Characterization of the genome of bald cypress
<p>Abstract</p> <p>Background</p> <p>Bald cypress (<it>Taxodium distichum var. distichum</it>) is a coniferous tree of tremendous ecological and economic importance. It is a member of the family Cupressaceae which also includes cypresses, redwoods, sequoias,...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2011-11-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/12/553 |
| _version_ | 1818569919121326080 |
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| author | Liu Wenxuan Thummasuwan Supaphan Sehgal Sunish K Chouvarine Philippe Peterson Daniel G |
| author_facet | Liu Wenxuan Thummasuwan Supaphan Sehgal Sunish K Chouvarine Philippe Peterson Daniel G |
| author_sort | Liu Wenxuan |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Bald cypress (<it>Taxodium distichum var. distichum</it>) is a coniferous tree of tremendous ecological and economic importance. It is a member of the family Cupressaceae which also includes cypresses, redwoods, sequoias, thujas, and junipers. While the bald cypress genome is more than three times the size of the human genome, its 1C DNA content is amongst the smallest of any conifer. To learn more about the genome of bald cypress and gain insight into the evolution of Cupressaceae genomes, we performed a Cot analysis and used Cot filtration to study <it>Taxodium </it>DNA. Additionally, we constructed a 6.7 genome-equivalent BAC library that we screened with known <it>Taxodium </it>genes and select repeats.</p> <p>Results</p> <p>The bald cypress genome is composed of 90% repetitive DNA with most sequences being found in low to mid copy numbers. The most abundant repeats are found in fewer than 25,000 copies per genome. Approximately 7.4% of the genome is single/low-copy DNA (i.e., sequences found in 1 to 5 copies). Sequencing of highly repetitive Cot clones indicates that most <it>Taxodium </it>repeats are highly diverged from previously characterized plant repeat sequences. The bald cypress BAC library consists of 606,336 clones (average insert size of 113 kb) and collectively provides 6.7-fold genome equivalent coverage of the bald cypress genome. Macroarray screening with known genes produced, on average, about 1.5 positive clones per probe per genome-equivalent. Library screening with Cot-1 DNA revealed that approximately 83% of BAC clones contain repetitive sequences iterated 10<sup>3 </sup>to 10<sup>4 </sup>times per genome.</p> <p>Conclusions</p> <p>The BAC library for bald cypress is the first to be generated for a conifer species outside of the family Pinaceae. The <it>Taxodium </it>BAC library was shown to be useful in gene isolation and genome characterization and should be an important tool in gymnosperm comparative genomics, physical mapping, genome sequencing, and gene/polymorphism discovery. The single/low-copy (SL) component of bald cypress is 4.6 times the size of the <it>Arabidopsis </it>genome. As suggested for other gymnosperms, the large amount of SL DNA in <it>Taxodium </it>is likely the result of divergence among ancient repeat copies and gene/pseudogene duplication.</p> |
| first_indexed | 2024-12-14T06:53:59Z |
| format | Article |
| id | doaj.art-c525f01843234cefaa55900c20120251 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T06:53:59Z |
| publishDate | 2011-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-c525f01843234cefaa55900c201202512022-12-21T23:12:48ZengBMCBMC Genomics1471-21642011-11-0112155310.1186/1471-2164-12-553Characterization of the genome of bald cypressLiu WenxuanThummasuwan SupaphanSehgal Sunish KChouvarine PhilippePeterson Daniel G<p>Abstract</p> <p>Background</p> <p>Bald cypress (<it>Taxodium distichum var. distichum</it>) is a coniferous tree of tremendous ecological and economic importance. It is a member of the family Cupressaceae which also includes cypresses, redwoods, sequoias, thujas, and junipers. While the bald cypress genome is more than three times the size of the human genome, its 1C DNA content is amongst the smallest of any conifer. To learn more about the genome of bald cypress and gain insight into the evolution of Cupressaceae genomes, we performed a Cot analysis and used Cot filtration to study <it>Taxodium </it>DNA. Additionally, we constructed a 6.7 genome-equivalent BAC library that we screened with known <it>Taxodium </it>genes and select repeats.</p> <p>Results</p> <p>The bald cypress genome is composed of 90% repetitive DNA with most sequences being found in low to mid copy numbers. The most abundant repeats are found in fewer than 25,000 copies per genome. Approximately 7.4% of the genome is single/low-copy DNA (i.e., sequences found in 1 to 5 copies). Sequencing of highly repetitive Cot clones indicates that most <it>Taxodium </it>repeats are highly diverged from previously characterized plant repeat sequences. The bald cypress BAC library consists of 606,336 clones (average insert size of 113 kb) and collectively provides 6.7-fold genome equivalent coverage of the bald cypress genome. Macroarray screening with known genes produced, on average, about 1.5 positive clones per probe per genome-equivalent. Library screening with Cot-1 DNA revealed that approximately 83% of BAC clones contain repetitive sequences iterated 10<sup>3 </sup>to 10<sup>4 </sup>times per genome.</p> <p>Conclusions</p> <p>The BAC library for bald cypress is the first to be generated for a conifer species outside of the family Pinaceae. The <it>Taxodium </it>BAC library was shown to be useful in gene isolation and genome characterization and should be an important tool in gymnosperm comparative genomics, physical mapping, genome sequencing, and gene/polymorphism discovery. The single/low-copy (SL) component of bald cypress is 4.6 times the size of the <it>Arabidopsis </it>genome. As suggested for other gymnosperms, the large amount of SL DNA in <it>Taxodium </it>is likely the result of divergence among ancient repeat copies and gene/pseudogene duplication.</p>http://www.biomedcentral.com/1471-2164/12/553 |
| spellingShingle | Liu Wenxuan Thummasuwan Supaphan Sehgal Sunish K Chouvarine Philippe Peterson Daniel G Characterization of the genome of bald cypress BMC Genomics |
| title | Characterization of the genome of bald cypress |
| title_full | Characterization of the genome of bald cypress |
| title_fullStr | Characterization of the genome of bald cypress |
| title_full_unstemmed | Characterization of the genome of bald cypress |
| title_short | Characterization of the genome of bald cypress |
| title_sort | characterization of the genome of bald cypress |
| url | http://www.biomedcentral.com/1471-2164/12/553 |
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