SpotlightA showcase of research and scholarship in selected articles from 2014
EDITOR-IN-CHIEF
Brenda J. AndrewsUniversity of Toronto
EXECUTIVE EDITOR
Tracey DePellegrin
DEPUTY EDITOR, COMPLEX TRAITS
Dirk Jan de KoningSwedish University of Agricultural Sciences
DEPUTY EDITOR, HUMAN GENETICS
Stephen W. SchererThe Hospital for Sick Children & University of Toronto
SENIOR EDITORS
Katrien M. DevosUniversity of Georgia
Susan L. ForsburgUniversity of Southern California
R. Scott HawleyStowers Institute for Medical Research
Stephen I. WrightUniversity of Toronto
ASSISTANT EDITOR
Cristy Gelling
ASSISTANT MANAGING EDITOR
Ruth Isaacson
ASSOCIATE EDITORS
Eduard AkhunovKansas State University
Danika L. BannaschUniversity of California, Davis
Judith BermanUniversity of Minnesota & Tel Aviv University
James A. BirchlerUniversity of Missouri
Charles BooneUniversity of Toronto
Michael BoutrosDKFZ & University of Heidelberg
Rachel BremBuck Institute for Research on Aging
Julie BrillThe Hospital for Sick Children
David T. BurkeUniversity of Michigan Medical School
Rita M. CantorUniversity of California, Los Angeles
Susan CelnikerLawrence Berkeley National Laboratory
Aravinda ChakravartiJohns Hopkins University School of Medicine
J. Michael CherryStanford University
Timothy J. CloseUniversity of California, Riverside
Barak A. CohenWashington University School of Medicine
Josep M. ComeronUniversity of Iowa
Gloria M. CoruzziNew York University
William S. DavidsonSimon Fraser University
Kelly DaweUniversity of Georgia
2014 Editorial Board
Gustavo A. de los CamposUniversity of Alabama at Birmingham
Job DekkerUniversity of Massachusetts Medical School
Fred S. DietrichDuke University Medical Center
Rebecca W. DoergePurdue University
Aime M. Dudley1BDJD/PSUIXFTUDiabetes Research Institute
Jay C. DunlapDartmouth Medical School
Mark EstelleUniversity of California, San Diego
Justin D. FarisUSDA-ARS Cereal Crops Research Unit
David S. FayUniversity of Wyoming
Justin C. FayWashington University in St. Louis
Audrey GaschUniversity of Wisconsin-Madison
David J. GreshamNew York University
Erich GrotewoldThe Ohio State University
David J. GrunwaldThe University of Utah
Kris GunsalusNew York University
Ira M. HallWashington University School of Medicine
Jay R. HesselberthUniversity of Colorado School of Medicine
Charles S. HoffmanBoston College
James B. HollandUSDA & North Carolina State University
Emma HuangCSIRO
Timothy R. HughesUniversity of Toronto
Scott A. JacksonUniversity of Georgia
Sue L. JaspersenStowers Institute for Medical Research
Stephen L. JohnsonWashington University School of Medicine
Nicholas KatsanisDuke University
Cynthia KenyonUniversity of California, San Francisco
John K. KimUniversity of Michigan
Yuseob KimEwha Womans University
Rob J. KulathinalTemple University
Siu Sylvia LeeCornell University
Howard D. LipshitzUniversity of Toronto
Jianxin MaPurdue University
