Hequan Sun1, Jia Ding2, Mathieu Piednoël1, Korbinian Schneeberger1. 1. Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany. 2. Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
Abstract
Motivation: Analyzing k-mer frequencies in whole-genome sequencing data is becoming a common method for estimating genome size (GS). However, it remains uninvestigated how accurate the method is, especially if it can capture intra-species GS variation. Results: We present findGSE, which fits skew normal distributions to k-mer frequencies to estimate GS. findGSE outperformed existing tools in an extensive simulation study. Estimating GSs of 89 Arabidopsis thaliana accessions, findGSE showed the highest capability in capturing GS variations. In an application with 71 female and 71 male human individuals, findGSE delivered an average of 3039 Mb as haploid human GS, while female genomes were on average 41 Mb larger than male genomes, in astonishing agreement with size difference of the X and Y chromosomes. Further analysis showed that human GS variations link to geographical patterns and significant differences between populations, which can be explained by variable abundances of LINE-1 retrotransposons. Availability and implementation: R package of findGSE is freely available at https://github.com/schneebergerlab/findGSE and supported on linux and Mac systems. Contact: schneeberger@mpipz.mpg.de. Supplementary information: Supplementary data are available at Bioinformatics online.
Motivation: Analyzing k-mer frequencies in whole-genome sequencing data is becoming a common method for estimating genome size (GS). However, it remains uninvestigated how accurate the method is, especially if it can capture intra-species GS variation. Results: We present findGSE, which fits skew normal distributions to k-mer frequencies to estimate GS. findGSE outperformed existing tools in an extensive simulation study. Estimating GSs of 89 Arabidopsis thaliana accessions, findGSE showed the highest capability in capturing GS variations. In an application with 71 female and 71 male human individuals, findGSE delivered an average of 3039 Mb as haploid humanGS, while female genomes were on average 41 Mb larger than male genomes, in astonishing agreement with size difference of the X and Y chromosomes. Further analysis showed that humanGS variations link to geographical patterns and significant differences between populations, which can be explained by variable abundances of LINE-1 retrotransposons. Availability and implementation: R package of findGSE is freely available at https://github.com/schneebergerlab/findGSE and supported on linux and Mac systems. Contact: schneeberger@mpipz.mpg.de. Supplementary information: Supplementary data are available at Bioinformatics online.
Authors: Loïc Yengo; Sailaja Vedantam; Eirini Marouli; Julia Sidorenko; Eric Bartell; Saori Sakaue; Marielisa Graff; Anders U Eliasen; Yunxuan Jiang; Sridharan Raghavan; Jenkai Miao; Joshua D Arias; Sarah E Graham; Ronen E Mukamel; Cassandra N Spracklen; Xianyong Yin; Shyh-Huei Chen; Teresa Ferreira; Heather H Highland; Yingjie Ji; Tugce Karaderi; Kuang Lin; Kreete Lüll; Deborah E Malden; Carolina Medina-Gomez; Moara Machado; Amy Moore; Sina Rüeger; Xueling Sim; Scott Vrieze; Tarunveer S Ahluwalia; Masato Akiyama; Matthew A Allison; Marcus Alvarez; Mette K Andersen; Alireza Ani; Vivek Appadurai; Liubov Arbeeva; Seema Bhaskar; Lawrence F Bielak; Sailalitha Bollepalli; Lori L Bonnycastle; Jette Bork-Jensen; Jonathan P Bradfield; Yuki Bradford; Peter S Braund; Jennifer A Brody; Kristoffer S Burgdorf; Brian E Cade; Hui Cai; Qiuyin Cai; Archie Campbell; Marisa Cañadas-Garre; Eulalia Catamo; Jin-Fang Chai; Xiaoran Chai; Li-Ching Chang; Yi-Cheng Chang; Chien-Hsiun Chen; Alessandra Chesi; Seung Hoan Choi; Ren-Hua Chung; Massimiliano Cocca; Maria Pina Concas; Christian Couture; Gabriel Cuellar-Partida; Rebecca Danning; E Warwick Daw; Frauke Degenhard; Graciela E Delgado; Alessandro Delitala; Ayse Demirkan; Xuan Deng; Poornima Devineni; Alexander Dietl; Maria Dimitriou; Latchezar Dimitrov; Rajkumar Dorajoo; Arif B Ekici; Jorgen E Engmann; Zammy Fairhurst-Hunter; Aliki-Eleni Farmaki; Jessica D Faul; Juan-Carlos Fernandez-Lopez; Lukas Forer; Margherita Francescatto; Sandra Freitag-Wolf; Christian Fuchsberger; Tessel E Galesloot; Yan Gao; Zishan Gao; Frank Geller; Olga Giannakopoulou; Franco Giulianini; Anette P Gjesing; Anuj Goel; Scott D Gordon; Mathias Gorski; Jakob Grove; Xiuqing Guo; Stefan Gustafsson; Jeffrey Haessler; Thomas F Hansen; Aki S Havulinna; Simon J Haworth; Jing He; Nancy Heard-Costa; Prashantha Hebbar; George Hindy; Yuk-Lam A Ho; Edith Hofer; Elizabeth Holliday; Katrin Horn; Whitney E Hornsby; Jouke-Jan Hottenga; Hongyan Huang; Jie Huang; Alicia Huerta-Chagoya; Jennifer E Huffman; Yi-Jen Hung; Shaofeng Huo; Mi Yeong Hwang; Hiroyuki Iha; Daisuke D Ikeda; Masato Isono; Anne U Jackson; Susanne Jäger; Iris E Jansen; Ingegerd Johansson; Jost B Jonas; Anna Jonsson; Torben Jørgensen; Ioanna-Panagiota Kalafati; Masahiro Kanai; Stavroula Kanoni; Line L Kårhus; Anuradhani Kasturiratne; Tomohiro Katsuya; Takahisa Kawaguchi; Rachel L Kember; Katherine A Kentistou; Han-Na Kim; Young Jin Kim; Marcus E Kleber; Maria J Knol; Azra Kurbasic; Marie Lauzon; Phuong Le; Rodney Lea; Jong-Young Lee; Hampton L Leonard; Shengchao A Li; Xiaohui Li; Xiaoyin Li; Jingjing Liang; Honghuang Lin; Shih-Yi Lin; Jun Liu; Xueping Liu; Ken Sin Lo; Jirong Long; Laura Lores-Motta; Jian'an Luan; Valeriya Lyssenko; Leo-Pekka Lyytikäinen; Anubha Mahajan; Vasiliki Mamakou; Massimo Mangino; Ani Manichaikul; Jonathan Marten; Manuel Mattheisen; Laven Mavarani; Aaron F McDaid; Karina Meidtner; Tori L Melendez; Josep