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HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

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HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

Auteurs : Wenwei Xiong ; Limei He ; Jinsheng Lai [République populaire de Chine] ; Hugo K. Dooner ; Chunguang Du

Source :

Proceedings of the National Academy of Sciences of the United States of America [ 0027-8424 ] ; 2014.

RBID : PMC:4104883

Abstract

Significance

Helitrons are unusual rolling-circle eukaryotic transposons with a remarkable ability to capture gene sequences, which makes them of considerable evolutionary importance. Because Helitrons lack typical transposon features, they are challenging to identify and are estimated to comprise at most 2% of sequenced genomes. Here, we describe HelitronScanner, a generalized tool for their identification based on a motif-extracting algorithm proposed initially in a study of natural languages. HelitronScanner overcomes the divergence of Helitron termini among species by using conserved nucleotides at potentially variable locations. Many new Helitrons were identified in all organisms examined, resulting in a major reassessment of their abundance in eukaryotic genomes. In maize, they make up >6% of the genome and are the most abundant DNA transposons identified.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104883

DOI: 10.1073/pnas.1410068111
PubMed: 24982153
PubMed Central: 4104883

Affiliations:

République populaire de Chine

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PMC:4104883

Le document en format XML

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 transposons in many plant genomes</title>
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 07043;</nlm:aff>
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<author><name sortKey="He, Limei" sort="He, Limei" uniqKey="He L" first="Limei" last="He">Limei He</name>
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, Beijing 100083,<country>China</country>
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<country xml:lang="fr">République populaire de Chine</country>
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<affiliation><nlm:aff id="aff4">Department of Plant Biology,<institution>Rutgers, the State University of New Jersey</institution>
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<author><name sortKey="Du, Chunguang" sort="Du, Chunguang" uniqKey="Du C" first="Chunguang" last="Du">Chunguang Du</name>
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 transposons in many plant genomes</title>
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 08854;</nlm:aff>
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, New Brunswick,<addr-line>NJ</addr-line>
 08801</nlm:aff>
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 lack typical transposon features, they are challenging to identify and are estimated to comprise at most 2% of sequenced genomes. Here, we describe HelitronScanner, a generalized tool for their identification based on a motif-extracting algorithm proposed initially in a study of natural languages. HelitronScanner overcomes the divergence of <italic>Helitron</italic>
 termini among species by using conserved nucleotides at potentially variable locations. Many new <italic>Helitrons</italic>
 were identified in all organisms examined, resulting in a major reassessment of their abundance in eukaryotic genomes. In maize, they make up >6% of the genome and are the most abundant DNA transposons identified.</p>
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HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

Source :

Abstract

Links toward previous steps (curation, corpus...)

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki