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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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Hypothetical evolutionary scenarios for plastomic rearrangements in Taxaceae. Plastomes are circular but here are shown in gray horizontal bars (beginning at psbA) for pairwise comparisons. Color triangles within the gray horizontal bars denote LCBs with their relative orientations. Gray bars from top to bottom indicate the corresponding plastomes in the common ancestor of Taxaceae, intermediate ancestors, and extant representative species. Inversions between two plastomes are linked by orange curved lines. Ancestral gene orders before the occurrence of specific inversions are shown along tree branches. Primer pairs (black arrows) for amplification of the corresponding ancestral fragments are labeled: Tax-1 to 4 for Taxus mairei, Ame-1 to 2 for Amentotaxus formosana, and Cep-1 to 5 for Cephalotaxus wilsoniana (see supplementary table S1, Supplementary Material online, for primer sequences).
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evu165-F3: Hypothetical evolutionary scenarios for plastomic rearrangements in Taxaceae. Plastomes are circular but here are shown in gray horizontal bars (beginning at psbA) for pairwise comparisons. Color triangles within the gray horizontal bars denote LCBs with their relative orientations. Gray bars from top to bottom indicate the corresponding plastomes in the common ancestor of Taxaceae, intermediate ancestors, and extant representative species. Inversions between two plastomes are linked by orange curved lines. Ancestral gene orders before the occurrence of specific inversions are shown along tree branches. Primer pairs (black arrows) for amplification of the corresponding ancestral fragments are labeled: Tax-1 to 4 for Taxus mairei, Ame-1 to 2 for Amentotaxus formosana, and Cep-1 to 5 for Cephalotaxus wilsoniana (see supplementary table S1, Supplementary Material online, for primer sequences).

Mentions: Ten pairs of specific primers used for amplification of nupt sequences were designed and their sequences and corresponding locations are in supplementary table S1, Supplementary Material online and figure 3. PCR amplification involved use of the long-range PCR Tag (TaKaRa LA Taq, Takara Bio Inc.) under the thermo-cycling condition 98 °C for 3 min, followed by 30 cycles of 98 °C for 15 s, 55 °C for 15 s, and 68 °C for 4 min, and a final extension at 72 °C for 10 min. Amplicons were checked by electrophoresis. Amplicons with expected lengths were collected and cloned into yT&A vectors (Yeastern Biotech Co., Taipei) that were then proliferated in Escherichia coli. Sequencing the proliferated amplicons involved M13-F and M13-R primers on an ABI 3730xl DNA Sequencer (Life Technologies).


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

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

Hypothetical evolutionary scenarios for plastomic rearrangements in Taxaceae. Plastomes are circular but here are shown in gray horizontal bars (beginning at psbA) for pairwise comparisons. Color triangles within the gray horizontal bars denote LCBs with their relative orientations. Gray bars from top to bottom indicate the corresponding plastomes in the common ancestor of Taxaceae, intermediate ancestors, and extant representative species. Inversions between two plastomes are linked by orange curved lines. Ancestral gene orders before the occurrence of specific inversions are shown along tree branches. Primer pairs (black arrows) for amplification of the corresponding ancestral fragments are labeled: Tax-1 to 4 for Taxus mairei, Ame-1 to 2 for Amentotaxus formosana, and Cep-1 to 5 for Cephalotaxus wilsoniana (see supplementary table S1, Supplementary Material online, for primer sequences).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu165-F3: Hypothetical evolutionary scenarios for plastomic rearrangements in Taxaceae. Plastomes are circular but here are shown in gray horizontal bars (beginning at psbA) for pairwise comparisons. Color triangles within the gray horizontal bars denote LCBs with their relative orientations. Gray bars from top to bottom indicate the corresponding plastomes in the common ancestor of Taxaceae, intermediate ancestors, and extant representative species. Inversions between two plastomes are linked by orange curved lines. Ancestral gene orders before the occurrence of specific inversions are shown along tree branches. Primer pairs (black arrows) for amplification of the corresponding ancestral fragments are labeled: Tax-1 to 4 for Taxus mairei, Ame-1 to 2 for Amentotaxus formosana, and Cep-1 to 5 for Cephalotaxus wilsoniana (see supplementary table S1, Supplementary Material online, for primer sequences).
Mentions: Ten pairs of specific primers used for amplification of nupt sequences were designed and their sequences and corresponding locations are in supplementary table S1, Supplementary Material online and figure 3. PCR amplification involved use of the long-range PCR Tag (TaKaRa LA Taq, Takara Bio Inc.) under the thermo-cycling condition 98 °C for 3 min, followed by 30 cycles of 98 °C for 15 s, 55 °C for 15 s, and 68 °C for 4 min, and a final extension at 72 °C for 10 min. Amplicons were checked by electrophoresis. Amplicons with expected lengths were collected and cloned into yT&A vectors (Yeastern Biotech Co., Taipei) that were then proliferated in Escherichia coli. Sequencing the proliferated amplicons involved M13-F and M13-R primers on an ABI 3730xl DNA Sequencer (Life Technologies).

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