Christian R. MarshallThe Hospital for Sick Children
Andrew S. McCallionJohns Hopkins University School of Medicine
John H. McCuskerDuke University Medical Center
Kim S. McKimRutgers University
Donald G. MoermanUniversity of British Columbia
Chad L. MyersUniversity of Minnesota
Corey NislowUniversity of British Columbia
Andrew H. PatersonUniversity of Georgia
Peter PfaffelhuberUniversity of Freiburg
Patrick C. PhillipsUniversity of Oregon
Eric M. PhizickyUniversity of Rochester Medical Center
Craig S. PikaardIndiana University
David D. PollockUniversity of Colorado School of Medicine
Julia E. RichardsUniversity of Michigan School of Public Health
Jasper RineUniversity of California, Berkeley
Antonis RokasVanderbilt University
Jeffrey Ross-IbarraUniversity of California, Davis
Fritz P. RothUniversity of Toronto
Matthew S. SachsTexas A&M University
Helen K. SalzCase Western Reserve University
Michael J. ScanlonCornell University
David S. SchneiderStanford University
Robert A. SclafaniUniversity of Colorado School of Medicine
Tanja SlotteUniversity of Stockholm
Marcus B. SmolkaCornell University
Lars M. SteinmetzEuropean Molecular Biology Laboratory & Stanford University
Hidenori TachidaKyushu University
Kevin ThorntonUniversity of California, Irvine
David W. ThreadgillTexas A&M University
Sarah A. TishkoffUniversity of Pennsylvania
Olga TroyanskayaPrinceton University
Mike TyersUniversit de Montral
Veronica J. VielandNationwide Childrens Hospital
Marian WalhoutUniversity of Massachusetts Medical School
Marilyn WarburtonUSDA-ARS Corn Host Plant Resistance Research Unit
Jonathan F. WendelIowa State University
Brian S. YandellUniversity of Wisconsin-Madison
Zhenbiao YangUniversity of California, Riverside
Nevin D. YoungUniversity of Minnesota
Dani ZamirThe Hebrew University of Jerusalem
Monique ZetkaMcGill University
2Extensive Differences in Gene Expression Between Symbiotic and Aposymbiotic Cnidarians Erik M. Lehnert, Morgan E. Mouchka, Matthew S. Burriesci, Natalya D. Gallo, Jodi A. Schwarz, and John R. PringleG3: Genes | Genomes | Genetics February 2014 4:277295
SEA ANEMONE & FRIENDS Coral reefs around the world are bleaching, a threat caused by breakdown of the symbiosis between the coral animals and the dinoflagellate algae that live within their cells. Unfortunately, this crucial symbiotic partnership is poorly understood. Lehnert et al. studied gene expression patterns associated with the symbiotic state using the sea anemone Aiptasia. This fast-growing cousin of corals maintains a similar symbiotic relationship with dinoflagellates, but it can also survive without its symbiotic friends. This image shows Aiptasia hosting different concentrations of dinoflagellate symbionts. Although the anemone tissue is nearly transparent, the dinoflagellates are visible via their red chlorophyll fluorescence. Image courtesy of Jan C. DeNofrio.
