<it>P </it>elements and MITE relatives in the whole genome sequence of <it>Anopheles gambiae</it>
<p>Abstract</p> <p>Background</p> <p>Miniature Inverted-repeat Terminal Elements (MITEs), which are particular class-II transposable elements (TEs), play an important role in genome evolution, because they have very high copy numbers and display recurrent bursts of tran...
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2006-08-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/7/214 |
| _version_ | 1811299362145304576 |
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| author | Nouaud Danielle Quesneville Hadi Anxolabéhère Dominique |
| author_facet | Nouaud Danielle Quesneville Hadi Anxolabéhère Dominique |
| author_sort | Nouaud Danielle |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Miniature Inverted-repeat Terminal Elements (MITEs), which are particular class-II transposable elements (TEs), play an important role in genome evolution, because they have very high copy numbers and display recurrent bursts of transposition. The 5' and 3' subterminal regions of a given MITE family often show a high sequence similarity with the corresponding regions of an autonomous Class-II TE family. However, the sustained presence over a prolonged evolutionary time of MITEs and TE master copies able to promote their mobility has been rarely reported within the same genome, and this raises fascinating evolutionary questions.</p> <p>Results</p> <p>We report here the presence of <it>P </it>transposable elements with related MITE families in the <it>Anopheles gambiae </it>genome. Using a TE annotation pipeline we have identified and analyzed all the <it>P </it>sequences in the sequenced <it>A. gambiae </it>PEST strain genome. More than 0.49% of the genome consists of <it>P </it>elements and derivates. <it>P </it>elements can be divided into 9 different subfamilies, separated by more than 30% of nucleotide divergence. Seven of them present full length copies. Ten MITE families are associated with 6 out of the 9 <it>P</it>subfamilies. Comparing their intra-element nucleotide diversities and their structures allows us to propose the putative dynamics of their emergence. In particular, one MITE family which has a hybrid structure, with ends each of which is related to a different <it>P</it>-subfamily, suggests a new mechanism for their emergence and their mobility.</p> <p>Conclusion</p> <p>This work contributes to a greater understanding of the relationship between full-length class-II TEs and MITEs, in this case <it>P </it>elements and their derivatives in the genome of <it>A. gambiae</it>. Moreover, it provides the most comprehensive catalogue to date of <it>P-</it>like transposons in this genome and provides convincing yet indirect evidence that some of the subfamilies have been recently active.</p> |
| first_indexed | 2024-04-13T06:34:57Z |
| format | Article |
| id | doaj.art-c2a79b6b640f4d3caa9e85bedd486999 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T06:34:57Z |
| publishDate | 2006-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-c2a79b6b640f4d3caa9e85bedd4869992022-12-22T02:57:57ZengBMCBMC Genomics1471-21642006-08-017121410.1186/1471-2164-7-214<it>P </it>elements and MITE relatives in the whole genome sequence of <it>Anopheles gambiae</it>Nouaud DanielleQuesneville HadiAnxolabéhère Dominique<p>Abstract</p> <p>Background</p> <p>Miniature Inverted-repeat Terminal Elements (MITEs), which are particular class-II transposable elements (TEs), play an important role in genome evolution, because they have very high copy numbers and display recurrent bursts of transposition. The 5' and 3' subterminal regions of a given MITE family often show a high sequence similarity with the corresponding regions of an autonomous Class-II TE family. However, the sustained presence over a prolonged evolutionary time of MITEs and TE master copies able to promote their mobility has been rarely reported within the same genome, and this raises fascinating evolutionary questions.</p> <p>Results</p> <p>We report here the presence of <it>P </it>transposable elements with related MITE families in the <it>Anopheles gambiae </it>genome. Using a TE annotation pipeline we have identified and analyzed all the <it>P </it>sequences in the sequenced <it>A. gambiae </it>PEST strain genome. More than 0.49% of the genome consists of <it>P </it>elements and derivates. <it>P </it>elements can be divided into 9 different subfamilies, separated by more than 30% of nucleotide divergence. Seven of them present full length copies. Ten MITE families are associated with 6 out of the 9 <it>P</it>subfamilies. Comparing their intra-element nucleotide diversities and their structures allows us to propose the putative dynamics of their emergence. In particular, one MITE family which has a hybrid structure, with ends each of which is related to a different <it>P</it>-subfamily, suggests a new mechanism for their emergence and their mobility.</p> <p>Conclusion</p> <p>This work contributes to a greater understanding of the relationship between full-length class-II TEs and MITEs, in this case <it>P </it>elements and their derivatives in the genome of <it>A. gambiae</it>. Moreover, it provides the most comprehensive catalogue to date of <it>P-</it>like transposons in this genome and provides convincing yet indirect evidence that some of the subfamilies have been recently active.</p>http://www.biomedcentral.com/1471-2164/7/214 |
| spellingShingle | Nouaud Danielle Quesneville Hadi Anxolabéhère Dominique <it>P </it>elements and MITE relatives in the whole genome sequence of <it>Anopheles gambiae</it> BMC Genomics |
| title | <it>P </it>elements and MITE relatives in the whole genome sequence of <it>Anopheles gambiae</it> |
| title_full | <it>P </it>elements and MITE relatives in the whole genome sequence of <it>Anopheles gambiae</it> |
| title_fullStr | <it>P </it>elements and MITE relatives in the whole genome sequence of <it>Anopheles gambiae</it> |
| title_full_unstemmed | <it>P </it>elements and MITE relatives in the whole genome sequence of <it>Anopheles gambiae</it> |
| title_short | <it>P </it>elements and MITE relatives in the whole genome sequence of <it>Anopheles gambiae</it> |
| title_sort | it p it elements and mite relatives in the whole genome sequence of it anopheles gambiae it |
| url | http://www.biomedcentral.com/1471-2164/7/214 |
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