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No ancient DNA damage in Actinobacteria from the Neanderthal bone.

Zaremba-Niedźwiedzka K, Andersson SG - PLoS ONE (2013)

Bottom Line: However, phylogenetic analyses did not identify any sediment clones that were closely related to the bone-derived sequences.We analysed the patterns of nucleotide differences in the individual sequence reads compared to the assembled consensus sequences of the rRNA gene sequences.Such studies can help identify targeted measures to increase the relative amount of endogenous DNA in the sample.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden.

ABSTRACT

Background: The Neanderthal genome was recently sequenced using DNA extracted from a 38,000-year-old fossil. At the start of the project, the fraction of mammalian and bacterial DNA in the sample was estimated to be <6% and 9%, respectively. Treatment with restriction enzymes prior to sequencing increased the relative proportion of mammalian DNA to 15%, but the large majority of sequences remain uncharacterized.

Principal findings: Our taxonomic profiling of 3.95 Gb of Neanderthal DNA isolated from the Vindija Neanderthal Vi33.16 fossil showed that 90% of about 50,000 rRNA gene sequence reads were of bacterial origin, of which Actinobacteria accounted for more than 75%. Actinobacteria also represented more than 80% of the PCR-amplified 16S rRNA gene sequences from a cave sediment sample taken from the same G layer as the Neanderthal bone. However, phylogenetic analyses did not identify any sediment clones that were closely related to the bone-derived sequences. We analysed the patterns of nucleotide differences in the individual sequence reads compared to the assembled consensus sequences of the rRNA gene sequences. The typical ancient nucleotide substitution pattern with a majority of C to T changes indicative of DNA damage was observed for the Neanderthal rRNA gene sequences, but not for the Streptomyces-like rRNA gene sequences.

Conclusions/significance: Our analyses suggest that the Actinobacteria, and especially members of the Streptomycetales, contribute the majority of sequences in the DNA extracted from the Neanderthal fossil Vi33.16. The bacterial DNA showed no signs of damage, and we hypothesize that it was derived from bacteria that have been enriched inside the bone. The bioinformatic approach used here paves the way for future studies of microbial compositions and patterns of DNA damage in bacteria from archaeological bones. Such studies can help identify targeted measures to increase the relative amount of endogenous DNA in the sample.

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Related in: MedlinePlus

Phylogeny of prolyl aminopeptidases.Propyl aminopeptidase consensus sequences are coloured red (Contigs C1103–C1106). The clade containing contig C1104 and two Streptomyces species is shown in yellow. The Streptomyces reference sequences from MEROPS S33 family are shown in green and family holotypes in blue. MEROPS id is indicated for each sequence. The phylogeny was inferred using the maximum likelihood method. Numbers refer to bootstrap support values higher than 75%.
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pone-0062799-g006: Phylogeny of prolyl aminopeptidases.Propyl aminopeptidase consensus sequences are coloured red (Contigs C1103–C1106). The clade containing contig C1104 and two Streptomyces species is shown in yellow. The Streptomyces reference sequences from MEROPS S33 family are shown in green and family holotypes in blue. MEROPS id is indicated for each sequence. The phylogeny was inferred using the maximum likelihood method. Numbers refer to bootstrap support values higher than 75%.

Mentions: To investigate the taxonomic affiliations of the S33 protein family, the identified reads were assembled, yielding more than a thousand contigs in total. The consensus protein sequences of the four contigs that contained a majority of reads were compared to reference protein sequences of the S33 family in the MEROPs database in a maximum likelihood analysis (Figure 6). Two of the consensus sequences (C1103 and C1104) belonged to a clade with actinobacterial tripeptidyl peptidase B (S33.006) for which the holotype sequence is from Streptomyces lividans (100% bootstrap support). C1104 was placed as a sister taxa to Streptomyces sviceus with 100% bootstrap support and there was some support for a clustering also of C1103 with Streptomyces. To ensure the best possible match, we included all S33.006 sequences and all S33 sequences from S. sviceus, and top hits from the search against the MEROPs database where consensus sequences were used as queries.