3What makes us different from other journals? G3 was DPRQJWKHUVWWROODQLPSRUWDQWQLFKHDVDVRFLHW\UXQopen access journal with the same high standards for VFLHQWLFULJRUuDQGWKHVDPHTXDOLW\RIUHYLHZVuDVLWVsister journal GENETICS. G3 has established itself as a IRUXPIRUQGLQJVDQGUHVRXUFHVXVHIXOWRWKHJHQHWLFVFRPPXQLW\UHJDUGOHVVRISHUFHLYHGLPSDFWRUQRYHOW\6XEPLVVLRQVODVW\HDUZHUHXSE\DQGZHpYHDGGHGeditors in human genetics, bioinformatics, statistical, FURSVKDQGSRSXODWLRQJHQHWLFVDQGJHQRPLFV
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GENESTOGENOMES.ORG
In 2014 the GSA journals launched Genes to Genomes, a blog about genetics and genomics research and scholarly publishing. The blog features the stories behind the latest research in GENETICS and G3, guest posts from young UHVHDUFKHUVDQGOHDGHUVLQWKHHOGDQGSXEOLVKLQJWLSVDQGDQQRXQFHPHQWVfrom our editors. Visit GSSOFDMDRSNFDMNLDRNQF to read the latest posts and subscribe! Below are a few popular posts from 2014:
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Genes to Genomes the GSA journals blog
'NVSGDB@SFNSHSRRONSR @MCGD@QHMFOQNAKDLR 7KHLQWULJXLQJUHDVRQPDQ\FDWVKDYHDwhite belly, white socks, or other patches of white fur. ,PDJHFUHGLW.R]LUR+DVHJDZD&&%
6INVESTIGATIONS
Species-Level Deconvolution of Metagenome Assemblies with Hi-CBased Contact Probability Maps )NRGT@-!TQSNM(U@M+H@BGJN,@HSQDX@)#TMG@L@MC)@X2GDMCTQD
G3: Genes | Genomes | Genetics July 2014 4:13391346
EDITORS NOTE7KHqPHWDJHQRPHVrSURGXFHGE\VKRWJXQVHTXHQFLQJRIPLFURELDOFRPPXQLWLHVDUHMXPEOHGFROOHFWLRQVRIVHTXHQFHVIURPGLIIHUHQWspecies and domains. Burton and Liachko et al. introduced a powerful QHZDSSURDFKWKDWDOORZVZKROHJHQRPHVHTXHQFHVRILQGLYLGXDOPLFURELDOVSHFLHVWREHXQWDQJOHGIURPPL[HGVDPSOHV&RYHUDJHRIWKLVZRUNZDVIHDWXUHGLQ%LR,7:RUOG7KH6FLHQWLVW*HQRPH:HEDQG%LWHVL]H%LR
ABSTRACT Microbial communities consist of mixed populations of organisms, including unknown species in unknown abundances. These communities DUHRIWHQVWXGLHGWKURXJKPHWDJHQRPLFVKRWJXQVHTXHQFLQJEXWVWDQGDUGOLEUDU\FRQVWUXFWLRQPHWKRGVUHPRYHORQJUDQJHFRQWLJXLW\LQIRUPDWLRQWKXVVKRWJXQVHTXHQFLQJDQGde novo assembly of a metagenome typically yield a collection of contigs that cannot readily be grouped by species. Methods IRUJHQHUDWLQJFKURPDWLQOHYHOFRQWDFWSUREDELOLW\PDSVe.g., as generated by WKH+L&PHWKRGSURYLGHDVLJQDORIFRQWLJXLW\WKDWLVFRPSOHWHO\LQWUDFHOOXODUand contains both intrachromosomal and interchromosomal information. Here, ZHGHPRQVWUDWHKRZWKLVVLJQDOFDQEHH[SORLWHGWRUHFRQVWUXFWWKHLQGLYLGXDOgenomes of microbial species present within a mixed sample. We apply this approach to two synthetic metagenome samples, successfully clustering the genome content of fungal, bacterial, and archaeal species with more than 99% DJUHHPHQWZLWKSXEOLVKHGUHIHUHQFHJHQRPHV:HDOVRVKRZWKDWWKH+L&signal can secondarily be used to create scaffolded genome assemblies of LQGLYLGXDOHXNDU\RWLFVSHFLHVSUHVHQWZLWKLQWKHPLFURELDOFRPPXQLW\ZLWKKLJKHUOHYHOVRIFRQWLJXLW\WKDQVRPHRIWKHVSHFLHVpSXEOLVKHGUHIHUHQFHJHQRPHV
7UNTANGLING THE MIX This soccer-ball-like network diagram from Burton and Liachko et al. illustrates the genomes of 12 yeast species assembled from a metagenomic sequencing sample. Image courtesy of Joshua N. Burton.
8INVESTIGATIONS
The Yeast Ess1 Prolyl Isomerase Controls Swi6 and Whi5 Nuclear Localization #@UHC SDMBHN"@RR@MCQ@!@QMDR3GNL@R,#TMB@M(@M,6HKKHR @MC2SDUDM#'@MDR
G3: Genes | Genomes | Genetics March 2014 4:523537
EDITORS NOTE3UHYLRXVO\WKHRQO\NQRZQWDUJHWRIWKH\HDVW(VVSURO\Oisomerase was RNA polymerase II. In this work, Atencio et al. showed that (VVLVFUXFLDOIRUWKHQXFOHDUORFDOL]DWLRQRIWZRFHOOF\FOHUHJXODWRUV7KH\proposed that Ess1 induces a conformational switch within the transcription IDFWRUVpQXFOHDUWDUJHWLQJVHTXHQFHVLQUHVSRQVHWRSKRVSKRU\ODWLRQE\F\FOLQGHSHQGHQWNLQDVHV
ABSTRACT The Ess1 prolyl isomerase from Saccharomyces cerevisiae and its human ortholog, Pin1, play critical roles in transcription by regulating 51$SRO\PHUDVH,,,QKXPDQFHOOV3LQDOVRUHJXODWHVDYDULHW\RIVLJQDOLQJSURWHLQVDQG3LQPLVH[SUHVVLRQLVOLQNHGWRVHYHUDOKXPDQGLVHDVHV7Rgain insight into Ess1/Pin1 function, we carried out a synthetic genetic array VFUHHQWRLGHQWLI\QRYHOWDUJHWVRI(VVLQ\HDVW:HLGHQWLHGSRWHQWLDOWDUJHWVRI(VVLQWUDQVFULSWLRQVWUHVVDQGFHOOF\FOHSDWKZD\V:HIRFXVHGRQWKHFHOOF\FOHUHJXODWRUV6ZLDQG:KLERWKRIZKLFKVKRZKLJKO\regulated nucleocytoplasmic shuttling during the cell cycle. Surprisingly, Ess1 did not control their transcription but instead was necessary for their nuclear localization. Ess1 associated with Swi6 and Whi5 in vivo and bound GLUHFWO\WRSHSWLGHVFRUUHVSRQGLQJWRWKHLUQXFOHDUORFDOL]DWLRQVHTXHQFHVin vitro%LQGLQJE\(VVZDVVLJQLFDQWRQO\LIWKH6ZLDQG:KLSHSWLGHVZHUHSKRVSKRU\ODWHGDW6HU3URPRWLIVWKHWDUJHWVLWHVRIF\FOLQGHSHQGHQWkinases. On the basis of these results, we propose a model in which Ess1 induces a conformational switch (cis-transLVRPHUL]DWLRQDWSKRVSKR6HU3URVLWHVZLWKLQWKHQXFOHDUWDUJHWLQJVHTXHQFHVRI6ZLDQG:KL7KLVVZLWFKwould promote nuclear entry and/or retention during late M and G1 phases and might work by stimulating dephosphorylation at these sites by the Cdc14 SKRVSKDWDVH7KLVLVWKHUVWVWXG\WRLGHQWLI\WDUJHWVRI(VVLQ\HDVWRWKHUthan RNA polymerase II.
9INVESTIGATIONS
Pattern and Distribution of Deleterious Mutations in Maize 2N@MD,DYLNTJ@MC)DEEQDX1NRR(A@QQ@
G3: Genes | Genomes | Genetics January 2014 4:163171
EDITORS NOTE )ROORZLQJWKHODQGPDUNGLVFRYHU\RIKHWHURVLVK\EULGYLJRULQPDL]HWKHEXONRIWKHFURSLVQRZJURZQIURPK\EULGVRILQEUHGOLQHVOne model for the extreme success of hybrid maize is that complementation masks the effects of many deleterious mutations. This work reported the results RIWKHUVWVFDQIRUGHOHWHULRXVPXWDWLRQVLQPDL]HVXJJHVWLQJDPHDQLQJIXOUROHfor complementation in heterosis.
ABSTRACT Most nonsynonymous mutations are thought to be deleterious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ogether, these data are consistent with the dominance model of heterosis, LQZKLFKFRPSOHPHQWDWLRQRIQXPHURXVORZIUHTXHQF\ZHDNGHOHWHULRXVYDULDQWVFRQWULEXWHWRK\EULGYLJRU
