Literature DB >> 35962045

Author Correction: Comparative and demographic analysis of orang-utan genomes.

Devin P Locke1, LaDeana W Hillier2, Wesley C Warren3, Kim C Worley4, Lynne V Nazareth4, Donna M Muzny4, Shiaw-Pyng Yang2, Zhengyuan Wang2, Asif T Chinwalla2, Pat Minx2, Makedonka Mitreva2, Lisa Cook2, Kim D Delehaunty2, Catrina Fronick2, Heather Schmidt2, Lucinda A Fulton2, Robert S Fulton2, Joanne O Nelson2, Vincent Magrini2, Craig Pohl2, Tina A Graves2, Chris Markovic2, Andy Cree4, Huyen H Dinh4, Jennifer Hume4, Christie L Kovar4, Gerald R Fowler4, Gerton Lunter5,6, Stephen Meader5, Andreas Heger5, Chris P Ponting5, Tomas Marques-Bonet7,8, Can Alkan7, Lin Chen7, Ze Cheng7, Jeffrey M Kidd7, Evan E Eichler7,9, Simon White10, Stephen Searle10, Albert J Vilella11, Yuan Chen11, Paul Flicek11, Jian Ma12,13, Brian Raney12, Bernard Suh12, Richard Burhans14, Javier Herrero11, David Haussler12, Rui Faria8,15, Olga Fernando8,16, Fleur Darré8, Domènec Farré8, Elodie Gazave8, Meritxell Oliva8, Arcadi Navarro8,17, Roberta Roberto18, Oronzo Capozzi18, Nicoletta Archidiacono18, Giuliano Della Valle19, Stefania Purgato19, Mariano Rocchi18, Miriam K Konkel20, Jerilyn A Walker20, Brygg Ullmer21, Mark A Batzer20, Arian F A Smit22, Robert Hubley22, Claudio Casola23, Daniel R Schrider23, Matthew W Hahn23, Victor Quesada24, Xose S Puente24, Gonzalo R Ordoñez24, Carlos López-Otín24, Tomas Vinar25, Brona Brejova25, Aakrosh Ratan14, Robert S Harris14, Webb Miller14, Carolin Kosiol26, Heather A Lawson27, Vikas Taliwal28, André L Martins28, Adam Siepel28, Arindam RoyChoudhury29, Xin Ma28, Jeremiah Degenhardt28, Carlos D Bustamante30, Ryan N Gutenkunst31, Thomas Mailund32, Julien Y Dutheil32, Asger Hobolth32, Mikkel H Schierup32, Oliver A Ryder33, Yuko Yoshinaga34, Pieter J de Jong34, George M Weinstock2, Jeffrey Rogers4, Elaine R Mardis2, Richard A Gibbs4, Richard K Wilson2.   

Abstract

Entities:  

Year:  2022        PMID: 35962045      PMCID: PMC9402433          DOI: 10.1038/s41586-022-04799-7

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   69.504


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Correction to: Nature 10.1038/nature09687 Published online 26 January 2011 In this Article, we reported genome sequencing data from five Sumatran and five Bornean orang-utans. In re-analysing these data, Banes et al.[1] found that eight of the ten samples were mislabelled, and we wish to correct the original publication according to their findings. In addition, Banes et al.[1] find that one of the orang-utans that we had labelled as a male Sumatran is in fact a female Tapanuli orang-utan (an orang-utan species that was unknown at the time of publication of our original Article and that was first reported in 2017 (ref. [2])). While we here correct the original tables to display the correct names and IDs of the individuals studied, we do not correct the analyses in the original paper since the Tapanuli species was discovered only after we had concluded our study. We refer the reader to Banes et al.[1] for further information. In the main text, the sentence “We also sequenced the genomes of 10 additional unrelated wild-caught orang-utans, five Sumatran and five Bornean, using a short read sequencing platform (297 Gb of data in total; Supplementary Information section 4)” should have read “We also sequenced the genomes of 10 additional unrelated wild-caught orang-utans, four Sumatran, five Bornean and one Tapanuli, using a short read sequencing platform (297 Gb of data in total; Supplementary Information section 4)”. In addition, the sentence “We then called single nucleotide polymorphisms (SNPs) from the alignment of all short read data from 10 individuals (five Bornean, including the 20-fold coverage mentioned above, and five Sumatran) (Supplementary Information section 4)” should have read “We then called single nucleotide polymorphisms (SNPs) from the alignment of all short read data from 10 individuals (five Bornean, including the 20-fold coverage mentioned above, four Sumatran and one Tapanuli) (Supplementary Information section 4). Supplementary Data to this Amendment corrects the sample ID in the original Supplementary Data (‘Accession Table for Bornean and Sumatran Orangutan Short Read Data’) for animal sample ID KB9258 from a Sumatran male to a Tapanuli female (line 204). In Supplemental Section S4 of the original Supplementary Information, the first sentence “The orangutan population diversity survey utilized DNA from 5 Sumatran and 5 Bornean wild-caught orang-utans […]” should have read “The orangutan population diversity survey utilized DNA from 4 Sumatran, 5 Bornean and 1 Tapanuli wild-caught orang-utans […]”. Supplementary Table 1 to this Amendment shows a corrected version of the original Supplementary Table S4-1, reproduced with modifications from Banes et al.[1]. None of these corrections affect the results and conclusions of the original Article with the exception of Fig. 5 in the main text. The estimates of SNPs in panel a, allele counts in panel b and estimates of population (Ne) should be recalculated for the Sumatran and Tapanuli separately in the future. Our Bornean estimates in Fig. 5 are unaffected by this sample mislabelling, as noted in Banes et al.[1]. The original Article has not been corrected online. A corrected version of the original Supplementary Table S4-1 (Next generation sequence data summary). A corrected version of the original Supplementary Data (Accession table for Bornean and Sumatran orang-utan short read data).
  1 in total

1.  Orangutan genome mix-up muddies conservation efforts.

Authors:  Freda Kreier
Journal:  Nature       Date:  2022-10-19       Impact factor: 69.504

  1 in total

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