No ancient DNA damage in Actinobacteria from the Neanderthal bone.

Zaremba-Niedźwiedzka K, Andersson SG - PLoS ONE (2013)

Phylogeny of prolyl aminopeptidases.Propyl aminopeptidase consensus sequences are coloured red (Contigs C1103–C1106). The clade containing contig C1104 and two Streptomyces species is shown in yellow. The Streptomyces reference sequences from MEROPS S33 family are shown in green and family holotypes in blue. MEROPS id is indicated for each sequence. The phylogeny was inferred using the maximum likelihood method. Numbers refer to bootstrap support values higher than 75%.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3643900&req=5

pone-0062799-g006: Phylogeny of prolyl aminopeptidases.Propyl aminopeptidase consensus sequences are coloured red (Contigs C1103–C1106). The clade containing contig C1104 and two Streptomyces species is shown in yellow. The Streptomyces reference sequences from MEROPS S33 family are shown in green and family holotypes in blue. MEROPS id is indicated for each sequence. The phylogeny was inferred using the maximum likelihood method. Numbers refer to bootstrap support values higher than 75%.
Mentions: To investigate the taxonomic affiliations of the S33 protein family, the identified reads were assembled, yielding more than a thousand contigs in total. The consensus protein sequences of the four contigs that contained a majority of reads were compared to reference protein sequences of the S33 family in the MEROPs database in a maximum likelihood analysis (Figure 6). Two of the consensus sequences (C1103 and C1104) belonged to a clade with actinobacterial tripeptidyl peptidase B (S33.006) for which the holotype sequence is from Streptomyces lividans (100% bootstrap support). C1104 was placed as a sister taxa to Streptomyces sviceus with 100% bootstrap support and there was some support for a clustering also of C1103 with Streptomyces. To ensure the best possible match, we included all S33.006 sequences and all S33 sequences from S. sviceus, and top hits from the search against the MEROPs database where consensus sequences were used as queries.

Bottom Line: However, phylogenetic analyses did not identify any sediment clones that were closely related to the bone-derived sequences.We analysed the patterns of nucleotide differences in the individual sequence reads compared to the assembled consensus sequences of the rRNA gene sequences.Such studies can help identify targeted measures to increase the relative amount of endogenous DNA in the sample.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden.

ABSTRACT

Background: The Neanderthal genome was recently sequenced using DNA extracted from a 38,000-year-old fossil. At the start of the project, the fraction of mammalian and bacterial DNA in the sample was estimated to be <6% and 9%, respectively. Treatment with restriction enzymes prior to sequencing increased the relative proportion of mammalian DNA to 15%, but the large majority of sequences remain uncharacterized.

Principal findings: Our taxonomic profiling of 3.95 Gb of Neanderthal DNA isolated from the Vindija Neanderthal Vi33.16 fossil showed that 90% of about 50,000 rRNA gene sequence reads were of bacterial origin, of which Actinobacteria accounted for more than 75%. Actinobacteria also represented more than 80% of the PCR-amplified 16S rRNA gene sequences from a cave sediment sample taken from the same G layer as the Neanderthal bone. However, phylogenetic analyses did not identify any sediment clones that were closely related to the bone-derived sequences. We analysed the patterns of nucleotide differences in the individual sequence reads compared to the assembled consensus sequences of the rRNA gene sequences. The typical ancient nucleotide substitution pattern with a majority of C to T changes indicative of DNA damage was observed for the Neanderthal rRNA gene sequences, but not for the Streptomyces-like rRNA gene sequences.

Conclusions/significance: Our analyses suggest that the Actinobacteria, and especially members of the Streptomycetales, contribute the majority of sequences in the DNA extracted from the Neanderthal fossil Vi33.16. The bacterial DNA showed no signs of damage, and we hypothesize that it was derived from bacteria that have been enriched inside the bone. The bioinformatic approach used here paves the way for future studies of microbial compositions and patterns of DNA damage in bacteria from archaeological bones. Such studies can help identify targeted measures to increase the relative amount of endogenous DNA in the sample.

Show MeSH
Related in: MedlinePlus