A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing Export

@article{citeulike:3099748, abstract = {Although it is well established that Neandertals are the hominid form most closely related to present-day humans, their exact relationship with modern humans remains a topic of debate (Hublin et al., 2006, Soficaru et al., 2006, Harvati et al., 2007). Molecular genetic data first spoke to this issue in 1997, when a 379 base pair section of the hypervariable region I (HVRI) of the mitochondrial genome (mtDNA) was determined from the Neandertal-type specimen found in 1856 in Neander Valley, near D\"{u}sseldorf, Germany (Krings et al., 1997). Since then, a total of 15 complete or partial Neandertal HVRI sequences, as well as two HVRII sequences (Krings et al., 1999, Krings et al., 2000), have been described. Phylogenetic analyses of these suggest that Neandertal mtDNA falls outside the variation of modern human mtDNA. Since the mtDNA genome is maternally inherited without recombination, these results indicate that Neandertals made no lasting contribution to the modern human mtDNA gene pool (Krings et al., 1997, Currat et al., 2004, Serre et al., 2004). High-throughput 454 sequencing techniques have recently been applied to ancient DNA (Green et al., 2006, Poinar et al., 2006, Stiller et al., 2006). These methods open new possibilities for the retrieval of ancient DNA that has hitherto relied either on the cloning of random molecules in bacteria (Higuchi et al., 1984, P\"{a}\"{a}bo, 1985, Noonan et al., 2005, Noonan et al., 2006) or on the PCR amplification of individual DNA sequences of interest (P\"{a}\"{a}bo et al., 1988, P\"{a}\"{a}bo et al., 2004). The main benefit of the 454 sequencing technique is the sheer volume of sequence data that make it practical to undertake genome-scale ancient DNA sequencing projects. This is particularly feasible for mitochondrial genomes (Gilbert et al., 2007), given their smaller size relative to the nuclear genome and their abundance in cells, where, typically, several hundred mtDNAs per nuclear genome exist. The 454 sequence data from ancient DNA have also allowed an increased understanding of DNA diagenesis (i.e., how DNA is modified during deposition in a burial context). In particular, they have allowed a quantitative model of how DNA degradation and chemical modification occurs, and how the effects of these processes interact with the molecular manipulations used to generate sequencing libraries (Briggs et al., 2007). Notably, although it was previously known that a high rate of cytosine deamination occurs in ancient DNA (Hofreiter et al., 2001), it has become clear that this is particularly prevalent in the ends of the ancient molecules, presumably because these are often single stranded (Briggs et al., 2007). Deamination of cytosine residues results in uracil residues that are read as thymine by DNA polymerases, leading to a high rate of C-to-T transitions. A high rate of G-to-A transitions observed near the 3′ ends of sequence reads is thought to be caused by deaminated cytosine residues on the complementary strands used as templates during the fill-in reaction to create blunt ends when sequencing libraries are constructed (Briggs et al., 2007). By 454 sequencing, we have generated 34.9-fold coverage of the Neandertal mtDNA genome from a Neandertal bone (Vindija bone 33.16) excavated in 1980 from Vindija Cave, Croatia (Malez et al., 1982). It has been dated to 38,310 ± 2130 years before present (Serre et al., 2004). Previously, the mtDNA HVRI sequence of this bone has been determined (Serre et al., 2004), as well as 2414 bp of mtDNA sequences by 454 sequencing (Green et al., 2006). Here, we present its complete mtDNA sequence, as well as the insights it allows into recent human and Neandertal mtDNA evolution.}, author = {Green, Richard E. and Malaspinas, Anna-Sapfo and Krause, Johannes and Briggs, Adrian W. and Johnson, Philip L. F. and Uhler, Caroline and Meyer, Matthias and Good, Jeffrey M. and Maricic, Tomislav and Stenzel, Udo and Pr\"{u}fer, Kay and Siebauer, Michael and Burbano, Hern\'{a}n A. and Ronan, Michael and Rothberg, Jonathan M. and Egholm, Michael and Rudan, Pavao and Brajkovi\'{c}, Dejana and Ku\'{c}an, \v{Z}eljko and Gu\v{s}i\'{c}, Ivan and Wikstr\"{o}m, M\r{a}rten and Laakkonen, Liisa and Kelso, Janet and Slatkin, Montgomery and P\"{a}\"{a}bo, Svante}, citeulike-article-id = {3099748}, citeulike-linkout-0 = {http://www.cell.com/content/article/fulltext?uid=PIIS0092867408007733}, journal = {Cell}, keywords = {200808, adn-mitochondrial, neandertalien, paleobiochimie, paleolithique-moyen}, pages = {416--426}, posted-at = {2008-08-08 11:14:38}, priority = {2}, title = {A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing}, url = {http://www.cell.com/content/article/fulltext?uid=PIIS0092867408007733}, volume = {134}, year = {2008} }

TY - JOUR ID - citeulike:3099748 L3 - citeulike-article-id:3099748 N2 - Although it is well established that Neandertals are the hominid form most closely related to present-day humans, their exact relationship with modern humans remains a topic of debate (Hublin et al., 2006, Soficaru et al., 2006, Harvati et al., 2007). Molecular genetic data first spoke to this issue in 1997, when a 379 base pair section of the hypervariable region I (HVRI) of the mitochondrial genome (mtDNA) was determined from the Neandertal-type specimen found in 1856 in Neander Valley, near Düsseldorf, Germany (Krings et al., 1997). Since then, a total of 15 complete or partial Neandertal HVRI sequences, as well as two HVRII sequences (Krings et al., 1999, Krings et al., 2000), have been described. Phylogenetic analyses of these suggest that Neandertal mtDNA falls outside the variation of modern human mtDNA. Since the mtDNA genome is maternally inherited without recombination, these results indicate that Neandertals made no lasting contribution to the modern human mtDNA gene pool (Krings et al., 1997, Currat et al., 2004, Serre et al., 2004). High-throughput 454 sequencing techniques have recently been applied to ancient DNA (Green et al., 2006, Poinar et al., 2006, Stiller et al., 2006). These methods open new possibilities for the retrieval of ancient DNA that has hitherto relied either on the cloning of random molecules in bacteria (Higuchi et al., 1984, Pääbo, 1985, Noonan et al., 2005, Noonan et al., 2006) or on the PCR amplification of individual DNA sequences of interest (Pääbo et al., 1988, Pääbo et al., 2004). The main benefit of the 454 sequencing technique is the sheer volume of sequence data that make it practical to undertake genome-scale ancient DNA sequencing projects. This is particularly feasible for mitochondrial genomes (Gilbert et al., 2007), given their smaller size relative to the nuclear genome and their abundance in cells, where, typically, several hundred mtDNAs per nuclear genome exist. The 454 sequence data from ancient DNA have also allowed an increased understanding of DNA diagenesis (i.e., how DNA is modified during deposition in a burial context). In particular, they have allowed a quantitative model of how DNA degradation and chemical modification occurs, and how the effects of these processes interact with the molecular manipulations used to generate sequencing libraries (Briggs et al., 2007). Notably, although it was previously known that a high rate of cytosine deamination occurs in ancient DNA (Hofreiter et al., 2001), it has become clear that this is particularly prevalent in the ends of the ancient molecules, presumably because these are often single stranded (Briggs et al., 2007). Deamination of cytosine residues results in uracil residues that are read as thymine by DNA polymerases, leading to a high rate of C-to-T transitions. A high rate of G-to-A transitions observed near the 3′ ends of sequence reads is thought to be caused by deaminated cytosine residues on the complementary strands used as templates during the fill-in reaction to create blunt ends when sequencing libraries are constructed (Briggs et al., 2007). By 454 sequencing, we have generated 34.9-fold coverage of the Neandertal mtDNA genome from a Neandertal bone (Vindija bone 33.16) excavated in 1980 from Vindija Cave, Croatia (Malez et al., 1982). It has been dated to 38,310 ± 2130 years before present (Serre et al., 2004). Previously, the mtDNA HVRI sequence of this bone has been determined (Serre et al., 2004), as well as 2414 bp of mtDNA sequences by 454 sequencing (Green et al., 2006). Here, we present its complete mtDNA sequence, as well as the insights it allows into recent human and Neandertal mtDNA evolution. JF - Cell EP - 426 TI - A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing VL - 134 SP - 416 KW - 200808 KW - adn-mitochondrial KW - neandertalien KW - paleobiochimie KW - paleolithique-moyen AU - Green, Richard AU - Malaspinas, Anna-Sapfo AU - Krause, Johannes AU - Briggs, Adrian AU - Johnson, Philip AU - Uhler, Caroline AU - Meyer, Matthias AU - Good, Jeffrey AU - Maricic, Tomislav AU - Stenzel, Udo AU - Prüfer, Kay AU - Siebauer, Michael AU - Burbano, Hernán AU - Ronan, Michael AU - Rothberg, Jonathan AU - Egholm, Michael AU - Rudan, Pavao AU - Brajković, Dejana AU - Kućan, Željko AU - Gušić, Ivan AU - Wikström, Mårten AU - Laakkonen, Liisa AU - Kelso, Janet AU - Slatkin, Montgomery AU - Pääbo, Svante PY - 2008/// UR - http://www.cell.com/content/article/fulltext?uid=PIIS0092867408007733 ER -