Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis.
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Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. / Gilbert, M Thomas P; Binladen, Jonas; Miller, Webb; Wiuf, Carsten; Willerslev, Eske; Poinar, Hendrik; Carlson, John E; Leebens-Mack, James H; Schuster, Stephan C.
In: Nucleic Acids Research, Vol. 35, No. 1, 2007, p. 1-10.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis.
AU - Gilbert, M Thomas P
AU - Binladen, Jonas
AU - Miller, Webb
AU - Wiuf, Carsten
AU - Willerslev, Eske
AU - Poinar, Hendrik
AU - Carlson, John E
AU - Leebens-Mack, James H
AU - Schuster, Stephan C
N1 - Keywords: Animals; DNA Damage; DNA, Chloroplast; DNA-Directed DNA Polymerase; Data Interpretation, Statistical; Elephants; Fossils; Genomics; Polymerase Chain Reaction; Templates, Genetic
PY - 2007
Y1 - 2007
N2 - Although ancient DNA (aDNA) miscoding lesions have been studied since the earliest days of the field, their nature remains a source of debate. A variety of conflicting hypotheses exist about which miscoding lesions constitute true aDNA damage as opposed to PCR polymerase amplification error. Furthermore, considerable disagreement and speculation exists on which specific damage events underlie observed miscoding lesions. The root of the problem is that it has previously been difficult to assemble sufficient data to test the hypotheses, and near-impossible to accurately determine the specific strand of origin of observed damage events. With the advent of emulsion-based clonal amplification (emPCR) and the sequencing-by-synthesis technology this has changed. In this paper we demonstrate how data produced on the Roche GS20 genome sequencer can determine miscoding lesion strands of origin, and subsequently be interpreted to enable characterization of the aDNA damage behind the observed phenotypes. Through comparative analyses on 390,965 bp of modern chloroplast and 131,474 bp of ancient woolly mammoth GS20 sequence data we conclusively demonstrate that in this sample at least, a permafrost preserved specimen, Type 2 (cytosine-->thymine/guanine-->adenine) miscoding lesions represent the overwhelming majority of damage-derived miscoding lesions. Additionally, we show that an as yet unidentified guanine-->adenine analogue modification, not the conventionally argued cytosine-->uracil deamination, underpins a significant proportion of Type 2 damage. How widespread these implications are for aDNA will become apparent as future studies analyse data recovered from a wider range of substrates.
AB - Although ancient DNA (aDNA) miscoding lesions have been studied since the earliest days of the field, their nature remains a source of debate. A variety of conflicting hypotheses exist about which miscoding lesions constitute true aDNA damage as opposed to PCR polymerase amplification error. Furthermore, considerable disagreement and speculation exists on which specific damage events underlie observed miscoding lesions. The root of the problem is that it has previously been difficult to assemble sufficient data to test the hypotheses, and near-impossible to accurately determine the specific strand of origin of observed damage events. With the advent of emulsion-based clonal amplification (emPCR) and the sequencing-by-synthesis technology this has changed. In this paper we demonstrate how data produced on the Roche GS20 genome sequencer can determine miscoding lesion strands of origin, and subsequently be interpreted to enable characterization of the aDNA damage behind the observed phenotypes. Through comparative analyses on 390,965 bp of modern chloroplast and 131,474 bp of ancient woolly mammoth GS20 sequence data we conclusively demonstrate that in this sample at least, a permafrost preserved specimen, Type 2 (cytosine-->thymine/guanine-->adenine) miscoding lesions represent the overwhelming majority of damage-derived miscoding lesions. Additionally, we show that an as yet unidentified guanine-->adenine analogue modification, not the conventionally argued cytosine-->uracil deamination, underpins a significant proportion of Type 2 damage. How widespread these implications are for aDNA will become apparent as future studies analyse data recovered from a wider range of substrates.
U2 - 10.1093/nar/gkl483
DO - 10.1093/nar/gkl483
M3 - Journal article
C2 - 16920744
VL - 35
SP - 1
EP - 10
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 1
ER -
ID: 3848623