Amplicons of maize zein genes are conserved within genic but expanded and constricted in intergenic regions

Llaca, Víctor; Messing, Joachim

doi:10.1046/j.1365-313x.1998.00200.x

Cited by 50 publications

(45 citation statements)

References 40 publications

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“…Thus, the gene density in this gene cluster is one gene per 9.8 kb, which is five times higher than the calculated average gene density of one gene per 50 kb (5). A shorter length of DNA uninterrupted by retrotransposons has been reported in the 22-kDa zein cluster, where one apparently functional zein gene and four pseudogenes occur within the first 26 kb of a 78-kb cosmid contig (6).…”

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confidence: 66%

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The highly recombinogenic bz locus lies in an unusually gene-rich region of the maize genome

Park

Yan

et al. 2001

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

102

107

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The bronze (bz) locus exhibits the highest rate of recombination of any gene in higher plants. To investigate the possible basis of this high rate of recombination, we have analyzed the physical organization of the region around the bz locus. Two adjacent bacterial artificial chromosome clones, comprising a 240-kb contig centered around the Bz-McC allele, were isolated, and 60 kb of contiguous DNA spanning the two bacterial artificial chromosome clones was sequenced. We find that the bz locus lies in an unusually gene-rich region of the maize genome. Ten genes, at least eight of which are shown to be transcribed, are contained in a 32-kb stretch of DNA that is uninterrupted by retrotransposons. We have isolated nearly full length cDNAs corresponding to the five proximal genes in the cluster. The average intertranscript distance between them is just 1 kb, revealing a surprisingly compact packaging of adjacent genes in this part of the genome. At least 11 small insertions, including several previously described miniature inverted repeat transposable elements, were detected in the introns and 3 untranslated regions of genes and between genes. The gene-rich region is flanked at the proximal and distal ends by retrotransposon blocks. Thus, the maize genome appears to have scattered regions of high gene density similar to those found in other plants. The unusually high rate of intragenic recombination seen in bz may be related to the very high gene density of the region.

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confidence: 66%

“…The 32-kb gene-rich sequence in the bz region appears to be flanked on either side by large retrotransposon blocks similar to those found in the Adh1 (1) and 22-kDa zein regions (6). To obtain a general picture of the organization of these blocks, we sequenced 18 kb of the proximal cluster and 8 kb of the distal cluster.…”

Section: Hypro1mentioning

confidence: 97%

The highly recombinogenic bz locus lies in an unusually gene-rich region of the maize genome

Park

Yan

et al. 2001

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

102

107

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“…Additionally, clustered retrotransposon regions should be expected given the finding that retroelements preferentially insert into existing retroelements (San Miguel et al 1996;Suoniemi et al 1997). On the other hand, Tikhonov et al (1999), Chen et al (1998), and Llaca and Messing (1998) sequenced syntenic regions of rice, sorghum, and maize (Adh-1, Sh1-a2, zein genes) and demonstrated genome expansion by retrotransposon insertion into intergenic spaces. Based on the distribution of the most abundant repeats in BAC clones and on the correlation observed between the size of the BACs and the number of different repetitive elements, we conclude that repeats are, in general, randomly distributed in the genome.…”

Section: Genome Research 1671mentioning

confidence: 99%

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

Meyers

Tingey²,

Morgante³

2001

Genome Res.

373

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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“…In a few cases, including within tandem gene families or the rare unrelated gene cluster (Llaca and Messing 1998;Fu et al 2001), gene-rich regions may extend for 50 kb or more. In most cases, however, gene-rich chromosome segments only contain 1-4 genes in a region of 20 kb or less.…”

mentioning

confidence: 99%

“…In most cases, however, gene-rich chromosome segments only contain 1-4 genes in a region of 20 kb or less. The repetitive DNAs found in the intermixed repeat blocks are usually nested insertions of a class of mobile DNAs called long terminal repeat-(LTR-) retrotransposons (SanMiguel et al 1996;Llaca and Messing 1998;Panstruga et al 1998;Kumar and Bennetzen 1999;Tikhonov et al 1999;Dubcovsky et al 2001;Fu et al 2001;Wicker et al 2001). These nested LTR-retrotransposons can make up well over 50% of total genomic DNA, with most of this DNA coming from only a handful of different element families that have copy numbers of several thousand per nuclear genome (SanMiguel and Bennetzen 1998;Kumar and Bennetzen 1999;Vicient et al 1999;Meyers et al 2001).…”

mentioning

confidence: 99%

Methylation-Spanning Linker Libraries Link Gene-Rich Regions and Identify Epigenetic Boundaries in Zea mays

Yuan¹

2002

Genome Res.

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Complex cereal genomes are largely composed of small gene-rich regions intermixed with 5 kb to 200 kb blocks of repetitive DNA. The repetitive DNA blocks are usually 5-methylated at 5Ј-CG-3Ј and 5Ј-CNG-3Ј cytosines in most or all adult tissues, while the genes are generally unmethylated at these sites. We have developed methylation-spanning linker library (MSLL) technology as a tool to span large methylated DNA blocks and thereby link unmethylated genic regions. MSLL clones contain insertions of large fragments that are size fractionated over gels after complete digestion of total genomic DNA with restriction enzymes that are sensitive to the 5-methylation of cytosines in 5Ј-CG-3Ј and 5Ј-CNG-3Ј sequences. Our data indicate that the end sequences of maize MSLL clones are greatly depleted in repetitive DNAs and enriched in genes relative to total genomic DNA. Combined with other gene-enrichment approaches, MSLL technology can efficiently generate fully-linked contiguous sequences in complex genomes that are resistant to shotgun sequencing.

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Amplicons of maize zein genes are conserved within genic but expanded and constricted in intergenic regions

Abstract: SummaryThe 78

Cited by 50 publications

References 40 publications

The highly recombinogenic bz locus lies in an unusually gene-rich region of the maize genome

The highly recombinogenic bz locus lies in an unusually gene-rich region of the maize genome

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

Methylation-Spanning Linker Libraries Link Gene-Rich Regions and Identify Epigenetic Boundaries in Zea mays

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