Literature DB >> 26003218

It's more than stamp collecting: how genome sequencing can unify biological research.

Stephen Richards1.   

Abstract

The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, while the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence information. Here, I identify neglected areas of biology and describe how both targeted species sequencing and more broad taxonomic surveys of the tree of life can address important biological questions. I enumerate the significant benefits that would accrue from sequencing a broader range of taxa, as well as discuss the technical advances in sequencing and assembly methods that would allow for wide-ranging application of whole-genome analysis. Finally, I suggest that in addition to 'big science' survey initiatives to sequence the tree of life, a modified infrastructure-funding paradigm would better support reference genome sequence generation for research communities most in need.
Copyright © 2015 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  DNA sequencing; Long read sequencing technologies; eukaryotes; eukaryotic genomics; genome analysis; genome assembly; genome infrastructure funding; genome reference sequences; taxanomic genome surveys; tree of life

Mesh:

Year:  2015        PMID: 26003218      PMCID: PMC4490122          DOI: 10.1016/j.tig.2015.04.007

Source DB:  PubMed          Journal:  Trends Genet        ISSN: 0168-9525            Impact factor:   11.639


  98 in total

1.  Evolutionary genomics: detecting selection needs comparative data.

Authors:  Rasmus Nielsen; Melissa J Hubisz
Journal:  Nature       Date:  2005-01-20       Impact factor: 49.962

2.  A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor.

Authors:  Chaoyang Zhao; Lucio Navarro Escalante; Hang Chen; Thiago R Benatti; Jiaxin Qu; Sanjay Chellapilla; Robert M Waterhouse; David Wheeler; Martin N Andersson; Riyue Bao; Matthew Batterton; Susanta K Behura; Kerstin P Blankenburg; Doina Caragea; James C Carolan; Marcus Coyle; Mustapha El-Bouhssini; Liezl Francisco; Markus Friedrich; Navdeep Gill; Tony Grace; Cornelis J P Grimmelikhuijzen; Yi Han; Frank Hauser; Nicolae Herndon; Michael Holder; Panagiotis Ioannidis; LaRonda Jackson; Mehwish Javaid; Shalini N Jhangiani; Alisha J Johnson; Divya Kalra; Viktoriya Korchina; Christie L Kovar; Fremiet Lara; Sandra L Lee; Xuming Liu; Christer Löfstedt; Robert Mata; Tittu Mathew; Donna M Muzny; Swapnil Nagar; Lynne V Nazareth; Geoffrey Okwuonu; Fiona Ongeri; Lora Perales; Brittany F Peterson; Ling-Ling Pu; Hugh M Robertson; Brandon J Schemerhorn; Steven E Scherer; Jacob T Shreve; DeNard Simmons; Subhashree Subramanyam; Rebecca L Thornton; Kun Xue; George M Weissenberger; Christie E Williams; Kim C Worley; Dianhui Zhu; Yiming Zhu; Marion O Harris; Richard H Shukle; John H Werren; Evgeny M Zdobnov; Ming-Shun Chen; Susan J Brown; Jeffery J Stuart; Stephen Richards
Journal:  Curr Biol       Date:  2015-02-05       Impact factor: 10.834

3.  Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.

Authors:  Ludovic Orlando; Aurélien Ginolhac; Guojie Zhang; Duane Froese; Anders Albrechtsen; Mathias Stiller; Mikkel Schubert; Enrico Cappellini; Bent Petersen; Ida Moltke; Philip L F Johnson; Matteo Fumagalli; Julia T Vilstrup; Maanasa Raghavan; Thorfinn Korneliussen; Anna-Sapfo Malaspinas; Josef Vogt; Damian Szklarczyk; Christian D Kelstrup; Jakob Vinther; Andrei Dolocan; Jesper Stenderup; Amhed M V Velazquez; James Cahill; Morten Rasmussen; Xiaoli Wang; Jiumeng Min; Grant D Zazula; Andaine Seguin-Orlando; Cecilie Mortensen; Kim Magnussen; John F Thompson; Jacobo Weinstock; Kristian Gregersen; Knut H Røed; Véra Eisenmann; Carl J Rubin; Donald C Miller; Douglas F Antczak; Mads F Bertelsen; Søren Brunak; Khaled A S Al-Rasheid; Oliver Ryder; Leif Andersson; John Mundy; Anders Krogh; M Thomas P Gilbert; Kurt Kjær; Thomas Sicheritz-Ponten; Lars Juhl Jensen; Jesper V Olsen; Michael Hofreiter; Rasmus Nielsen; Beth Shapiro; Jun Wang; Eske Willerslev
Journal:  Nature       Date:  2013-06-26       Impact factor: 49.962

4.  Convergent evolution of the genomes of marine mammals.

Authors:  Andrew D Foote; Yue Liu; Gregg W C Thomas; Tomáš Vinař; Jessica Alföldi; Jixin Deng; Shannon Dugan; Cornelis E van Elk; Margaret E Hunter; Vandita Joshi; Ziad Khan; Christie Kovar; Sandra L Lee; Kerstin Lindblad-Toh; Annalaura Mancia; Rasmus Nielsen; Xiang Qin; Jiaxin Qu; Brian J Raney; Nagarjun Vijay; Jochen B W Wolf; Matthew W Hahn; Donna M Muzny; Kim C Worley; M Thomas P Gilbert; Richard A Gibbs
Journal:  Nat Genet       Date:  2015-01-26       Impact factor: 38.330

5.  Evolution of Darwin's finches and their beaks revealed by genome sequencing.

Authors:  Sangeet Lamichhaney; Jonas Berglund; Markus Sällman Almén; Khurram Maqbool; Manfred Grabherr; Alvaro Martinez-Barrio; Marta Promerová; Carl-Johan Rubin; Chao Wang; Neda Zamani; B Rosemary Grant; Peter R Grant; Matthew T Webster; Leif Andersson
Journal:  Nature       Date:  2015-02-11       Impact factor: 49.962

Review 6.  The future is now: single-cell genomics of bacteria and archaea.

Authors:  Paul C Blainey
Journal:  FEMS Microbiol Rev       Date:  2013-02-11       Impact factor: 16.408

7.  Mutation mapping and identification by whole-genome sequencing.

Authors:  Ignaty Leshchiner; Kristen Alexa; Peter Kelsey; Ivan Adzhubei; Christina A Austin-Tse; Jeffrey D Cooney; Heidi Anderson; Matthew J King; Rolf W Stottmann; Maija K Garnaas; Seungshin Ha; Iain A Drummond; Barry H Paw; Trista E North; David R Beier; Wolfram Goessling; Shamil R Sunyaev
Journal:  Genome Res       Date:  2012-05-03       Impact factor: 9.043

8.  The complete genome sequence of a Neanderthal from the Altai Mountains.

Authors:  Kay Prüfer; Fernando Racimo; Nick Patterson; Flora Jay; Sriram Sankararaman; Susanna Sawyer; Anja Heinze; Gabriel Renaud; Peter H Sudmant; Cesare de Filippo; Heng Li; Swapan Mallick; Michael Dannemann; Qiaomei Fu; Martin Kircher; Martin Kuhlwilm; Michael Lachmann; Matthias Meyer; Matthias Ongyerth; Michael Siebauer; Christoph Theunert; Arti Tandon; Priya Moorjani; Joseph Pickrell; James C Mullikin; Samuel H Vohr; Richard E Green; Ines Hellmann; Philip L F Johnson; Hélène Blanche; Howard Cann; Jacob O Kitzman; Jay Shendure; Evan E Eichler; Ed S Lein; Trygve E Bakken; Liubov V Golovanova; Vladimir B Doronichev; Michael V Shunkov; Anatoli P Derevianko; Bence Viola; Montgomery Slatkin; David Reich; Janet Kelso; Svante Pääbo
Journal:  Nature       Date:  2013-12-18       Impact factor: 49.962

9.  Genome analysis of the platypus reveals unique signatures of evolution.

Authors:  Wesley C Warren; LaDeana W Hillier; Jennifer A Marshall Graves; Ewan Birney; Chris P Ponting; Frank Grützner; Katherine Belov; Webb Miller; Laura Clarke; Asif T Chinwalla; Shiaw-Pyng Yang; Andreas Heger; Devin P Locke; Pat Miethke; Paul D Waters; Frédéric Veyrunes; Lucinda Fulton; Bob Fulton; Tina Graves; John Wallis; Xose S Puente; Carlos López-Otín; Gonzalo R Ordóñez; Evan E Eichler; Lin Chen; Ze Cheng; Janine E Deakin; Amber Alsop; Katherine Thompson; Patrick Kirby; Anthony T Papenfuss; Matthew J Wakefield; Tsviya Olender; Doron Lancet; Gavin A Huttley; Arian F A Smit; Andrew Pask; Peter Temple-Smith; Mark A Batzer; Jerilyn A Walker; Miriam K Konkel; Robert S Harris; Camilla M Whittington; Emily S W Wong; Neil J Gemmell; Emmanuel Buschiazzo; Iris M Vargas Jentzsch; Angelika Merkel; Juergen Schmitz; Anja Zemann; Gennady Churakov; Jan Ole Kriegs; Juergen Brosius; Elizabeth P Murchison; Ravi Sachidanandam; Carly Smith; Gregory J Hannon; Enkhjargal Tsend-Ayush; Daniel McMillan; Rosalind Attenborough; Willem Rens; Malcolm Ferguson-Smith; Christophe M Lefèvre; Julie A Sharp; Kevin R Nicholas; David A Ray; Michael Kube; Richard Reinhardt; Thomas H Pringle; James Taylor; Russell C Jones; Brett Nixon; Jean-Louis Dacheux; Hitoshi Niwa; Yoko Sekita; Xiaoqiu Huang; Alexander Stark; Pouya Kheradpour; Manolis Kellis; Paul Flicek; Yuan Chen; Caleb Webber; Ross Hardison; Joanne Nelson; Kym Hallsworth-Pepin; Kim Delehaunty; Chris Markovic; Pat Minx; Yucheng Feng; Colin Kremitzki; Makedonka Mitreva; Jarret Glasscock; Todd Wylie; Patricia Wohldmann; Prathapan Thiru; Michael N Nhan; Craig S Pohl; Scott M Smith; Shunfeng Hou; Mikhail Nefedov; Pieter J de Jong; Marilyn B Renfree; Elaine R Mardis; Richard K Wilson
Journal:  Nature       Date:  2008-05-08       Impact factor: 49.962