M Mercader; Yuri Milaneschi; Jason E Miller; Iona Y Millwood; Pashupati P Mishra; Ruth E Mitchell; Line T Møllehave; Anna Morgan; Soeren Mucha; Matthias Munz; Masahiro Nakatochi; Christopher P Nelson; Maria Nethander; Chu Won Nho; Aneta A Nielsen; Ilja M Nolte; Suraj S Nongmaithem; Raymond Noordam; Ioanna Ntalla; Teresa Nutile; Anita Pandit; Paraskevi Christofidou; Katri Pärna; Marc Pauper; Eva R B Petersen; Liselotte V Petersen; Niina Pitkänen; Ozren Polašek; Alaitz Poveda; Michael H Preuss; Saiju Pyarajan; Laura M Raffield; Hiromi Rakugi; Julia Ramirez; Asif Rasheed; Dennis Raven; Nigel W Rayner; Carlos Riveros; Rebecca Rohde; Daniela Ruggiero; Sanni E Ruotsalainen; Kathleen A Ryan; Maria Sabater-Lleal; Richa Saxena; Markus Scholz; Anoop Sendamarai; Botong Shen; Jingchunzi Shi; Jae Hun Shin; Carlo Sidore; Colleen M Sitlani; Roderick C Slieker; Roelof A J Smit; Albert V Smith; Jennifer A Smith; Laura J Smyth; Lorraine Southam; Valgerdur Steinthorsdottir; Liang Sun; Fumihiko Takeuchi; Divya Sri Priyanka Tallapragada; Kent D Taylor; Bamidele O Tayo; Catherine Tcheandjieu; Natalie Terzikhan; Paola Tesolin; Alexander Teumer; Elizabeth Theusch; Deborah J Thompson; Gudmar Thorleifsson; Paul R H J Timmers; Stella Trompet; Constance Turman; Simona Vaccargiu; Sander W van der Laan; Peter J van der Most; Jan B van Klinken; Jessica van Setten; Shefali S Verma; Niek Verweij; Yogasudha Veturi; Carol A Wang; Chaolong Wang; Lihua Wang; Zhe Wang; Helen R Warren; Wen Bin Wei; Ananda R Wickremasinghe; Matthias Wielscher; Kerri L Wiggins; Bendik S Winsvold; Andrew Wong; Yang Wu; Matthias Wuttke; Rui Xia; Tian Xie; Ken Yamamoto; Jingyun Yang; Jie Yao; Hannah Young; Noha A Yousri; Lei Yu; Lingyao Zeng; Weihua Zhang; Xinyuan Zhang; Jing-Hua Zhao; Wei Zhao; Wei Zhou; Martina E Zimmermann; Magdalena Zoledziewska; Linda S Adair; Hieab H H Adams; Carlos A Aguilar-Salinas; Fahd Al-Mulla; Donna K Arnett; Folkert W Asselbergs; Bjørn Olav Åsvold; John Attia; Bernhard Banas; Stefania Bandinelli; David A Bennett; Tobias Bergler; Dwaipayan Bharadwaj; Ginevra Biino; Hans Bisgaard; Eric Boerwinkle; Carsten A Böger; Klaus Bønnelykke; Dorret I Boomsma; Anders D Børglum; Judith B Borja; Claude Bouchard; Donald W Bowden; Ivan Brandslund; Ben Brumpton; Julie E Buring; Mark J Caulfield; John C Chambers; Giriraj R Chandak; Stephen J Chanock; Nish Chaturvedi; Yii-Der Ida Chen; Zhengming Chen; Ching-Yu Cheng; Ingrid E Christophersen; Marina Ciullo; John W Cole; Francis S Collins; Richard S Cooper; Miguel Cruz; Francesco Cucca; L Adrienne Cupples; Michael J Cutler; Scott M Damrauer; Thomas M Dantoft; Gert J de Borst; Lisette C P G M de Groot; Philip L De Jager; Dominique P V de Kleijn; H Janaka de Silva; George V Dedoussis; Anneke I den Hollander; Shufa Du; Douglas F Easton; Petra J M Elders; A Heather Eliassen; Patrick T Ellinor; Sölve