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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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Alignment of seven rps8 sequences. The left orange arrow highlights a specific C-to-U RNA-editing site at the second codon position of the initial codon in the four sampled Taxus. mairei plastomes. A normal initial codon, ATG (black rectangle), was common among Cephalotaxus, Amentotaxus, and Tax-4. These data imply the creation of the “ACT” RNA-editing site after the transfer of Tax-4. The red rectangle denotes the initial codon annotated in the sequences from NCBI GenBank.
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evu165-F6: Alignment of seven rps8 sequences. The left orange arrow highlights a specific C-to-U RNA-editing site at the second codon position of the initial codon in the four sampled Taxus. mairei plastomes. A normal initial codon, ATG (black rectangle), was common among Cephalotaxus, Amentotaxus, and Tax-4. These data imply the creation of the “ACT” RNA-editing site after the transfer of Tax-4. The red rectangle denotes the initial codon annotated in the sequences from NCBI GenBank.

Mentions: Most importantly, nupts can also help in probing RNA-editing sites and improving gene annotations. Figure 6 clearly reveals that the previously annotated rps8 of T. mairei (vouchers NN014, WC052, and SNJ046) is truncated. Our newly predicted initial codon, “ACG,” locates 48 bp upstream of the previously predicted site. This ACG initial codon was predicted to be corrected to “AUG” via a C-to-U RNA-editing because the corresponding sequence of Tax-4 nupt and other conifers retain a normal initial codon of “ATG” (fig. 6). These data also imply that in T. mairei, the transfer of Tax-4 nupt predates the T-to-C mutation at the second codon position in the initial codon of rps8.Fig. 6.—


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

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

Alignment of seven rps8 sequences. The left orange arrow highlights a specific C-to-U RNA-editing site at the second codon position of the initial codon in the four sampled Taxus. mairei plastomes. A normal initial codon, ATG (black rectangle), was common among Cephalotaxus, Amentotaxus, and Tax-4. These data imply the creation of the “ACT” RNA-editing site after the transfer of Tax-4. The red rectangle denotes the initial codon annotated in the sequences from NCBI GenBank.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu165-F6: Alignment of seven rps8 sequences. The left orange arrow highlights a specific C-to-U RNA-editing site at the second codon position of the initial codon in the four sampled Taxus. mairei plastomes. A normal initial codon, ATG (black rectangle), was common among Cephalotaxus, Amentotaxus, and Tax-4. These data imply the creation of the “ACT” RNA-editing site after the transfer of Tax-4. The red rectangle denotes the initial codon annotated in the sequences from NCBI GenBank.
Mentions: Most importantly, nupts can also help in probing RNA-editing sites and improving gene annotations. Figure 6 clearly reveals that the previously annotated rps8 of T. mairei (vouchers NN014, WC052, and SNJ046) is truncated. Our newly predicted initial codon, “ACG,” locates 48 bp upstream of the previously predicted site. This ACG initial codon was predicted to be corrected to “AUG” via a C-to-U RNA-editing because the corresponding sequence of Tax-4 nupt and other conifers retain a normal initial codon of “ATG” (fig. 6). These data also imply that in T. mairei, the transfer of Tax-4 nupt predates the T-to-C mutation at the second codon position in the initial codon of rps8.Fig. 6.—

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