Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element family<i>Heartbreaker</i>into genic regions of maize

Zhang, Qiang; Arbuckle, John; Wessler, Susan R.

doi:10.1073/pnas.97.3.1160

Cited by 166 publications

(125 citation statements)

References 43 publications

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“…Six MITE DNA transposons were identified, three in RC3 and two in RC13, inserted close to each other within each cluster. This is in contrast to other results that show that MITEs preferentially insert into the 3# upstream regulatory regions of genes (Mao et al, 2000;Zhang et al, 2000). Six solo LTRs were identified across the two rf1-associated contigs.…”

Section: Te Annotation Reveals Large Repeat Clusterscontrasting

confidence: 53%

Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-Associated Region of Maize

Kronmiller

Wise

2009

Plant Physiology

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The architecture of grass genomes varies on multiple levels. Large long terminal repeat retrotransposon clusters occupy significant portions of the intergenic regions, and islands of protein-encoding genes are interspersed among the repeat clusters. Hence, advanced assembly techniques are required to obtain completely finished genomes as well as to investigate gene and transposable element distributions. To characterize the organization and distribution of repeat clusters and gene islands across large grass genomes, we present 961-and 594-kb contiguous sequence contigs associated with the rf1 (for restorer of fertility1) locus in the near-centromeric region of maize (Zea mays) chromosome 3. We present two methods for computational finishing of highly repetitive bacterial artificial chromosome clones that have proved successful to close all sequence gaps caused by transposable element insertions. Sixteen repeat clusters were observed, ranging in length from 23 to 155 kb. These repeat clusters are almost exclusively long terminal repeat retrotransposons, of which the paleontology of insertion varies throughout the cluster. Gene islands contain from one to four predicted genes, resulting in a gene density of one gene per 16 kb in gene islands and one gene per 111 kb over the entire sequenced region. The two sequence contigs, when compared with the rice (Oryza sativa) and sorghum (Sorghum bicolor) genomes, retain gene colinearity of 50% and 71%, respectively, and 70% and 100%, respectively, for high-confidence gene models. Collinear genes on single gene islands show that while most expansion of the maize genome has occurred in the repeat clusters, gene islands are not immune and have experienced growth in both intragene and intergene locations.

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Section: Te Annotation Reveals Large Repeat Clusterscontrasting

confidence: 53%

Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-Associated Region of Maize

Kronmiller

Wise

2009

Plant Physiology

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“…MITEs, for example, are often found in close association with genes, and they are believed to contribute regulatory sequences that may alter gene expression (Zhang et al, 2000). A similar role can be suggested for CACTA elements.…”

Section: The Contribution Of Cacta Elements To Genome Evolutionmentioning

confidence: 99%

CACTA Transposons in Triticeae. A Diverse Family of High-Copy Repetitive Elements

et al. 2003

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In comparison with retrotransposons, which comprise the majority of the Triticeae genomes, very few class 2 transposons have been described in these genomes. Based on the recent discovery of a local accumulation of CACTA elements at the Glu-A3 loci in the two wheat species Triticum monococcum and Triticum durum, we performed a database search for additional such elements in Triticeae spp. A combination of BLAST search and dot-plot analysis of publicly available Triticeae sequences led to the identification of 41 CACTA elements. Only seven of them encode a protein similar to known transposases, whereas the other 34 are considered to be deletion derivatives. A detailed characterization of the identified elements allowed a further classification into seven subgroups. The major subgroup, designated the "Caspar " family, was shown by hybridization to be present in at least 3,000 copies in the T. monococcum genome. The close association of numerous CACTA elements with genes and the identification of several similar elements in sorghum (Sorghum bicolor) and rice (Oryza sativa) led to the conclusion that CACTA elements contribute significantly to genome size and to organization and evolution of grass genomes.

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“…Taxa such as Brassica and Secale, which show particularly high rates of chromosome structural rearrangement (see Paterson et al, 1996), might be fertile systems for investigating the structural mutation process. New methods also promise to reveal more detail about the arrangements of repetitive DNA elements on a genome-wide scale (Lin et al, 2000;Zhang et al, 2000). An especially intriguing issue is how and why parallel gene order is preserved along the chromosomes of taxa that have been reproductively isolated for millions of years despite rapidly changing arrangements of intergenic DNA.…”

Section: Synthesismentioning

confidence: 99%

Comparative Genomics of Plant Chromosomes

et al. 2000

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FOUNDATIONS OF COMPARATIVE GENOMICSComparative genomics, the study of the similarities and differences in structure and function of hereditary information across taxa, uses molecular tools to investigate many notions that long preceded identification of DNA as the hereditary molecule. Vavilov's (1922) law of homologous series in variation was an early suggestion of the similarities in the genetic blueprints of many (plant) species. Genetic analysis based on morphological and isoenzyme markers hinted at parallel arrangements of genes along the chromosomes of various taxa. These hints were later borne out at the DNA level, in seminal investigations of nightshades (Tanksley et al., 1988; Bonierbale et al., 1988) and grasses (Hulbert et al., 1990).Over the past two decades, multiple investigations of many additional taxa have delivered two broad messages: (1) In most plants, the evolution of the small but essential portion of the genome that actually encodes the organism's genes has proceeded relatively slowly; as a result, taxa that have been reproductively isolated for millions of years have retained recognizable intragenic DNA sequences as well as similar arrangements of genes along the chromosomes. (2) A wide range of factors, such as ancient chromosomal or segmental duplications, mobility of DNA sequences, gene deletion, and localized rearrangements, has been superimposed on the relatively slow tempo of chromosomal evolution and causes many deviations from colinearity. COMPARATIVE MAPS IN CROP TAXA The BrassicaceaeThe Brassicaceae comprise 360 genera, organized into 13 tribes (Shultz, 1936; Al-Shehbaz, 1973). The most economically important species are in the genus Brassica (tribe Brassiceae), six species of which are cultivated worldwide.

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Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element familyHeartbreakerinto genic regions of maize

Cited by 166 publications

References 43 publications

Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-Associated Region of Maize

Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-Associated Region of Maize

CACTA Transposons in Triticeae. A Diverse Family of High-Copy Repetitive Elements

Comparative Genomics of Plant Chromosomes

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