SINEs and LINEs: symbionts of eukaryotic genomes with a common tail

Ohshima, Kousei; Okada, Norihiro

doi:10.1159/000084981

Cited by 148 publications

(134 citation statements)

References 257 publications

(141 reference statements)

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“…That LTR retrotransposons are long (,10 kb), highly repetitive and often nested 21 supports our assumption that short reads either collapsed or did not assemble. Short interspersed elements (SINEs) 22 , short (80-600 bp) non-autonomous retrotransposons that are highly repeated in barley, showed no differential exclusion from the assemblies. However, miniature invertedrepeat transposable elements (MITEs), small non-autonomous DNA transposons 23 , were twofold enriched in the whole-genome shotgun assemblies compared with BES reads or random BACs, consistent with the gene richness of the assemblies and their association with genes 23 .…”

Section: Repetitive Nature Of the Barley Genomementioning

confidence: 99%

A physical, genetic and functional sequence assembly of the barley genome

2012

Nature

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Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement

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Section: Repetitive Nature Of the Barley Genomementioning

confidence: 99%

A physical, genetic and functional sequence assembly of the barley genome

2012

Nature

1,300

880

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“…A substantial fraction of SINEs (20%; Table 1; Figures 1a and b) has a 30-100 bp region of similarity with the 3 0 -terminal sequence of LINE, whose RT is involved in SINE amplification (Ohshima and Okada, 2005). Such regions are not only found in most of the SINEs in fishes (Matveev and Okada, 2009), but also occur in other groups including mammals.…”

Section: Da Kramerov and Ns Vassetzkymentioning

confidence: 99%

“…The last subclass of retrotransposons is Short INterspersed Elements (SINEs), whose length ranges from 100 to 600 bp (Kramerov and Vassetzky, 2005;Ohshima and Okada, 2005;Deragon and Zhang, 2006). The genomes can contain tens or hundreds of thousands of SINE copies.…”

Section: Introductionmentioning

confidence: 99%

Origin and evolution of SINEs in eukaryotic genomes

2011

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“…Compiling an inventory of potentially useful retrotransposons is beyond the scope of this commentary. However, for interested researchers, Ohshima and Okada (2005) provided a useful list in their 2005 discussion of LINE/SINE interactions.…”

Section: Extensions To Other Organismsmentioning

confidence: 99%

Reading TE leaves: New approaches to the identification of transposable element insertions

Ray¹,

Batzer²

2011

Genome Res.

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Transposable elements (TEs) are a tremendous source of genome instability and genetic variation. Of particular interest to investigators of human biology and human evolution are retrotransposon insertions that are recent and/or polymorphic in the human population. As a consequence, the ability to assay large numbers of polymorphic TEs in a given genome is valuable. Five recent manuscripts each propose methods to scan whole human genomes to identify, map, and, in some cases, genotype polymorphic retrotransposon insertions in multiple human genomes simultaneously. These technologies promise to revolutionize our ability to analyze human genomes for TE-based variation important to studies of human variability and human disease. Furthermore, the approaches hold promise for researchers interested in nonhuman genomic variability. Herein, we explore the methods reported in the manuscripts and discuss their applications to aspects of human biology and the biology of other organisms.

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SINEs and LINEs: symbionts of eukaryotic genomes with a common tail

Cited by 148 publications

References 257 publications

A physical, genetic and functional sequence assembly of the barley genome

A physical, genetic and functional sequence assembly of the barley genome

Origin and evolution of SINEs in eukaryotic genomes

Reading TE leaves: New approaches to the identification of transposable element insertions

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