Deciphering the complex leaf transcriptome of the allotetraploid species <it>Nicotiana tabacum</it>: a phylogenomic perspective
<p>Abstract</p> <p>Background</p> <p>Polyploidization is an important mechanism in plant evolution. By analyzing the leaf transcriptomes taken from the allotetraploid <it>Nicotiana tabacum</it> (tobacco) and parental genome donors, <it>N. sylvesteris&l...
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| Format: | Article |
| Language: | English |
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BMC
2012-08-01
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| Series: | BMC Genomics |
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| Online Access: | http://www.biomedcentral.com/1471-2164/13/406 |
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| author | Bombarely Aureliano Edwards Kieron D Sanchez-Tamburrino Juan Mueller Lukas A |
| author_facet | Bombarely Aureliano Edwards Kieron D Sanchez-Tamburrino Juan Mueller Lukas A |
| author_sort | Bombarely Aureliano |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Polyploidization is an important mechanism in plant evolution. By analyzing the leaf transcriptomes taken from the allotetraploid <it>Nicotiana tabacum</it> (tobacco) and parental genome donors, <it>N. sylvesteris</it> (S-Genome) and <it>N. tomentosiformis</it> (T-Genome), a phylogenomic approach was taken to map the fate of homeologous gene pairs in this plant.</p> <p>Results</p> <p>A comparison between the genes present in the leaf transcriptomes of <it>N. tabacum</it> and modern day representatives of its progenitor species demonstrated that only 33% of assembled transcripts could be distinguished based on their sequences. A large majority of the genes (83.6% of the non parent distinguishable and 87.2% of the phylogenetic topology analyzed clusters) expressed above background level (more than 5 reads) showed similar overall expression levels. Homeologous sequences could be identified for 968 gene clusters, and 90% (6% of all genes) of the set maintained expression of only one of the tobacco homeologs. When both homeologs were expressed, only 15% (0.5% of the total) showed evidence of differential expression, providing limited evidence of subfunctionalization. Comparing the rate of synonymous nucleotide substitution (Ks) and non-synonymous nucleotide substitution (Kn) provided limited evidence for positive selection during the evolution of tobacco since the polyploidization event took place.</p> <p>Conclusions</p> <p>Polyploidization is a powerful mechanism for plant speciation that can occur during one generation; however millions of generations may be necessary for duplicate genes to acquire a new function. Analysis of the tobacco leaf transcriptome reveals that polyploidization, even in a young tetraploid such as tobacco, can lead to complex changes in gene expression. Gene loss and gene silencing, or subfunctionalization may explain why both homeologs are not expressed by the associated genes. With Whole Genome Duplication (WGD) events, polyploid genomes usually maintain a high percentage of gene duplicates. The data provided little evidence of preferential maintenance of gene expression from either the T- or S-genome. Additionally there was little evidence of neofunctionalization in <it>Nicotiana tabacum</it> suggesting it occurs at a low frequency in young polyploidy.</p> |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
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| publishDate | 2012-08-01 |
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| spelling | doaj.art-4f691b5be0a04b348e682e51246723f92022-12-21T20:55:44ZengBMCBMC Genomics1471-21642012-08-0113140610.1186/1471-2164-13-406Deciphering the complex leaf transcriptome of the allotetraploid species <it>Nicotiana tabacum</it>: a phylogenomic perspectiveBombarely AurelianoEdwards Kieron DSanchez-Tamburrino JuanMueller Lukas A<p>Abstract</p> <p>Background</p> <p>Polyploidization is an important mechanism in plant evolution. By analyzing the leaf transcriptomes taken from the allotetraploid <it>Nicotiana tabacum</it> (tobacco) and parental genome donors, <it>N. sylvesteris</it> (S-Genome) and <it>N. tomentosiformis</it> (T-Genome), a phylogenomic approach was taken to map the fate of homeologous gene pairs in this plant.</p> <p>Results</p> <p>A comparison between the genes present in the leaf transcriptomes of <it>N. tabacum</it> and modern day representatives of its progenitor species demonstrated that only 33% of assembled transcripts could be distinguished based on their sequences. A large majority of the genes (83.6% of the non parent distinguishable and 87.2% of the phylogenetic topology analyzed clusters) expressed above background level (more than 5 reads) showed similar overall expression levels. Homeologous sequences could be identified for 968 gene clusters, and 90% (6% of all genes) of the set maintained expression of only one of the tobacco homeologs. When both homeologs were expressed, only 15% (0.5% of the total) showed evidence of differential expression, providing limited evidence of subfunctionalization. Comparing the rate of synonymous nucleotide substitution (Ks) and non-synonymous nucleotide substitution (Kn) provided limited evidence for positive selection during the evolution of tobacco since the polyploidization event took place.</p> <p>Conclusions</p> <p>Polyploidization is a powerful mechanism for plant speciation that can occur during one generation; however millions of generations may be necessary for duplicate genes to acquire a new function. Analysis of the tobacco leaf transcriptome reveals that polyploidization, even in a young tetraploid such as tobacco, can lead to complex changes in gene expression. Gene loss and gene silencing, or subfunctionalization may explain why both homeologs are not expressed by the associated genes. With Whole Genome Duplication (WGD) events, polyploid genomes usually maintain a high percentage of gene duplicates. The data provided little evidence of preferential maintenance of gene expression from either the T- or S-genome. Additionally there was little evidence of neofunctionalization in <it>Nicotiana tabacum</it> suggesting it occurs at a low frequency in young polyploidy.</p>http://www.biomedcentral.com/1471-2164/13/406<it>Nicotiana tabacum</it>PhylogenomicPolyploidSequence assemblyHomeolog identificationTree topologyTranscriptomeTobaccoNext generation sequencing454 |
| spellingShingle | Bombarely Aureliano Edwards Kieron D Sanchez-Tamburrino Juan Mueller Lukas A Deciphering the complex leaf transcriptome of the allotetraploid species <it>Nicotiana tabacum</it>: a phylogenomic perspective BMC Genomics <it>Nicotiana tabacum</it> Phylogenomic Polyploid Sequence assembly Homeolog identification Tree topology Transcriptome Tobacco Next generation sequencing 454 |
| title | Deciphering the complex leaf transcriptome of the allotetraploid species <it>Nicotiana tabacum</it>: a phylogenomic perspective |
| title_full | Deciphering the complex leaf transcriptome of the allotetraploid species <it>Nicotiana tabacum</it>: a phylogenomic perspective |
| title_fullStr | Deciphering the complex leaf transcriptome of the allotetraploid species <it>Nicotiana tabacum</it>: a phylogenomic perspective |
| title_full_unstemmed | Deciphering the complex leaf transcriptome of the allotetraploid species <it>Nicotiana tabacum</it>: a phylogenomic perspective |
| title_short | Deciphering the complex leaf transcriptome of the allotetraploid species <it>Nicotiana tabacum</it>: a phylogenomic perspective |
| title_sort | deciphering the complex leaf transcriptome of the allotetraploid species it nicotiana tabacum it a phylogenomic perspective |
| topic | <it>Nicotiana tabacum</it> Phylogenomic Polyploid Sequence assembly Homeolog identification Tree topology Transcriptome Tobacco Next generation sequencing 454 |
| url | http://www.biomedcentral.com/1471-2164/13/406 |
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