Mononucleotide repeats are asymmetrically distributed in fungal genes
<p>Abstract</p> <p>Background</p> <p>Systematic analyses of sequence features have resulted in a better characterisation of the organisation of the genome. A previous study in prokaryotes on the distribution of sequence repeats, which are notoriously variable and can di...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-12-01
|
| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/9/596 |
| _version_ | 1818208236415746048 |
|---|---|
| author | de Graaff Leo H van Passel Mark WJ |
| author_facet | de Graaff Leo H van Passel Mark WJ |
| author_sort | de Graaff Leo H |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Systematic analyses of sequence features have resulted in a better characterisation of the organisation of the genome. A previous study in prokaryotes on the distribution of sequence repeats, which are notoriously variable and can disrupt the reading frame in genes, showed that these motifs are skewed towards gene termini, specifically the 5' end of genes. For eukaryotes no such intragenic analysis has been performed, though this could indicate the pervasiveness of this distribution bias, thereby helping to expose the selective pressures causing it.</p> <p>Results</p> <p>In fungal gene repertoires we find a similar 5' bias of intragenic mononucleotide repeats, most notably for <it>Candida </it>spp., whereas e.g. <it>Coccidioides </it>spp. display no such bias. With increasing repeat length, ever larger discrepancies are observed in genome repertoire fractions containing such repeats, with up to an 80-fold difference in gene fractions at repeat lengths of 10 bp and longer. This species-specific difference in gene fractions containing large repeats could be attributed to variations in intragenic repeat tolerance. Furthermore, long transcripts experience an even more prominent bias towards the gene termini, with possibly a more adaptive role for repeat-containing short transcripts.</p> <p>Conclusion</p> <p>Mononucleotide repeats are intragenically biased in numerous fungal genomes, similar to earlier studies on prokaryotes, indicative of a similar selective pressure in gene organization.</p> |
| first_indexed | 2024-12-12T04:41:36Z |
| format | Article |
| id | doaj.art-6c73f6e319344603bdbe14319a3679e6 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T04:41:36Z |
| publishDate | 2008-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-6c73f6e319344603bdbe14319a3679e62022-12-22T00:37:48ZengBMCBMC Genomics1471-21642008-12-019159610.1186/1471-2164-9-596Mononucleotide repeats are asymmetrically distributed in fungal genesde Graaff Leo Hvan Passel Mark WJ<p>Abstract</p> <p>Background</p> <p>Systematic analyses of sequence features have resulted in a better characterisation of the organisation of the genome. A previous study in prokaryotes on the distribution of sequence repeats, which are notoriously variable and can disrupt the reading frame in genes, showed that these motifs are skewed towards gene termini, specifically the 5' end of genes. For eukaryotes no such intragenic analysis has been performed, though this could indicate the pervasiveness of this distribution bias, thereby helping to expose the selective pressures causing it.</p> <p>Results</p> <p>In fungal gene repertoires we find a similar 5' bias of intragenic mononucleotide repeats, most notably for <it>Candida </it>spp., whereas e.g. <it>Coccidioides </it>spp. display no such bias. With increasing repeat length, ever larger discrepancies are observed in genome repertoire fractions containing such repeats, with up to an 80-fold difference in gene fractions at repeat lengths of 10 bp and longer. This species-specific difference in gene fractions containing large repeats could be attributed to variations in intragenic repeat tolerance. Furthermore, long transcripts experience an even more prominent bias towards the gene termini, with possibly a more adaptive role for repeat-containing short transcripts.</p> <p>Conclusion</p> <p>Mononucleotide repeats are intragenically biased in numerous fungal genomes, similar to earlier studies on prokaryotes, indicative of a similar selective pressure in gene organization.</p>http://www.biomedcentral.com/1471-2164/9/596 |
| spellingShingle | de Graaff Leo H van Passel Mark WJ Mononucleotide repeats are asymmetrically distributed in fungal genes BMC Genomics |
| title | Mononucleotide repeats are asymmetrically distributed in fungal genes |
| title_full | Mononucleotide repeats are asymmetrically distributed in fungal genes |
| title_fullStr | Mononucleotide repeats are asymmetrically distributed in fungal genes |
| title_full_unstemmed | Mononucleotide repeats are asymmetrically distributed in fungal genes |
| title_short | Mononucleotide repeats are asymmetrically distributed in fungal genes |
| title_sort | mononucleotide repeats are asymmetrically distributed in fungal genes |
| url | http://www.biomedcentral.com/1471-2164/9/596 |
| work_keys_str_mv | AT degraaffleoh mononucleotiderepeatsareasymmetricallydistributedinfungalgenes AT vanpasselmarkwj mononucleotiderepeatsareasymmetricallydistributedinfungalgenes |