Targeted isolation, sequence assembly and characterization of two white spruce (<it>Picea glauca</it>) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome
<p>Abstract</p> <p>Background</p> <p>Conifers are a large group of gymnosperm trees which are separated from the angiosperms by more than 300 million years of independent evolution. Conifer genomes are extremely large and contain considerable amounts of repetitive DNA....
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2009-08-01
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| Series: | BMC Plant Biology |
| Online Access: | http://www.biomedcentral.com/1471-2229/9/106 |
| _version_ | 1811244672656343040 |
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| author | Ritland Carol Keeling Christopher I Hamberger Britta Oddy Claire Yuen Mack Hall Dawn Hamberger Björn Ritland Kermit Bohlmann Jörg |
| author_facet | Ritland Carol Keeling Christopher I Hamberger Britta Oddy Claire Yuen Mack Hall Dawn Hamberger Björn Ritland Kermit Bohlmann Jörg |
| author_sort | Ritland Carol |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Conifers are a large group of gymnosperm trees which are separated from the angiosperms by more than 300 million years of independent evolution. Conifer genomes are extremely large and contain considerable amounts of repetitive DNA. Currently, conifer sequence resources exist predominantly as expressed sequence tags (ESTs) and full-length (FL)cDNAs. There is no genome sequence available for a conifer or any other gymnosperm. Conifer defence-related genes often group into large families with closely related members. The goals of this study are to assess the feasibility of targeted isolation and sequence assembly of conifer BAC clones containing specific genes from two large gene families, and to characterize large segments of genomic DNA sequence for the first time from a conifer.</p> <p>Results</p> <p>We used a PCR-based approach to identify BAC clones for two target genes, a terpene synthase (3-carene synthase; 3CAR) and a cytochrome P450 (CYP720B4) from a non-arrayed genomic BAC library of white spruce (<it>Picea glauca</it>). Shotgun genomic fragments isolated from the BAC clones were sequenced to a depth of 15.6- and 16.0-fold coverage, respectively. Assembly and manual curation yielded sequence scaffolds of 172 kbp (3CAR) and 94 kbp (CYP720B4) long. Inspection of the genomic sequences revealed the intron-exon structures, the putative promoter regions and putative <it>cis</it>-regulatory elements of these genes. Sequences related to transposable elements (TEs), high complexity repeats and simple repeats were prevalent and comprised approximately 40% of the sequenced genomic DNA. An <it>in silico </it>simulation of the effect of sequencing depth on the quality of the sequence assembly provides direction for future efforts of conifer genome sequencing.</p> <p>Conclusion</p> <p>We report the first targeted cloning, sequencing, assembly, and annotation of large segments of genomic DNA from a conifer. We demonstrate that genomic BAC clones for individual members of multi-member gene families can be isolated in a gene-specific fashion. The results of the present work provide important new information about the structure and content of conifer genomic DNA that will guide future efforts to sequence and assemble conifer genomes.</p> |
| first_indexed | 2024-04-12T14:29:21Z |
| format | Article |
| id | doaj.art-044be638fb414afd95c02a51885bb749 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-12T14:29:21Z |
| publishDate | 2009-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-044be638fb414afd95c02a51885bb7492022-12-22T03:29:21ZengBMCBMC Plant Biology1471-22292009-08-019110610.1186/1471-2229-9-106Targeted isolation, sequence assembly and characterization of two white spruce (<it>Picea glauca</it>) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genomeRitland CarolKeeling Christopher IHamberger BrittaOddy ClaireYuen MackHall DawnHamberger BjörnRitland KermitBohlmann Jörg<p>Abstract</p> <p>Background</p> <p>Conifers are a large group of gymnosperm trees which are separated from the angiosperms by more than 300 million years of independent evolution. Conifer genomes are extremely large and contain considerable amounts of repetitive DNA. Currently, conifer sequence resources exist predominantly as expressed sequence tags (ESTs) and full-length (FL)cDNAs. There is no genome sequence available for a conifer or any other gymnosperm. Conifer defence-related genes often group into large families with closely related members. The goals of this study are to assess the feasibility of targeted isolation and sequence assembly of conifer BAC clones containing specific genes from two large gene families, and to characterize large segments of genomic DNA sequence for the first time from a conifer.</p> <p>Results</p> <p>We used a PCR-based approach to identify BAC clones for two target genes, a terpene synthase (3-carene synthase; 3CAR) and a cytochrome P450 (CYP720B4) from a non-arrayed genomic BAC library of white spruce (<it>Picea glauca</it>). Shotgun genomic fragments isolated from the BAC clones were sequenced to a depth of 15.6- and 16.0-fold coverage, respectively. Assembly and manual curation yielded sequence scaffolds of 172 kbp (3CAR) and 94 kbp (CYP720B4) long. Inspection of the genomic sequences revealed the intron-exon structures, the putative promoter regions and putative <it>cis</it>-regulatory elements of these genes. Sequences related to transposable elements (TEs), high complexity repeats and simple repeats were prevalent and comprised approximately 40% of the sequenced genomic DNA. An <it>in silico </it>simulation of the effect of sequencing depth on the quality of the sequence assembly provides direction for future efforts of conifer genome sequencing.</p> <p>Conclusion</p> <p>We report the first targeted cloning, sequencing, assembly, and annotation of large segments of genomic DNA from a conifer. We demonstrate that genomic BAC clones for individual members of multi-member gene families can be isolated in a gene-specific fashion. The results of the present work provide important new information about the structure and content of conifer genomic DNA that will guide future efforts to sequence and assemble conifer genomes.</p>http://www.biomedcentral.com/1471-2229/9/106 |
| spellingShingle | Ritland Carol Keeling Christopher I Hamberger Britta Oddy Claire Yuen Mack Hall Dawn Hamberger Björn Ritland Kermit Bohlmann Jörg Targeted isolation, sequence assembly and characterization of two white spruce (<it>Picea glauca</it>) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome BMC Plant Biology |
| title | Targeted isolation, sequence assembly and characterization of two white spruce (<it>Picea glauca</it>) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome |
| title_full | Targeted isolation, sequence assembly and characterization of two white spruce (<it>Picea glauca</it>) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome |
| title_fullStr | Targeted isolation, sequence assembly and characterization of two white spruce (<it>Picea glauca</it>) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome |
| title_full_unstemmed | Targeted isolation, sequence assembly and characterization of two white spruce (<it>Picea glauca</it>) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome |
| title_short | Targeted isolation, sequence assembly and characterization of two white spruce (<it>Picea glauca</it>) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome |
| title_sort | targeted isolation sequence assembly and characterization of two white spruce it picea glauca it bac clones for terpenoid synthase and cytochrome p450 genes involved in conifer defence reveal insights into a conifer genome |
| url | http://www.biomedcentral.com/1471-2229/9/106 |
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