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INVESTIGATIONS
Genomic and Phenotypic Characterization of a Wild Medaka Population: Towards the Establishment of an Isogenic Population Genetic Resource in Fish ,HJG@HK2OHU@JNU3GNL@R. TDQ1@UHMCQ@/DQ@U@KH(@M#TMG@L#HQJ#NKKD
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*HXNRGH-@QTRD$V@M!HQMDX@MC)N@BGHL6HSSAQNCS
G3: Genes | Genomes | Genetics March 2014 4:433445
EDITORS NOTE7KHPHGDNDLVDFHQWXU\ROGJHQHWLFPRGHORQWKHULVHDJDLQ/RQJVWXGLHGE\VFLHQWLVWVLQ-DSDQLWKDVEHHQUHGLVFRYHUHGE\WKHZLGHUUHVHDUFKFRPPXQLW\GXULQJWKHODVWGHFDGHDVDH[LEOHWRROIRUYHUWHEUDWHJHQHWLFV3DUWRIWKHPHGDNDpVDSSHDORYHULWV]HEUDVKUHODWLYHVLVLWVDPHQDELOLW\WRLQEUHHGLQJ,QWKLVZRUN6SLYDNRYDQG$XHUet al. laid the groundwork for a SODQQHGQHDULVRJHQLFSDQHORIOLQHVGHULYHGIURPDZLOGSRSXODWLRQ
ABSTRACT Oryzias latipesPHGDNDKDVEHHQHVWDEOLVKHGDVDYHUWHEUDWHJHQHWLFPRGHOIRUPRUHWKDQDFHQWXU\DQGUHFHQWO\KDVEHHQUHGLVFRYHUHGRXWVLGHLWVQDWLYH-DSDQ7KHSRZHURIQHZVHTXHQFLQJPHWKRGVQRZPDNHVLWSRVVLEOHWRUHLQYLJRUDWHPHGDNDJHQHWLFVLQSDUWLFXODUE\HVWDEOLVKLQJDQHDULVRJHQLFSDQHOGHULYHGIURPDVLQJOHZLOGSRSXODWLRQ+HUHZHFKDUDFWHUL]HWKHgenomes of wild medaka catches obtained from a single Southern Japanese SRSXODWLRQLQ.L\RVXDVDSUHFXUVRUIRUWKHHVWDEOLVKPHQWRIDQHDULVRJHQLFSDQHORIZLOGOLQHV7KHSRSXODWLRQLVIUHHRIVLJQLFDQWGHWULPHQWDOSRSXODWLRQVWUXFWXUHDQGKDVDGYDQWDJHRXVOLQNDJHGLVHTXLOLEULXPSURSHUWLHVVXLWDEOHfor the establishment of the proposed panel. Analysis of morphometric traits LQYHUHSUHVHQWDWLYHLQEUHGVWUDLQVVXJJHVWVSKHQRW\SLFPDSSLQJZLOOEHIHDVLEOHLQWKHSDQHO,QDGGLWLRQKLJKWKURXJKSXWJHQRPHVHTXHQFLQJRIWKHVHPHGDNDVWUDLQVFRQUPVWKHLUHYROXWLRQDU\UHODWLRQVKLSVRQOLQHVRIJHRJUDSKLFVHSDUDWLRQDQGSURYLGHVIXUWKHUHYLGHQFHWKDWWKHUHKDVEHHQOLWWOHVLJQLFDQWLQWHUEUHHGLQJEHWZHHQWKH6RXWKHUQDQG1RUWKHUQPHGDNDSRSXODWLRQVLQFHWKH6RXWKHUQ1RUWKHUQSRSXODWLRQVSOLW7KHVHTXHQFHdata suggest that the Southern Japanese medaka existed as a larger older SRSXODWLRQWKDWZHQWWKURXJKDUHODWLYHO\UHFHQWERWWOHQHFNDSSUR[LPDWHO\\HDUVDJR,QDGGLWLRQZHGHWHFWSDWWHUQVRIUHFHQWSRVLWLYHVHOHFWLRQin the Southern population. These data indicate that the genetic structure of WKH.L\RVXPHGDNDVDPSOHVLVVXLWDEOHIRUWKHHVWDEOLVKPHQWRIDYHUWHEUDWHQHDULVRJHQLFSDQHODQGWKHUHIRUHLQEUHHGLQJRIOLQHVEDVHGRQWKLVpopulation has commenced. Progress of this project can be tracked at KWWSZZZHELDFXNELUQH\VUYPHGDNDUHISDQHO.
11
OLD & NEW Medaka have been kept as aquarium fish since the 17th century, with domesticated varieties in a range of colors. Body color mutants were key to early medaka research, including Tatuo Aidas 1921 GENETICS paper that was the first to demonstrate Y-linked inheritance in any organism. This 1835 illustration by Baien Mouri shows white and orange-red medaka varieties. From the National Diet Library Digital Collections, Japan, http://www.ndl.go.jp.
