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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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Distribution of SNPs, indels, and SSRs in the plastomes of Taxus mairei. The outermost circle is the plastome map of T. mairei (AP014575) with genes that are transcribed counter-clockwise (outer boxes) and clockwise (inner boxes), respectively. The immediately next circle denotes a scale of 5-kb units beginning at psbA gene (the 3 o’clock position). In the gray zone, three histograms from outer to inner are 1) counts of SNPs, 2) counts of indels, and 3) total indel lengths within nonoverlapping 200-bp bins across the entire plastome. Triangles mark locations of SSRs.
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evu165-F2: Distribution of SNPs, indels, and SSRs in the plastomes of Taxus mairei. The outermost circle is the plastome map of T. mairei (AP014575) with genes that are transcribed counter-clockwise (outer boxes) and clockwise (inner boxes), respectively. The immediately next circle denotes a scale of 5-kb units beginning at psbA gene (the 3 o’clock position). In the gray zone, three histograms from outer to inner are 1) counts of SNPs, 2) counts of indels, and 3) total indel lengths within nonoverlapping 200-bp bins across the entire plastome. Triangles mark locations of SSRs.

Mentions: We also performed a pairwise genome comparison between our T. mairei and voucher NN014 because the latter was designated as the reference sequence (RefSeq) in NCBI GenBank. We detected 858 SNPs and 218 indels. Supplementary figure S3, Supplementary Material online, shows that the intergenic spacers and coding regions contained nearly equal numbers of SNPs. Most of the indels were found in the intergenic spacers. We found 33 indels in the coding regions, but none caused frameshifts. Figure 2 illustrates the distribution of SNPs, indels, and SSRs in the plastome of our sampled T. mairei. Interestingly, the abundance of SSRs was positively correlated with that of SNPs (Pearson, r = 0.52, P < 0.01), with no correlation between SSRs and indels (Pearson, r = 0.02, P = 0.89). In legumes, the region that contains ycf4, psaI, accD, and rps16 was found to be hypermutable (Magee et al. 2010). In the plastome of T. mairei, three 200-bp bins that locate in the sequence of 5′clpP (position 55,001–55,200), that of 5′ycf1 (pos. 124,201–124,400), and the intergenic spacer between rrn16 and rrn23 (pos. 96,801–97,000) contained the highest sum of SNPs, indels, and SSRs (fig. 2). Therefore, these loci can be considered intraspecies mutational hotspots in T. mairei and can be potentially high-resolution DNA barcodes in the study of population genetics.Fig. 2.—


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

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

Distribution of SNPs, indels, and SSRs in the plastomes of Taxus mairei. The outermost circle is the plastome map of T. mairei (AP014575) with genes that are transcribed counter-clockwise (outer boxes) and clockwise (inner boxes), respectively. The immediately next circle denotes a scale of 5-kb units beginning at psbA gene (the 3 o’clock position). In the gray zone, three histograms from outer to inner are 1) counts of SNPs, 2) counts of indels, and 3) total indel lengths within nonoverlapping 200-bp bins across the entire plastome. Triangles mark locations of SSRs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu165-F2: Distribution of SNPs, indels, and SSRs in the plastomes of Taxus mairei. The outermost circle is the plastome map of T. mairei (AP014575) with genes that are transcribed counter-clockwise (outer boxes) and clockwise (inner boxes), respectively. The immediately next circle denotes a scale of 5-kb units beginning at psbA gene (the 3 o’clock position). In the gray zone, three histograms from outer to inner are 1) counts of SNPs, 2) counts of indels, and 3) total indel lengths within nonoverlapping 200-bp bins across the entire plastome. Triangles mark locations of SSRs.
Mentions: We also performed a pairwise genome comparison between our T. mairei and voucher NN014 because the latter was designated as the reference sequence (RefSeq) in NCBI GenBank. We detected 858 SNPs and 218 indels. Supplementary figure S3, Supplementary Material online, shows that the intergenic spacers and coding regions contained nearly equal numbers of SNPs. Most of the indels were found in the intergenic spacers. We found 33 indels in the coding regions, but none caused frameshifts. Figure 2 illustrates the distribution of SNPs, indels, and SSRs in the plastome of our sampled T. mairei. Interestingly, the abundance of SSRs was positively correlated with that of SNPs (Pearson, r = 0.52, P < 0.01), with no correlation between SSRs and indels (Pearson, r = 0.02, P = 0.89). In legumes, the region that contains ycf4, psaI, accD, and rps16 was found to be hypermutable (Magee et al. 2010). In the plastome of T. mairei, three 200-bp bins that locate in the sequence of 5′clpP (position 55,001–55,200), that of 5′ycf1 (pos. 124,201–124,400), and the intergenic spacer between rrn16 and rrn23 (pos. 96,801–97,000) contained the highest sum of SNPs, indels, and SSRs (fig. 2). Therefore, these loci can be considered intraspecies mutational hotspots in T. mairei and can be potentially high-resolution DNA barcodes in the study of population genetics.Fig. 2.—

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