10.  The common marmoset genome provides insight into primate biology and evolution.

Authors: 
Journal:  Nat Genet       Date:  2014-07-20       Impact factor: 38.330

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  12 in total

1.  A golden goat genome.

Authors:  Kim C Worley
Journal:  Nat Genet       Date:  2017-03-30       Impact factor: 38.330

2.  Cytochrome P450 diversity in the tree of life.

Authors:  David R Nelson
Journal:  Biochim Biophys Acta Proteins Proteom       Date:  2017-05-11       Impact factor: 3.036

3.  Earth BioGenome Project: Sequencing life for the future of life.

Authors:  Harris A Lewin; Gene E Robinson; W John Kress; William J Baker; Jonathan Coddington; Keith A Crandall; Richard Durbin; Scott V Edwards; Félix Forest; M Thomas P Gilbert; Melissa M Goldstein; Igor V Grigoriev; Kevin J Hackett; David Haussler; Erich D Jarvis; Warren E Johnson; Aristides Patrinos; Stephen Richards; Juan Carlos Castilla-Rubio; Marie-Anne van Sluys; Pamela S Soltis; Xun Xu; Huanming Yang; Guojie Zhang
Journal:  Proc Natl Acad Sci U S A       Date:  2018-04-24       Impact factor: 11.205

4.  An Outsider's Perspective on Why We Climb Mountains and Why Projects Like the i5k Matter.

Authors:  David C Molik
Journal:  J Insect Sci       Date:  2022-07-01       Impact factor: 2.066

5.  A strategy for the identification of patterns in the biosynthesis of nonribosomal peptides by Betaproteobacteria species.

Authors:  João Luiz Baldim; Bruna Lidiane da Silva; Daniela Aparecida Chagas-Paula; João Henrique G Lago; Marisi G Soares
Journal:  Sci Rep       Date:  2017-09-04       Impact factor: 4.379

Review 6.  A Metagenomic Approach to Cyanobacterial Genomics.

Authors:  Danillo O Alvarenga; Marli F Fiore; Alessandro M Varani
Journal:  Front Microbiol       Date:  2017-05-09       Impact factor: 5.640

7.  Molecular classification based on apomorphic amino acids (Arthropoda, Hexapoda): Integrative taxonomy in the era of phylogenomics.

Authors:  Hao-Yang Wu; Yan-Hui Wang; Qiang Xie; Yun-Ling Ke; Wen-Jun Bu
Journal:  Sci Rep       Date:  2016-06-17       Impact factor: 4.379

8.  The Genome and Methylome of a Beetle with Complex Social Behavior, Nicrophorus vespilloides (Coleoptera: Silphidae).

Authors:  Christopher B Cunningham; Lexiang Ji; R Axel W Wiberg; Jennifer Shelton; Elizabeth C McKinney; Darren J Parker; Richard B Meagher; Kyle M Benowitz; Eileen M Roy-Zokan; Michael G Ritchie; Susan J Brown; Robert J Schmitz; Allen J Moore
Journal:  Genome Biol Evol       Date:  2015-10-09       Impact factor: 3.416

9.  A new strategy to infer circularity applied to four new complete frog mitogenomes.

Authors:  Denis Jacob Machado; Daniel Janies; Cory Brouwer; Taran Grant
Journal:  Ecol Evol       Date:  2018-03-25       Impact factor: 2.912

10.  sppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing.

Authors:  Quinn K Langdon; David Peris; Brian Kyle; Chris Todd Hittinger
Journal:  Mol Biol Evol       Date:  2018-11-01       Impact factor: 16.240

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