An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data

被引：10

作者：

Xu, Wenhao ^{[1
,2
]}

Lin, Yu ^{[3
,4
]}

Zhao, Keliang ^{[5
]}

Li, Haimeng ^{[3
,6
]}

Tian, Yinping ^{[3
]}

Ngatia, Jacob Njaramba ^{[7
]}

Ma, Yue ^{[7
]}

Sahu, Sunil Kumar ^{[3
]}

Guo, Huabing ^{[8
]}

Guo, Xiaosen ^{[3
,9
]}

Xu, Yan Chun ^{[7
]}

Liu, Huan ^{[3
,10
]}

Kristiansen, Karsten ^{[3
,10
]}

Lan, Tianming ^{[3
,10
]}

Zhou, Xinying ^{[1
,5
]}

机构：

[1] Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, 142 Xizhimenwai St, Beijing 100044, Peoples R China

[2] Huazhong Agr Univ, Coll Informat, Wuhan, Peoples R China

[3] BGI Shenzhen, State Key Lab Agr Genom, Shenzhen 518083, Peoples R China

[4] BGI Shenzhen, Guangdong Prov Key Lab Genome Read & Write, Shenzhen, Peoples R China

[5] CAS Ctr Excellence Life & Paleoenvironm, Beijing, Peoples R China

[6] Univ Chinese Acad Sci, Sch Future Technol, Beijing, Peoples R China

[7] Northeast Forestry Univ, Coll Wildlife Resources, Harbin, Peoples R China

[8] Forest Inventory & Planning Inst Jilin Prov, Changchun, Peoples R China

[9] BGI Shenzhen, Guangdong Prov Acad Workstat BGI Synthet Genom, Shenzhen, Peoples R China

[10] Univ Copenhagen, Lab Genom & Mol Biomed, Dept Biol, Copenhagen, Denmark

来源：

ECOLOGY AND EVOLUTION | 2021年 / 11卷 / 01期

关键词：

ancient DNA; BWA mem; deamination; DNA damage; genome mapping; POPULATION HISTORY; READ ALIGNMENT; EXTINCT; DAMAGE;

D O I：

10.1002/ece3.7056

中图分类号：

Q14 [生态学（生物生态学）];

学科分类号：

071012 ; 0713 ;

摘要：

Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next-generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degradation of ancient DNA and high levels of contamination, especially homologous contamination that has extremely similar genetic background with that of the real ancient DNA. In this study, we collected whole-genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from homologous contaminations, we attempted to recover reads based on ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing homologous contaminations to very low proportions. Our goal in this research was to develop useful recommendations for ancient DNA mapping and for separation of endogenous DNA to facilitate future studies of ancient DNA.

引用

页码：390 / 401

页数：12

共 38 条

[1] Population genomics of Bronze Age Eurasia [J].

Allentoft, Morten E. ;

Sikora, Martin ;

Sjogren, Karl-Goran ;

Rasmussen, Simon ;

Rasmussen, Morten ;

Stenderup, Jesper ;

Damgaard, Peter B. ;

Schroeder, Hannes ;

Ahlstrom, Torbjorn ;

Vinner, Lasse ;

Malaspinas, Anna-Sapfo ;

Margaryan, Ashot ;

Higham, Tom ;

Chivall, David ;

Lynnerup, Niels ;

Harvig, Lise ;

Baron, Justyna ;

Della Casa, Philippe ;

Dabrowski, Pawel ;

Duffy, Paul R. ;

Ebel, Alexander V. ;

Epimakhov, Andrey ;

Frei, Karin ;

Furmanek, Miroslaw ;

Gralak, Tomasz ;

Gromov, Andrey ;

Gronkiewicz, Stanislaw ;

Grupe, Gisela ;

Hajdu, Tamas ;

Jarysz, Radoslaw ;

Khartanovich, Valeri ;

Khokhlov, Alexandr ;

Kiss, Viktoria ;

Kolar, Jan ;

Kriiska, Aivar ;

Lasak, Irena ;

Longhi, Cristina ;

McGlynn, George ;

Merkevicius, Algimantas ;

Merkyte, Inga ;

Metspalu, Mait ;

Mkrtchyan, Ruzan ;

Moiseyev, Vyacheslav ;

Paja, Laszlo ;

Palfi, Gyoergy ;

Pokutta, Dalia ;

Pospieszny, Lukasz ;

Price, T. Douglas ;

Saag, Lehti ;

Sablin, Mikhail .

NATURE, 2015, 522 (7555) :167-+

[2] Patterns of damage in genomic DNA sequences from a Neandertal [J].

Briggs, Adrian W. ;

Stenzel, Udo ;

Johnson, Philip L. F. ;

Green, Richard E. ;

Kelso, Janet ;

Pruefer, Kay ;

Meyer, Matthias ;

Krause, Johannes ;

Ronan, Michael T. ;

Lachmann, Michael ;

Paeaebo, Svante .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (37) :14616-14621

[3] The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis [J].

Chang, Dan ;

Knapp, Michael ;

Enk, Jacob ;

Lippold, Sebastian ;

Kircher, Martin ;

Lister, Adrian ;

MacPhee, Ross D. E. ;

Widga, Christopher ;

Czechowski, Paul ;

Sommer, Robert ;

Hodges, Emily ;

Stuempel, Nikolaus ;

Barnes, Ian ;

Dalen, Love ;

Derevianko, Anatoly ;

Germonpre, Mietje ;

Hillebrand-Voiculescu, Alexandra ;

Constantin, Silviu ;

Kuznetsova, Tatyana ;

Mol, Dick ;

Rathgeber, Thomas ;

Rosendahl, Wilfried ;

Tikhonov, Alexey N. ;

Willerslev, Eske ;

Hannon, Greg ;

Lalueza-Fox, Carles ;

Joger, Ulrich ;

Poinar, Hendrik ;

Hofreiter, Michael ;

Shapiro, Beth .

SCIENTIFIC REPORTS, 2017, 7

[4] Ancient DNA Damage [J].

Dabney, Jesse ;

Meyer, Matthias ;

Paeaebo, Svante .

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY, 2013, 5 (07)

[5] Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments [J].

Dabney, Jesse ;

Knapp, Michael ;

Glocke, Isabelle ;

Gansauge, Marie-Theres ;

Weihmann, Antje ;

Nickel, Birgit ;

Valdiosera, Cristina ;

Garcia, Nuria ;

Paeaebo, Svante ;

Arsuaga, Juan-Luis ;

Meyer, Matthias .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2013, 110 (39) :15758-15763

[6] Ancient goat genomes reveal mosaic domestication in the Fertile Crescent [J].

Daly, Kevin G. ;

Delser, Pierpaolo Maisano ;

Mullin, Victoria E. ;

Scheu, Amelie ;

Mattiangeli, Valeria ;

Teasdale, Matthew D. ;

Hare, Andrew J. ;

Burger, Joachim ;

Verdugo, Marta Pereira ;

Collins, Matthew J. ;

Kehati, Ron ;

Erek, Cevdet Merih ;

Bar-Oz, Guy ;

Pompanon, Francois ;

Cumer, Tristan ;

Cakirlar, Canan ;

Mohaseb, Azadeh Fatemeh ;

Decruyenaere, Delphine ;

Davoudi, Hossein ;

Cevik, Ozlem ;

Rollefson, Gary ;

Vigne, Jean-Denis ;

Khazaeli, Roya ;

Fathi, Homa ;

Doost, Sanaz Beizaee ;

Sorkhani, Roghayeh Rahimi ;

Vahdati, Ali Akbar ;

Sauer, Eberhard W. ;

Kharanaghi, Hossein Azizi ;

Maziar, Sepideh ;

Gasparian, Boris ;

Pinhasi, Ron ;

Martin, Louise ;

Orton, David ;

Arbuckle, Benjamin S. ;

Benecke, Norbert ;

Manica, Andrea ;

Horwitz, Liora Kolska ;

Mashkour, Marjan ;

Bradley, Daniel G. .

SCIENCE, 2018, 361 (6397) :85-87

[7] Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths [J].