12
INVESTIGATIONS
Multigenic Natural Variation Underlies Caenorhabditis elegans Olfactory Preference for the Bacterial Pathogen Serratia marcescens $KHY@ADSG$&K@SDQ,@SSGDV51NBJL@M@MC"NQMDKH@(!@QFL@MM
G3: Genes | Genomes | Genetics February 2014 4:265276
EDITORS NOTE C. elegans smells its way through the world, using FKHPRVHQVDWLRQWRVHHNIRRGDYRLGGDQJHUDQGQGPDWHV7KLVZRUNdissected the complex genetic architecture of preference for the odor of certain bacteria. The authors also compared two common methods for identifying QTLs, and suggested that the odor preference QTLs were more GLIFXOWWRGHWHFWZLWKUHFRPELQDQWLQEUHGOLQHVWKDQZLWKLQWURJUHVVLRQOLQHVEHFDXVHRIH[WHQVLYHHSLVWDWLFLQWHUDFWLRQV
ABSTRACT The nematode Caenorhabditis elegans can use olfaction to discriminate among different kinds of bacteria, its major food source. We DVNHGKRZQDWXUDOJHQHWLFYDULDWLRQFRQWULEXWHVWRFKRLFHEHKDYLRUIRFXVLQJRQGLIIHUHQFHVLQROIDFWRU\SUHIHUHQFHEHKDYLRUEHWZHHQWZRZLOGW\SHC. elegans strains. The laboratory strain N2 strongly prefers the odor of Serratia marcescens, a soil bacterium that is pathogenic to C. elegans, to the odor of Escherichia coli, a commonly used laboratory food source. The GLYHUJHQW+DZDLLDQVWUDLQ&%KDVDZHDNHUDWWUDFWLRQWRSerratia than the 1VWUDLQDQGWKLVEHKDYLRUDOGLIIHUHQFHKDVDFRPSOH[JHQHWLFEDVLV$WOHDVWWKUHHTXDQWLWDWLYHWUDLWORFL47/VIURPWKH&%+DZDLLVWUDLQ+:ZLWKlarge effect sizes lead to reduced Serratia preference when introgressed into DQ1JHQHWLFEDFNJURXQG7KHVHORFLLQWHUDFWDQGKDYHHSLVWDWLFLQWHUDFWLRQVwith at least two antagonistic QTLs from HW that increase Serratia preference. The complex genetic architecture of this C. elegans trait is reminiscent of the DUFKLWHFWXUHRIPDPPDOLDQPHWDEROLFDQGEHKDYLRUDOWUDLWV
13
INVESTIGATIONS
Sequencing, Assembling, and Correcting Draft Genomes Using Recombinant Populations ,@SSGDV6'@GM2HLN59G@MF@MC+DNMHD",NXKD
G3: Genes | Genomes | Genetics April 2014 4:669679
EDITORS NOTE$VVHPEOLQJQRQPRGHORUJDQLVPJHQRPHVde novo is challenging. Current methods produce thousands of assembled pieces, none RIZKLFKDUHDVVLJQHGWRFKURPRVRPHVDQGPDQ\RIZKLFKKDYHHUURUV7KHPHWKRGGHVFULEHGLQWKLVZRUNVROYHVERWKRIWKHVHSUREOHPVE\VHTXHQFLQJDUHFRPELQDQWSRSXODWLRQZKLFKDOORZVDVVHPEO\RIDKLJKTXDOLW\JHQRPHVLPXOWDQHRXVZLWKKLJKFRQGHQFHPDUNHULGHQWLFDWLRQDQG47/PDSSLQJ
ABSTRACT Current de novoZKROHJHQRPHVHTXHQFLQJDSSURDFKHVRIWHQDUHLQDGHTXDWHIRURUJDQLVPVODFNLQJVXEVWDQWLDOSUHH[LVWLQJJHQHWLFGDWDProblems with these methods are manifest as: large numbers of scaffolds that DUHQRWRUGHUHGZLWKLQFKURPRVRPHVRUDVVLJQHGWRLQGLYLGXDOFKURPRVRPHVPLVDVVHPEO\RIDOOHOLFVHTXHQFHVDVVHSDUDWHORFLZKHQWKHLQGLYLGXDOVEHLQJVHTXHQFHGDUHKHWHUR]\JRXVDQGWKHFROODSVHRIUHFHQWO\GXSOLFDWHGVHTXHQFHVLQWRDVLQJOHORFXVUHJDUGOHVVRIOHYHOVRIKHWHUR]\JRVLW\+HUHZHpropose