Ancient nuclear plastid DNA in the yew family (taxaceae).
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.
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
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.—
Affiliation: Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan.