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Ancient nuclear plastid DNA in the yew family (taxaceae).

Hsu CY, Wu CS, Chaw SM - Genome Biol Evol (2014)

Bottom Line: These nupts have significantly accumulated GC-to-AT mutations, reflecting a nuclear mutational environment shaped by spontaneous deamination of 5-methylcytosin.These findings suggest that nupts can help recover scenarios of the nucleotide mutation process.We show that the Taxaceae nupts we retrieved may have been retained because the Cretaceous and they carry information of both ancestral genomic organization and nucleotide composition, which offer clues for understanding the plastome evolution in conifers.

View Article: PubMed Central - PubMed

Affiliation: Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan.

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Origin of the obtained PCR amplicons examined by ML phylogenetic analyses. PCR amplicons are labeled “PCR,” and their plastomic counterparts and orthologs of other gymnosperms are labeled “pt.” Taxa of the same conifer family are in the same color. Cycas and Ginkgo together are the outgroup. Bootstrapping values assessed with 1,000 replicates are shown along branches.
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evu165-F4: Origin of the obtained PCR amplicons examined by ML phylogenetic analyses. PCR amplicons are labeled “PCR,” and their plastomic counterparts and orthologs of other gymnosperms are labeled “pt.” Taxa of the same conifer family are in the same color. Cycas and Ginkgo together are the outgroup. Bootstrapping values assessed with 1,000 replicates are shown along branches.

Mentions: The obtained PCR amplicons were sequenced and annotated (supplementary table S2, Supplementary Material online). With the exception of chlB of Cep-2, all putative protein-coding genes contain no premature stop codons. The coding sequence (CDS) of each amplicon was aligned with its plastomic counterparts and orthologs of other cupressophytes, Ginkgo and Cycas. We used ML trees inferred from concatenated CDSs to examine the origins of these PCR amplicons, with Ginkgo and Cycas as the outgroup (fig. 4). In each tree, the plastomic sequences were divided into three groups (i.e., the Cupressaceae clade, the Taxaceae clade, and the clade comprising Araucariaceae and Podocarpaceae). Notably, the placements of our PCR amplicons are incongruent among the four trees. For example, both Ame-2 and Cep-2 were clustered with their plastomic counterparts (fig. 4A). In contrast, Cep-5, Cep-6, and Tax-4 were placed remotely from their individual plastomic counterparts, indicating that they originated via horizontal transfer (fig. 4B–D).Fig. 4.—


Ancient nuclear plastid DNA in the yew family (taxaceae).

Hsu CY, Wu CS, Chaw SM - Genome Biol Evol (2014)

Origin of the obtained PCR amplicons examined by ML phylogenetic analyses. PCR amplicons are labeled “PCR,” and their plastomic counterparts and orthologs of other gymnosperms are labeled “pt.” Taxa of the same conifer family are in the same color. Cycas and Ginkgo together are the outgroup. Bootstrapping values assessed with 1,000 replicates are shown along branches.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231637&req=5

evu165-F4: Origin of the obtained PCR amplicons examined by ML phylogenetic analyses. PCR amplicons are labeled “PCR,” and their plastomic counterparts and orthologs of other gymnosperms are labeled “pt.” Taxa of the same conifer family are in the same color. Cycas and Ginkgo together are the outgroup. Bootstrapping values assessed with 1,000 replicates are shown along branches.
Mentions: The obtained PCR amplicons were sequenced and annotated (supplementary table S2, Supplementary Material online). With the exception of chlB of Cep-2, all putative protein-coding genes contain no premature stop codons. The coding sequence (CDS) of each amplicon was aligned with its plastomic counterparts and orthologs of other cupressophytes, Ginkgo and Cycas. We used ML trees inferred from concatenated CDSs to examine the origins of these PCR amplicons, with Ginkgo and Cycas as the outgroup (fig. 4). In each tree, the plastomic sequences were divided into three groups (i.e., the Cupressaceae clade, the Taxaceae clade, and the clade comprising Araucariaceae and Podocarpaceae). Notably, the placements of our PCR amplicons are incongruent among the four trees. For example, both Ame-2 and Cep-2 were clustered with their plastomic counterparts (fig. 4A). In contrast, Cep-5, Cep-6, and Tax-4 were placed remotely from their individual plastomic counterparts, indicating that they originated via horizontal transfer (fig. 4B–D).Fig. 4.—

Bottom Line: These nupts have significantly accumulated GC-to-AT mutations, reflecting a nuclear mutational environment shaped by spontaneous deamination of 5-methylcytosin.These findings suggest that nupts can help recover scenarios of the nucleotide mutation process.We show that the Taxaceae nupts we retrieved may have been retained because the Cretaceous and they carry information of both ancestral genomic organization and nucleotide composition, which offer clues for understanding the plastome evolution in conifers.

View Article: PubMed Central - PubMed

Affiliation: Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan.

Show MeSH