a new approach for producing de novo ZKROHJHQRPHVHTXHQFHVuZKLFKZHFDOOUHFRPELQDQWSRSXODWLRQJHQRPHFRQVWUXFWLRQuWKDWVROYHVPDQ\of the problems encountered in standard genome assembly and that can be DSSOLHGLQPRGHODQGQRQPRGHORUJDQLVPV2XUDSSURDFKWDNHVDGYDQWDJHRIQH[WJHQHUDWLRQVHTXHQFLQJWHFKQRORJLHVWRVLPXOWDQHRXVO\EDUFRGHDQGVHTXHQFHDODUJHQXPEHURILQGLYLGXDOVIURPDUHFRPELQDQWSRSXODWLRQ7KHVHTXHQFHVRIDOOUHFRPELQDQWVFDQEHFRPELQHGWRFUHDWHDQLQLWLDOde novo DVVHPEO\IROORZHGE\WKHXVHRILQGLYLGXDOUHFRPELQDQWJHQRW\SHVWRFRUUHFWassembly splitting/collapsing and to order and orient scaffolds within linkage groups. Recombinant population genome construction can rapidly accelerate WKHWUDQVIRUPDWLRQRIQRQPRGHOVSHFLHVLQWRJHQRPHHQDEOHGV\VWHPVE\VLPXOWDQHRXVO\SURGXFLQJDKLJKTXDOLW\JHQRPHDVVHPEO\DQGSURYLGLQJJHQRPLFWRROVHJKLJKFRQGHQFHVLQJOHQXFOHRWLGHSRO\PRUSKLVPVIRUimmediate applications. In populations segregating for important functional WUDLWVWKLVDSSURDFKDOVRHQDEOHVVLPXOWDQHRXVPDSSLQJRITXDQWLWDWLYHWUDLWORFLWe demonstrate our method using simulated Illumina data from a recombinant population of Caenorhabditis elegans and show that the method can produce a KLJKGHOLW\KLJKTXDOLW\JHQRPHDVVHPEO\IRUERWKSDUHQWVRIWKHFURVV
14
INVESTIGATIONS
Distinct and Predictive Histone Lysine Acetylation Patterns at Promoters, Enhancers, and Gene Bodies -HRG@1@I@FNO@K)@RNM$QMRS/Q@CHOS@1@X)HD6T,HBG@DK9G@MF,@MNKHR*DKKHR
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G3: Genes | Genomes | Genetics1RYHPEHUt
EDITORS NOTE Because different types of histone lysine acetylations WHQGWRFRRFFXULQWKHJHQRPHWKH\DUHJHQHUDOO\FRQVLGHUHGUHGXQGDQW7KLVZRUNGHVFULEHGSUHGLFWLYHSDWWHUQVRIKLVWRQHDFHW\ODWLRQVXJJHVWLQJWKH\KDYHGLYHUVHDQGGLVWLQFWIXQFWLRQDOUROHV%HWWHUXQGHUVWDQGLQJWKHVHJHQRPLFSDWWHUQVFRXOGUHYHDOVWUDWHJLHVIRULQFUHDVLQJWKHVSHFLFLW\RIKLVWRQHGHDFHW\ODVHEDVHG+,9DQGFDQFHUWUHDWPHQWV
ABSTRACT,QHXNDU\RWLFFHOOVKLVWRQHO\VLQHVDUHIUHTXHQWO\DFHW\ODWHG+RZHYHUXQOLNHPRGLFDWLRQVVXFKDVPHWK\ODWLRQVKLVWRQHDFHW\ODWLRQPRGLFDWLRQVDUHRIWHQFRQVLGHUHGUHGXQGDQW$VVXFKWKHIXQFWLRQDOUROHVRIGLVWLQFWKLVWRQHDFHW\ODWLRQVDUHODUJHO\XQH[SORUHG:HSUHYLRXVO\GHYHORSHGDQDOJRULWKP5)(&6WRGLVFRYHUWKHPRVWLQIRUPDWLYHPRGLFDWLRQVDVVRFLDWHGZLWKWKHFODVVLFDWLRQRUSUHGLFWLRQRIPDPPDOLDQHQKDQFHUV+HUHZHXVHGWKLVWRROWRLGHQWLI\WKHPRGLFDWLRQVPRVWSUHGLFWLYHRISURPRWHUVHQKDQFHUVDQGJHQHbodies. Unexpectedly, we found that histone acetylation alone performs well in GLVWLQJXLVKLQJWKHVHXQLTXHJHQRPLFUHJLRQV)XUWKHUZHIRXQGWKHDVVRFLDWLRQof characteristic acetylation patterns with genic regions and association of FKURPDWLQVWDWHZLWKVSOLFLQJ7DNHQWRJHWKHURXUZRUNXQGHUVFRUHVWKHGLYHUVHIXQFWLRQDOUROHVRIKLVWRQHDFHW\ODWLRQLQJHQHUHJXODWLRQDQGSURYLGHVVHYHUDOtestable hypotheses to dissect these roles.