Delsuc, Frederic ;

Kuch, Melanie ;

Gibb, Gillian C. ;

Karpinski, Emil ;

Hackenberger, Dirk ;

Szpak, Paul ;

Martinez, Jorge G. ;

Mead, Jim, I ;

McDonald, H. Gregory ;

MacPhee, Ross D. E. ;

Billet, Guillaume ;

Hautier, Lionel ;

Poinar, Hendrik N. .

CURRENT BIOLOGY, 2019, 29 (12) :2031-+

[8] Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series [J].

Fages, Antoine ;

Hanghoj, Kristian ;

Khan, Naveed ;

Gaunitz, Charleen ;

Seguin-Orlando, Andaine ;

Leonardi, Michela ;

Constantz, Christian McCrory ;

Gamba, Cristina ;

Al-Rasheid, Khaled A. S. ;

Albizuri, Silvia ;

Alfarhan, Ahmed H. ;

Allentoft, Morten ;

Alquraishi, Saleh ;

Anthony, David ;

Baimukhanov, Nurbol ;

Barrett, James H. ;

Bayarsaikhan, Jamsranjav ;

Benecke, Norbert ;

Bernaldez-Sanchez, Eloisa ;

Berrocal-Rangel, Luis ;

Biglari, Fereidoun ;

Boessenkool, Sanne ;

Boldgiv, Bazartseren ;

Brem, Gottfried ;

Brown, Dorcas ;

Burger, Joachim ;

Crubezy, Eric ;

Daugnora, Linas ;

Davoudi, Hossein ;

Damgaard, Peter de Barros ;

de Chorro y de Villa-Ceballos, Maria de los Angeles ;

Deschler-Erb, Sabine ;

Detry, Cleia ;

Dill, Nadine ;

Oom, Maria do Mar ;

Dohr, Anna ;

Ellingvag, Sturla ;

Erdenebaatar, Diimaajav ;

Fathi, Homa ;

Felkel, Sabine ;

Fernandez-Rodriguez, Carlos ;

Garcia-Vinas, Esteban ;

Germonpre, Mietje ;

Granado, Jose D. ;

Hallsson, Jon H. ;

Hemmer, Helmut ;

Hofreiter, Michael ;

Kasparov, Aleksei ;

Khasanov, Mutalib ;

Khazaeli, Roya .

CELL, 2019, 177 (06) :1419-+

[9] The genetic history of Ice Age Europe [J].

Fu, Qiaomei ;

Posth, Cosimo ;

Hajdinjak, Mateja ;

Petr, Martin ;

Mallick, Swapan ;

Fernandes, Daniel ;

Furtwangler, Anja ;

Haak, Wolfgang ;

Meyer, Matthias ;

Mittnik, Alissa ;

Nickel, Birgit ;

Peltzer, Alexander ;

Rohland, Nadin ;

Slon, Viviane ;

Talamo, Sahra ;

Lazaridis, Iosif ;

Lipson, Mark ;

Mathieson, Iain ;

Schiffels, Stephan ;

Skoglund, Pontus ;

Derevianko, Anatoly P. ;

Drozdov, Nikolai ;

Slavinsky, Vyacheslav ;

Tsybankov, Alexander ;

Cremonesi, Renata Grifoni ;

Mallegni, Francesco ;

Gely, Bernard ;

Vacca, Eligio ;

Gonzalez Morales, Manuel R. ;

Straus, Lawrence G. ;

Neugebauer-Maresch, Christine ;

Teschler-Nicola, Maria ;

Constantin, Silviu ;

Moldovan, Oana Teodora ;

Benazzi, Stefano ;

Peresani, Marco ;

Coppola, Donato ;

Lari, Martina ;

Ricci, Stefano ;

Ronchitelli, Annamaria ;

Valentin, Frederique ;

Thevenet, Corinne ;

Wehrberger, Kurt ;

Grigorescu, Dan ;

Rougier, Helene ;

Crevecoeur, Isabelle ;

Flas, Damien ;

Semal, Patrick ;

Mannino, Marcello A. ;

Cupillard, Christophe .

NATURE, 2016, 534 (7606) :200-+

[10] Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA [J].

Gansauge, Marie-Theres ;

Meyer, Matthias .

NATURE PROTOCOLS, 2013, 8 (04) :737-748

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