Computational prediction and molecular confirmation of <it>Helitron </it>transposons in the maize genome
<p>Abstract</p> <p>Background</p> <p><it>Helitrons </it>represent a new class of transposable elements recently uncovered in plants and animals. One remarkable feature of <it>Helitrons </it>is their ability to capture gene sequences, which makes...
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-01-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/9/51 |
| _version_ | 1830214582698770432 |
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| author | He Limei Caronna Jason Du Chunguang Dooner Hugo K |
| author_facet | He Limei Caronna Jason Du Chunguang Dooner Hugo K |
| author_sort | He Limei |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Helitrons </it>represent a new class of transposable elements recently uncovered in plants and animals. One remarkable feature of <it>Helitrons </it>is their ability to capture gene sequences, which makes them of considerable potential evolutionary importance. However, because <it>Helitrons </it>lack the typical structural features of other DNA transposable elements, identifying them is a challenge. Currently, most researchers identify <it>Helitrons </it>manually by comparing sequences. With the maize whole genome sequencing project underway, an automated computational <it>Helitron </it>searching tool is needed. The characterization of <it>Helitron </it>activities in maize needs to be addressed in order to better understand the impact of <it>Helitrons </it>on the organization of the genome.</p> <p>Results</p> <p>We developed and implemented a heuristic searching algorithm in PERL for identifying <it>Helitrons</it>. Our HelitronFinder program will (i) take FASTA-formatted DNA sequences as input and identify the hairpin looping patterns, and (ii) exploit the consensus 5' and 3' end sequences of known <it>Helitrons </it>to identify putative ends. We randomly selected five predicted <it>Helitrons </it>from the program's high quality output for molecular verification. Four out of the five predicted <it>Helitrons </it>were confirmed by PCR assays and DNA sequencing in different maize inbred lines. The HelitronFinder program identified two head-to-head dissimilar <it>Helitrons </it>in a maize BAC sequence.</p> <p>Conclusion</p> <p>We have identified 140 new <it>Helitron </it>candidates in maize with our computational tool HelitronFinder by searching maize DNA sequences currently available in GenBank. Four out of five candidates were confirmed to be real by empirical methods, thus validating the predictions of HelitronFinder. Additional points to emerge from our study are that <it>Helitrons </it>do not always insert at an AT dinucleotide in the host sequences, that they can insert immediately adjacent to an existing <it>Helitron</it>, and that their movement may cause changes in the flanking region, such as deletions.</p> |
| first_indexed | 2024-12-18T06:46:23Z |
| format | Article |
| id | doaj.art-4a4e49267c944e82933ed87c0055a561 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-18T06:46:23Z |
| publishDate | 2008-01-01 |
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| spelling | doaj.art-4a4e49267c944e82933ed87c0055a5612022-12-21T21:17:29ZengBMCBMC Genomics1471-21642008-01-01915110.1186/1471-2164-9-51Computational prediction and molecular confirmation of <it>Helitron </it>transposons in the maize genomeHe LimeiCaronna JasonDu ChunguangDooner Hugo K<p>Abstract</p> <p>Background</p> <p><it>Helitrons </it>represent a new class of transposable elements recently uncovered in plants and animals. One remarkable feature of <it>Helitrons </it>is their ability to capture gene sequences, which makes them of considerable potential evolutionary importance. However, because <it>Helitrons </it>lack the typical structural features of other DNA transposable elements, identifying them is a challenge. Currently, most researchers identify <it>Helitrons </it>manually by comparing sequences. With the maize whole genome sequencing project underway, an automated computational <it>Helitron </it>searching tool is needed. The characterization of <it>Helitron </it>activities in maize needs to be addressed in order to better understand the impact of <it>Helitrons </it>on the organization of the genome.</p> <p>Results</p> <p>We developed and implemented a heuristic searching algorithm in PERL for identifying <it>Helitrons</it>. Our HelitronFinder program will (i) take FASTA-formatted DNA sequences as input and identify the hairpin looping patterns, and (ii) exploit the consensus 5' and 3' end sequences of known <it>Helitrons </it>to identify putative ends. We randomly selected five predicted <it>Helitrons </it>from the program's high quality output for molecular verification. Four out of the five predicted <it>Helitrons </it>were confirmed by PCR assays and DNA sequencing in different maize inbred lines. The HelitronFinder program identified two head-to-head dissimilar <it>Helitrons </it>in a maize BAC sequence.</p> <p>Conclusion</p> <p>We have identified 140 new <it>Helitron </it>candidates in maize with our computational tool HelitronFinder by searching maize DNA sequences currently available in GenBank. Four out of five candidates were confirmed to be real by empirical methods, thus validating the predictions of HelitronFinder. Additional points to emerge from our study are that <it>Helitrons </it>do not always insert at an AT dinucleotide in the host sequences, that they can insert immediately adjacent to an existing <it>Helitron</it>, and that their movement may cause changes in the flanking region, such as deletions.</p>http://www.biomedcentral.com/1471-2164/9/51 |
| spellingShingle | He Limei Caronna Jason Du Chunguang Dooner Hugo K Computational prediction and molecular confirmation of <it>Helitron </it>transposons in the maize genome BMC Genomics |
| title | Computational prediction and molecular confirmation of <it>Helitron </it>transposons in the maize genome |
| title_full | Computational prediction and molecular confirmation of <it>Helitron </it>transposons in the maize genome |
| title_fullStr | Computational prediction and molecular confirmation of <it>Helitron </it>transposons in the maize genome |
| title_full_unstemmed | Computational prediction and molecular confirmation of <it>Helitron </it>transposons in the maize genome |
| title_short | Computational prediction and molecular confirmation of <it>Helitron </it>transposons in the maize genome |
| title_sort | computational prediction and molecular confirmation of it helitron it transposons in the maize genome |
| url | http://www.biomedcentral.com/1471-2164/9/51 |
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