Comparative and demographic analysis of orang-utan genomes.
Devin P. Locke,LaDeana W. Hillier,Wesley C. Warren,Kim C. Worley,Lynne V. Nazareth,Donna M. Muzny,Shiaw-Pyng Yang,Zhengyuan Wang,Asif T. Chinwalla,Patrick Minx,Makedonka Mitreva,Lisa Cook,Kim D. Delehaunty,Catrina Fronick,Heather Schmidt,Lucinda Fulton,Robert S. Fulton,Joanne O. Nelson,Vincent Magrini,Craig Pohl,Tina Graves,Chris Markovic,Andy Cree,Huyen Dinh,Jennifer Hume,Christie Kovar,Gerald R. Fowler,Gerton Lunter,Gerton Lunter,Stephen Meader,Andreas Heger,Chris P. Ponting,Tomas Marques-Bonet,Tomas Marques-Bonet,Can Alkan,Lin Chen,Ze Cheng,Jeffrey M. Kidd,Evan E. Eichler,Evan E. Eichler,Simon D. M. White,Stephen M. J. Searle,Albert J. Vilella,Yuan Chen,Paul Flicek,Jian Ma,Jian Ma,Brian J. Raney,Bernard B. Suh,Richard Burhans,Javier Herrero,David Haussler,Rui Faria,Rui Faria,Olga Fernando,Olga Fernando,Fleur Darré,Domènec Farré,Elodie Gazave,Meritxell Oliva,Arcadi Navarro,Roberta Roberto,Oronzo Capozzi,Nicoletta Archidiacono,Giuliano Della Valle,Stefania Purgato,Mariano Rocchi,Miriam K. Konkel,Jerilyn A. Walker,Brygg Ullmer,Mark A. Batzer,Arian F.A. Smit,Robert Hubley,Claudio Casola,Daniel R. Schrider,Matthew W. Hahn,Víctor Quesada,Xose S. Puente,Gonzalo R. Ordóñez,Carlos López-Otín,Tomas Vinar,Brona Brejova,Aakrosh Ratan,Robert S. Harris,Webb Miller,Carolin Kosiol,Heather A. Lawson,Vikas Taliwal,André L. Martins,Adam Siepel,Arindam RoyChoudhury,Xin Ma,Jeremiah D. Degenhardt,Carlos Bustamante,Ryan N. Gutenkunst,Thomas Mailund,Julien Y. Dutheil,Asger Hobolth,Mikkel H. Schierup,Oliver A. Ryder,Yuko Yoshinaga,Pieter J. de Jong,George M. Weinstock,Jeffrey Rogers,Elaine R. Mardis,Richard A. Gibbs,Richard K. Wilson +106 more
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TLDR
The orang-utan species, Pongo abelii and Pongo pygmaeus, are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution and a primate polymorphic neocentromere, found in both Pongo species are described.Abstract:
'Orang-utan' is derived from a Malay term meaning 'man of the forest' and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (N(e)) expanded exponentially relative to the ancestral N(e) after the split, while Bornean N(e) declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.read more
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A high-coverage genome sequence from an archaic Denisovan individual
Matthias Meyer,Martin Kircher,Marie Theres Gansauge,Heng Li,Fernando Racimo,Swapan Mallick,Swapan Mallick,Joshua G. Schraiber,Flora Jay,Kay Prüfer,Cesare de Filippo,Peter H. Sudmant,Can Alkan,Can Alkan,Qiaomei Fu,Qiaomei Fu,Ron Do,Nadin Rohland,Nadin Rohland,Arti Tandon,Arti Tandon,Michael Siebauer,Richard E. Green,Katarzyna Bryc,Adrian W. Briggs,Udo Stenzel,Jesse Dabney,Jay Shendure,Jacob O. Kitzman,Michael F. Hammer,Michael V. Shunkov,A.P. Derevianko,Nick Patterson,Aida M. Andrés,Evan E. Eichler,Evan E. Eichler,Montgomery Slatkin,David Reich,David Reich,Janet Kelso,Svante Pääbo +40 more
TL;DR: The genomic sequence provides evidence for very low rates of heterozygosity in the Denisova, probably not because of recent inbreeding, but instead because of a small population size, and illuminates the relationships between humans and archaics, including Neandertals, and establishes a catalog of genetic changes within the human lineage.
Journal ArticleDOI
Differential expression in RNA-seq: A matter of depth
TL;DR: This work analyzed how sequencing depth affects the detection of transcripts and their identification as differentially expressed, and proposed a novel approach--NOISeq--that differs from existing methods in that it is data-adaptive and nonparametric.
Proceedings ArticleDOI
Searching and mining trillions of time series subsequences under dynamic time warping
Thanawin Rakthanmanon,Bilson Campana,Abdullah Mueen,Gustavo E. A. P. A. Batista,Brandon Westover,Qiang Zhu,Jesin Zakaria,Eamonn Keogh +7 more
TL;DR: This work shows that by using a combination of four novel ideas the authors can search and mine truly massive time series for the first time, and shows that in large datasets they can exactly search under DTW much more quickly than the current state-of-the-art Euclidean distance search algorithms.
