Retrotransposons in the flanking regions of normal plant genes: a role for copia-like elements in the evolution of gene structure and expression.

White, Shawn E.; Habera, Ledare F.; Wessler, Susan R.

doi:10.1073/pnas.91.25.11792

Cited by 252 publications

(169 citation statements)

References 54 publications

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“…The divergence within this family is higher than within any of the major families of maize. Many of the retroelements described previously and characterized in maize did not appear to be major components of the maize genome; such was the case for Hopscotch (White et al 1994), Stoner (Marillonnet andWessler 1998), Magellan, Reina, Fourf, Kake, Victim, andMilt (SanMiguel et al 1996;Tikhonov et al 1999). A repetitive sequence that represents 0.14% of the genome had a 95% probability of being found in our sample of 2157 sequences.…”

Section: Sample Sequencing Indicates the Maize Genome Is Highly Repetmentioning

confidence: 83%

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: Sample Sequencing Indicates the Maize Genome Is Highly Repetmentioning

confidence: 83%

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

Meyers

Tingey²,

Morgante³

2001

Genome Res.

376

313

View full text Add to dashboard Cite

show abstract

“…This transcript may originate from another Rim2 copy or ORF. Transposons in regions¯anking plant genes can affect gene structure and expression (White et al 1994), and have been proposed to be important in creating allelic diversity in disease resistance genes (Michelmore 1995;Song et al 1998). For example, 17 elements have been found within or closely linked to the Xa21 locus (Song et al 1997(Song et al , 1998.…”

Section: Discussionmentioning

confidence: 99%

The rice Rim2 transcript accumulates in response to Magnaporthe grisea and its predicted protein product shares similarity with TNP2-like proteins encoded by CACTA transposons

Dong

et al. 2000

Mol Gen Genet

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“…The ig1-mum allele contains a Mu8 insertion within the first intron, 86 nucleotides upstream of the start codon, and the ig1-O allele contains a Hopscotch retrotransposon insertion within codon 120 of ig1, 14 residues before the end of the LOB domain ( Figure 3). Hopscotch is one of a group of low-copy retrotransposons that are more commonly inserted into genes than the high-copy retroelements that make up the bulk of the maize genome (White et al, 1994). The ig1 gene contains four exons that constitute an mRNA 1264 bases in length (Figure 3).…”

Section: Fine Mapping and Cloning Of Ig1mentioning

confidence: 99%

Theindeterminate gametophyte1Gene of Maize Encodes a LOB Domain Protein Required for Embryo Sac and Leaf Development

2007

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Angiosperm embryo sac development begins with a phase of free nuclear division followed by cellularization and differentiation of cell types. The indeterminate gametophyte1 (ig1) gene of maize (Zea mays) restricts the proliferative phase of female gametophyte development. ig1 mutant female gametophytes have a prolonged phase of free nuclear divisions leading to a variety of embryo sac abnormalities, including extra egg cells, extra polar nuclei, and extra synergids. Positional cloning of ig1 was performed based on the genome sequence of the orthologous region in rice. ig1 encodes a LATERAL ORGAN BOUNDARIES domain protein with high similarity to ASYMMETRIC LEAVES2 of Arabidopsis thaliana. A second mutant allele of ig1 was identified in a noncomplementation screen using active Mutator transposable element lines. Homozygous ig1 mutants have abnormal leaf morphology as well as abnormal embryo sac development. Affected leaves have disrupted abaxial-adaxial polarity and fail to repress the expression of meristem-specific knotted-like homeobox (knox) genes in leaf primordia, causing a proliferative, stem cell identity to persist in these cells. Despite the superficial similarity of ig1-O leaves and embryo sacs, ectopic knox gene expression cannot be detected in ig1-O embryo sacs.

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Retrotransposons in the flanking regions of normal plant genes: a role for copia-like elements in the evolution of gene structure and expression.

Abstract: The wx-K mutation results from the insertion of a copia-like retrotransposon into exon 12 of the maize waxy gene.

Cited by 252 publications

References 54 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

The rice Rim2 transcript accumulates in response to Magnaporthe grisea and its predicted protein product shares similarity with TNP2-like proteins encoded by CACTA transposons

Theindeterminate gametophyte1Gene of Maize Encodes a LOB Domain Protein Required for Embryo Sac and Leaf Development

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