Rice Transposable Elements: A Survey of 73,000 Sequence-Tagged-Connectors

Mao, Long; Wood, Todd Charles; Yu, Yeisoo; Budiman, Muhammad A.; Tomkins, J. P.; Woo, Sung Sick; Sasinowski, Maciek; Presting, Gernot G.; Frisch, David; Goff, Steve; Dean, Ralph A.; Wing, Rod A.

doi:10.1101/gr.10.7.982

Cited by 193 publications

(148 citation statements)

References 39 publications

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“…Sample sequencing of other plant genomes will provide estimates of gene density, but classifying nongenic sequences will be difficult if intact repetitive elements from these plant species have not been described. For example, Mao et al (2000) analyzed 73,000 BAC-end sequences to determine that 4.5% of the rice genome is comprosed of transposable elements; lacking a set of distinct and well-characterized rice elements, these sequences could only be characterized into broadly defined categories (e.g., gypsy-or copia-like). Within the complete sequence of subgenomic regions (e.g., some BAC-sized contigs), it is likely that examples of the most common genome-specific retroelements will be found, as demonstrated by the analysis of the Adh-1 region of maize (SanMiguel et al 1996).…”

Section: Discussionmentioning

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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Section: Discussionmentioning

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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“…Traditionally, BAC fingerprinting and end sequencing was very time consuming and expensive (Mao et al, 2000;Chen et al, 2002). We have now optimized our methods so that we can produce one physical map in about 1-3 months depending on genome size.…”

Section: Development Of Wild Species Fpc/stc Physical Mapsmentioning

confidence: 99%

The Oryza Map Alignment Project: The Golden Path to Unlocking the Genetic Potential of Wild Rice Species

et al. 2005

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“…These clones were sequenced with 10-fold redundancy to ensure a sequence quality of 99.99% accuracy. By merging the above sequenced physical map with the CUGI (Clemson University Genomics Institute, USA) BAC contig map with the help of end sequences (Chen et al, 2002;Mao et al, 2000), 349 CUGI BAC clones were added to the maps for gap closure and contig extension. As of April 2003, the physical maps of chromosomes 1, 2, and 6±9 comprised 1814 PAC and BAC clones with only 20 physical gaps ( Figure 1; Table 1).…”

Section: Construction Of Physical Mapsmentioning

confidence: 99%

Physical maps and recombination frequency of six rice chromosomes

Wu¹,

Mizuno²,

et al. 2003

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These authors contributed equally to this work. SummaryWe constructed physical maps of rice chromosomes 1, 2, and 6±9 with P1-derived arti®cial chromosome (PAC) and bacterial arti®cial chromosome (BAC) clones. These maps, with only 20 gaps, cover more than 97% of the predicted length of the six chromosomes. We submitted a total of 193 Mbp of non-overlapping sequences to public databases. We analyzed the DNA sequences of 1316 genetic markers and six centromere-speci®c repeats to facilitate characterization of chromosomal recombination frequency and of the genomic composition and structure of the centromeric regions. We found marked changes in the relative recombination rate along the length of each chromosome. Chromosomal recombination at the centromere core and surrounding regions on the six chromosomes was completely suppressed. These regions have a total physical length of about 23 Mbp, corresponding to 11.4% of the entire size of the six chromosomes. Chromosome 6 has the longest quiescent region, with about 5.6 Mbp, followed by chromosome 8, with quiescent region about half this size. Repetitive sequences accounted for at least 40% of the total genomic sequence on the partly sequenced centromeric region of chromosome 1. Rice CentO satellite DNA is arrayed in clusters and is closely associated with the presence of Centromeric Retrotransposon of Rice (CRR )-and RIce RetroElement 7 (RIRE7 )-like retroelement sequences. We also detected relatively small coldspot regions outside the centromeric region; their repetitive content and gene density were similar to those of regions with normal recombination rates. Sequence analysis of these regions suggests that either the amount or the organization patterns of repetitive sequences may play a role in the inactivation of recombination.

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Rice Transposable Elements: A Survey of 73,000 Sequence-Tagged-Connectors

Cited by 193 publications

References 39 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 Oryza Map Alignment Project: The Golden Path to Unlocking the Genetic Potential of Wild Rice Species

Physical maps and recombination frequency of six rice chromosomes

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