Journal ArticleDOI
Comparative genomics reveals insights into avian genome evolution and adaptation.
Guojie Zhang,Guojie Zhang,Cai Li,Qiye Li,Bo Li,Denis M. Larkin,Chul Hee Lee,Jay F. Storz,Agostinho Antunes,Matthew J. Greenwold,Robert W. Meredith,Anders Ödeen,Jie Cui,Qi Zhou,Luohao Xu,Hailin Pan,Zongji Wang,Lijun Jin,Pei Zhang,Haofu Hu,Wei Yang,Jiang Hu,Jin Xiao,Zhikai Yang,Yang Liu,Qiaolin Xie,Hao Yu,Jinmin Lian,Ping Wen,Fang Zhang,Hui Li,Yongli Zeng,Zijun Xiong,Shiping Liu,Long Zhou,Zhiyong Huang,Na An,Jie Wang,Qiumei Zheng,Yingqi Xiong,Guangbiao Wang,Bo Wang,Jingjing Wang,Yu Fan,Rute R. da Fonseca,Alonzo Alfaro-Núñez,Mikkel Schubert,Ludovic Orlando,Tobias Mourier,Jason T. Howard,Ganeshkumar Ganapathy,Andreas R. Pfenning,Osceola Whitney,Miriam V. Rivas,Erina Hara,Julia Smith,Marta Farré,Jitendra Narayan,Gancho T. Slavov,Michael N Romanov,Rui Borges,João Paulo Machado,Imran Khan,Mark S. Springer,John Gatesy,Federico G. Hoffmann,Juan C. Opazo,Olle Håstad,Roger H. Sawyer,Heebal Kim,Kyu-Won Kim,Hyeon Jeong Kim,Seoae Cho,Ning Li,Yinhua Huang,Michael William Bruford,Xiangjiang Zhan,Andrew Dixon,Mads F. Bertelsen,Elizabeth P. Derryberry,Wesley C. Warren,Richard K. Wilson,Shengbin Li,David A. Ray,Richard E. Green,Stephen J. O'Brien,Darren K. Griffin,Warren E. Johnson,David Haussler,Oliver A. Ryder,Eske Willerslev,Gary R. Graves,Per Alström,Jon Fjeldså,David P. Mindell,Scott V. Edwards,Edward L. Braun,Carsten Rahbek,David W. Burt,Peter Houde,Yong Zhang,Huanming Yang,Jian Wang,Erich D. Jarvis,M. Thomas P. Gilbert,M. Thomas P. Gilbert,Jun Wang +106 more
TL;DR: This work explored bird macroevolution using full genomes from 48 avian species representing all major extant clades to reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
Journal ArticleDOI
The Ensembl gene annotation system.
Bronwen Aken,Bronwen Aken,Sarah Ayling,Daniel Barrell,Laura Clarke,Valery Curwen,Susan Fairley,Julio Fernandez Banet,Konstantinos Billis,Carlos García Girón,Thibaut Hourlier,Kevin L. Howe,Andreas Kähäri,Felix Kokocinski,Fergal J. Martin,Daniel N. Murphy,Rishi Nag,Magali Ruffier,Michael Schuster,Y. Amy Tang,Jan-Hinnerk Vogel,Simon D. M. White,Amonida Zadissa,Paul Flicek,Stephen M. J. Searle +24 more
TL;DR: The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects and generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets.
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
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Initial sequence of the chimpanzee genome and comparison with the human genome
Tarjei S. Mikkelsen,LaDeana W. Hillier,Evan E. Eichler,Michael C. Zody,David B. Jaffe,Shiaw-Pyng Yang,Wolfgang Enard,Ines Hellmann,Kerstin Lindblad-Toh,Tasha K. Altheide,Nicoletta Archidiacono,Peer Bork,Jonathan Butler,Jean L. Chang,Ze Cheng,Asif T. Chinwalla,Pieter J. de Jong,Kimberley D. Delehaunty,Catrina Fronick,Lucinda L. Fulton,Yoav Gilad,Gustavo Glusman,Sante Gnerre,Tina Graves,Toshiyuki Hayakawa,Karen E. Hayden,Xiaoqiu Huang,Hongkai Ji,W. James Kent,Mary Claire King,Edward J. Kulbokasl,Ming K. Lee,Ge Liu,Carlos López-Otín,Kateryna D. Makova,Orna Man,Elaine R. Mardis,Evan Mauceli,Tracie L. Miner,William E. Nash,Joanne O. Nelson,Svante Pääbo,Nick Patterson,Craig Pohl,Katherine S. Pollard,Kay Prüfer,Xose S. Puente,David Reich,Mariano Rocchi,Kate R. Rosenbloom,Maryellen Ruvolo,Daniel J. Richter,Stephen F. Schaffner,Arian F.A. Smit,Scott M. Smith,Mikita Suyama,James E. Taylor,David Torrents,Eray Tüzün,Ajit Varki,Gloria Velasco,Mario Ventura,John W. Wallis,Michael C. Wendl,Richard K. Wilson,Eric S. Lander,Robert H. Waterston +66 more
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Richard Cordaux,Mark A. Batzer +1 more
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