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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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Percentage of nucleotide mutation classes in nupts and their plastomic counterparts. Types of mutations are divided into six classes. For example, the class AT-to-GC denotes the pooled percentage of the A-to-G mutations and its complement T-to-C. Data are mean ± SD.
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evu165-F5: Percentage of nucleotide mutation classes in nupts and their plastomic counterparts. Types of mutations are divided into six classes. For example, the class AT-to-GC denotes the pooled percentage of the A-to-G mutations and its complement T-to-C. Data are mean ± SD.

Mentions: The sequence identity between the four nupts and their plastomic counterparts ranges from 61.71% to 99.08% (table 1). In fact, differences in aligned sites between nupts and their plastomic counterparts are derived from two types of mutations. One is the mutation in nupts and the other is that in plastomes. As shown in table 1, with the exception of Tax-4, all nupts accumulated more mutations than their plastomic counterparts. The low sequence identity between Tax-4 and its plastome sequences (61.71% in table 1) may be due to the unusually increased mutations in the latter. In all nupts except Cep-5, at least one potential protein-coding gene had the ratio of nonsynonymous (dn)/synonymous (ds) mutations >1, which reflects relaxed functional constraints in nupts. Figure 5 illustrates nucleotide mutation classes in nupts and their corresponding plastome sequences. We excluded the plastomic counterpart of Cep-2 from calculation because we observed only one mutation in the sequence. In all nupts, transitional mutations comprise over 50% of the total mutations. The mutation of G to A and its complement C to T (denoted GC-to-AT in fig. 5) had the highest frequency in both nupts and plastome sequences. To examine which of the mutation classes is statistically predominant, we compared the two most abundant classes of mutations. In nupts, the frequency was higher for GC-to-AT than AT-to-GC mutations (t-test, P = 0.018). However, GC-to-AT and AT-to-GC mutations did not differ in plastome sequences (t-test, P = 0.379), suggesting different mutational environments between nupts and their corresponding plastome sequences.Fig. 5.—


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

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

Percentage of nucleotide mutation classes in nupts and their plastomic counterparts. Types of mutations are divided into six classes. For example, the class AT-to-GC denotes the pooled percentage of the A-to-G mutations and its complement T-to-C. Data are mean ± SD.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu165-F5: Percentage of nucleotide mutation classes in nupts and their plastomic counterparts. Types of mutations are divided into six classes. For example, the class AT-to-GC denotes the pooled percentage of the A-to-G mutations and its complement T-to-C. Data are mean ± SD.
Mentions: The sequence identity between the four nupts and their plastomic counterparts ranges from 61.71% to 99.08% (table 1). In fact, differences in aligned sites between nupts and their plastomic counterparts are derived from two types of mutations. One is the mutation in nupts and the other is that in plastomes. As shown in table 1, with the exception of Tax-4, all nupts accumulated more mutations than their plastomic counterparts. The low sequence identity between Tax-4 and its plastome sequences (61.71% in table 1) may be due to the unusually increased mutations in the latter. In all nupts except Cep-5, at least one potential protein-coding gene had the ratio of nonsynonymous (dn)/synonymous (ds) mutations >1, which reflects relaxed functional constraints in nupts. Figure 5 illustrates nucleotide mutation classes in nupts and their corresponding plastome sequences. We excluded the plastomic counterpart of Cep-2 from calculation because we observed only one mutation in the sequence. In all nupts, transitional mutations comprise over 50% of the total mutations. The mutation of G to A and its complement C to T (denoted GC-to-AT in fig. 5) had the highest frequency in both nupts and plastome sequences. To examine which of the mutation classes is statistically predominant, we compared the two most abundant classes of mutations. In nupts, the frequency was higher for GC-to-AT than AT-to-GC mutations (t-test, P = 0.018). However, GC-to-AT and AT-to-GC mutations did not differ in plastome sequences (t-test, P = 0.379), suggesting different mutational environments between nupts and their corresponding plastome sequences.Fig. 5.—

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
Related in: MedlinePlus