific subfamily expansions. Compared with TF families from sequenced plant genomes, tobacco has a higher proportion of ERF/AP2, C2H2 zinc finger, homeodomain, GRF, TCP, zinc finger homeodomain, BES, and STERILE APETALA (SAP) genes and novel subfamilies of BES, C2H2 zinc finger, SAP, and NAC genes. The novel NAC subfamily, termed TNACS, appears restricted to the Solanaceae, as they are absent from currently sequenced plant genomes but present in tomato (Solanum lycopersicum), pepper (Capsicum annuum), and potato (Solanum tuberosum). They constitute approximately 25% of NAC genes in tobacco. Based on our phylogenetic studies, we predict that many of the more than 50 tobacco group IX ERF genes are involved in jasmonate responses. Consistent with this, over two-thirds of group IX ERF genes tested showed increased mRNA levels following jasmonate treatment. Our data are a major resource for the Solanaceae and fill a void in studies of TF families across the plant kingdom.

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Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA

Cited by 176 publications

References 47 publications

Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome

Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome

Oat–maize chromosome addition lines: A new system for mapping the maize genome

Tobacco Transcription Factors: Novel Insights into Transcriptional Regulation in the Solanaceae

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