Elmståhl; Jeanette Erdmann; Michele K Evans; Diane Fatkin; Bjarke Feenstra; Mary F Feitosa; Luigi Ferrucci; Ian Ford; Myriam Fornage; Andre Franke; Paul W Franks; Barry I Freedman; Paolo Gasparini; Christian Gieger; Giorgia Girotto; Michael E Goddard; Yvonne M Golightly; Clicerio Gonzalez-Villalpando; Penny Gordon-Larsen; Harald Grallert; Struan F A Grant; Niels Grarup; Lyn Griffiths; Vilmundur Gudnason; Christopher Haiman; Hakon Hakonarson; Torben Hansen; Catharina A Hartman; Andrew T Hattersley; Caroline Hayward; Susan R Heckbert; Chew-Kiat Heng; Christian Hengstenberg; Alex W Hewitt; Haretsugu Hishigaki; Carel B Hoyng; Paul L Huang; Wei Huang; Steven C Hunt; Kristian Hveem; Elina Hyppönen; William G Iacono; Sahoko Ichihara; M Arfan Ikram; Carmen R Isasi; Rebecca D Jackson; Marjo-Riitta Jarvelin; Zi-Bing Jin; Karl-Heinz Jöckel; Peter K Joshi; Pekka Jousilahti; J Wouter Jukema; Mika Kähönen; Yoichiro Kamatani; Kui Dong Kang; Jaakko Kaprio; Sharon L R Kardia; Fredrik Karpe; Norihiro Kato; Frank Kee; Thorsten Kessler; Amit V Khera; Chiea Chuen Khor; Lambertus A L M Kiemeney; Bong-Jo Kim; Eung Kweon Kim; Hyung-Lae Kim; Paulus Kirchhof; Mika Kivimaki; Woon-Puay Koh; Heikki A Koistinen; Genovefa D Kolovou; Jaspal S Kooner; Charles Kooperberg; Anna Köttgen; Peter Kovacs; Adriaan Kraaijeveld; Peter Kraft; Ronald M Krauss; Meena Kumari; Zoltan Kutalik; Markku Laakso; Leslie A Lange; Claudia Langenberg; Lenore J Launer; Loic Le Marchand; Hyejin Lee; Nanette R Lee; Terho Lehtimäki; Huaixing Li; Liming Li; Wolfgang Lieb; Xu Lin; Lars Lind; Allan Linneberg; Ching-Ti Liu; Jianjun Liu; Markus Loeffler; Barry London; Steven A Lubitz; Stephen J Lye; David A Mackey; Reedik Mägi; Patrik K E Magnusson; Gregory M Marcus; Pedro Marques Vidal; Nicholas G Martin; Winfried März; Fumihiko Matsuda; Robert W McGarrah; Matt McGue; Amy Jayne McKnight; Sarah E Medland; Dan Mellström; Andres Metspalu; Braxton D Mitchell; Paul Mitchell; Dennis O Mook-Kanamori; Andrew D Morris; Lorelei A Mucci; Patricia B Munroe; Mike A Nalls; Saman Nazarian; Amanda E Nelson; Matt J Neville; Christopher Newton-Cheh; Christopher S Nielsen; Markus M Nöthen; Claes Ohlsson; Albertine J Oldehinkel; Lorena Orozco; Katja Pahkala; Päivi Pajukanta; Colin N A Palmer; Esteban J Parra; Cristian Pattaro; Oluf Pedersen; Craig E Pennell; Brenda W J H Penninx; Louis Perusse; Annette Peters; Patricia A Peyser; David J Porteous; Danielle Posthuma; Chris Power; Peter P Pramstaller; Michael A Province; Qibin Qi; Jia Qu; Daniel J Rader; Olli T Raitakari; Sarju Ralhan; Loukianos S Rallidis; Dabeeru C Rao; Susan Redline; Dermot F Reilly; Alexander P Reiner; Sang Youl Rhee; Paul M Ridker; Michiel Rienstra; Samuli Ripatti; Marylyn D Ritchie; Dan M Roden; Frits R Rosendaal; Jerome I Rotter; Igor Rudan; Femke Rutters; Charumathi Sabanayagam; Danish Saleheen; Veikko Salomaa; Nilesh J Samani; Dharambir K Sanghera; Naveed Sattar; Börge Schmidt; Helena Schmidt; Reinhold Schmidt; Matthias B Schulze; Heribert Schunkert; Laura J Scott; Rodney J Scott; Peter Sever; Eric J Shiroma; M Benjamin Shoemaker; Xiao-Ou Shu; Eleanor M Simonsick; Mario Sims; Jai Rup Singh; Andrew B Singleton; Moritz F Sinner; J Gustav Smith; Harold Snieder; Tim D Spector; Meir J Stampfer; Klaus J Stark; David P Strachan; Leen M 't Hart; Yasuharu Tabara; Hua Tang; Jean-Claude Tardif; Thangavel A Thanaraj; Nicholas J Timpson; Anke Tönjes; Angelo Tremblay; Tiinamaija Tuomi; Jaakko Tuomilehto; Maria-Teresa Tusié-Luna; Andre G Uitterlinden; Rob M van Dam; Pim van der Harst; Nathalie Van der Velde; Cornelia M van Duijn; Natasja M van Schoor; Veronique Vitart; Uwe Völker; Peter Vollenweider; Henry Völzke; Niels H Wacher-Rodarte; Mark Walker; Ya Xing Wang; Nicholas J Wareham; Richard M Watanabe; Hugh Watkins; David R Weir; Thomas M Werge; Elisabeth Widen; Lynne R Wilkens; Gonneke Willemsen; Walter C Willett; James F Wilson; Tien-Yin Wong; Jeong-Taek Woo; Alan F Wright; Jer-Yuarn Wu; Huichun Xu; Chittaranjan S Yajnik; Mitsuhiro Yokota; Jian-Min Yuan; Eleftheria Zeggini; Babette S Zemel; Wei Zheng; Xiaofeng Zhu; Joseph M Zmuda; Alan B Zonderman; John-Anker Zwart; Daniel I Chasman; Yoon Shin Cho; Iris M Heid; Mark I McCarthy; Maggie C Y Ng; Christopher J O'Donnell; Fernando Rivadeneira; Unnur Thorsteinsdottir; Yan V Sun; E Shyong Tai; Michael Boehnke; Panos Deloukas; Anne E Justice; Cecilia M Lindgren; Ruth J F Loos; Karen L Mohlke; Kari E North; Kari Stefansson; Robin G Walters; Thomas W Winkler; Kristin L Young; Po-Ru Loh; Jian Yang; Tõnu Esko; Themistocles L Assimes; Adam Auton; Goncalo R Abecasis; Cristen J Willer; Adam E Locke; Sonja I Berndt; Guillaume Lettre; Timothy M Frayling; Yukinori Okada; Andrew R Wood; Peter M Visscher; Joel N Hirschhorn Journal: Nature Date: 2022-10-12 Impact factor: 69.504
Authors: Guilherme B Dias; Musaad A Altammami; Hamadttu A F El-Shafie; Fahad M Alhoshani; Mohamed B Al-Fageeh; Casey M Bergman; Manee M Manee Journal: Sci Rep Date: 2021-05-11 Impact factor: 4.379
Authors: Samira Mafi Moghaddam; Atena Oladzad; Chushin Koh; Larissa Ramsay; John P Hart; Sujan Mamidi; Genevieve Hoopes; Avinash Sreedasyam; Andrew Wiersma; Dongyan Zhao; Jane Grimwood; John P Hamilton; Jerry Jenkins; Brieanne Vaillancourt; Joshua C Wood; Jeremy Schmutz; Sateesh Kagale; Timothy Porch; Kirstin E Bett; C Robin Buell; Phillip E McClean Journal: Nat Commun Date: 2021-05-11 Impact factor: 14.919
Authors: Sampath Perumal; Chu Shin Koh; Lingling Jin; Miles Buchwaldt; Erin E Higgins; Chunfang Zheng; David Sankoff; Stephen J Robinson; Sateesh Kagale; Zahra-Katy Navabi; Lily Tang; Kyla N Horner; Zhesi He; Ian Bancroft; Boulos Chalhoub; Andrew G Sharpe; Isobel A P Parkin Journal: Nat Plants Date: 2020-08-10 Impact factor: 15.793