15
INVESTIGATIONS
The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now 2S@BH@1$MFDK%QDC2#HDSQHBG#H@MM@&%HRJ&@HK!HMJKDX1@L@!@K@JQHRGM@M
,@QH@""NRS@MYN2DKHM@2#VHFGS!DMI@LHM"'HSY*@KO@M@*@QQ@1NADQS2-@RG
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,@SS2HLHRNM@MC),HBG@DK"GDQQX
G3: Genes | Genomes | Genetics March 2014 4:389398
EDITORS NOTE$IWHU\HDUVWKHUVWHXNDU\RWLFJHQRPHHYHUVHTXHQFHGZDVXSJUDGHGWRDQHZUHIHUHQFHVHTXHQFHLQ%HVLGHVGHVFULELQJWKHUHVHTXHQFLQJDQGDQQRWDWLRQXSGDWHWKLVDUWLFOHGHWDLOVWKHJHQHDORJLFDOKLVWRU\RIWKH6&UHIHUHQFHVWUDLQDQGWKHKLVWRU\RIWKHHDUO\VHTXHQFLQJefforts during the 1990s.
ABSTRACT The genome of the budding yeast Saccharomyces cerevisiae was WKHUVWFRPSOHWHO\VHTXHQFHGIURPDHXNDU\RWH,WZDVUHOHDVHGLQDVWKHwork of a worldwide effort of hundreds of researchers. In the time since, the \HDVWJHQRPHKDVEHHQLQWHQVLYHO\VWXGLHGE\JHQHWLFLVWVPROHFXODUELRORJLVWVDQGFRPSXWDWLRQDOVFLHQWLVWVDOORYHUWKHZRUOG0DLQWHQDQFHDQGDQQRWDWLRQRIWKHJHQRPHVHTXHQFHKDYHORQJEHHQSURYLGHGE\WKHSaccharomyces Genome Database, one of the original model organism databases. To deepen our understanding of the eukaryotic genome, the S. cerevisiae strain S288C UHIHUHQFHJHQRPHVHTXHQFHZDVXSGDWHGUHFHQWO\LQLWVUVWPDMRUXSGDWHVLQFH7KHQHZYHUVLRQFDOOHGq6&rZDVGHWHUPLQHGIURPDVLQJOH\HDVWFRORQ\XVLQJPRGHUQVHTXHQFLQJWHFKQRORJLHVDQGVHUYHVDVWKHDQFKRUIRUIXUWKHULQQRYDWLRQVLQ\HDVWJHQRPLFVFLHQFH
16
INVESTIGATIONS
An X-Linked Sex Ratio Distorter in Drosophila simulans That Kills or Incapacitates Both Noncarrier Sperm and Sons 6HKKH@L11HBD
G3: Genes | Genomes | Genetics October 2014 4:18371848
EDITORS NOTE$QHZIRUPRIJHQRPLFFRQLFWZDVUHFHQWO\SUHGLFWHGE\WKHDXWKRURIWKLVZRUNVH[XDOO\DQWDJRQLVWLF]\JRWLFGULYHRIWKHVH[FKURPRVRPHV6$='6$='RFFXUVZKHQJHQHVRQRQHVH[FKURPRVRPHLQan XY father kill the sex of offspring that does not carry the killer chromosome. 7KLVZRUNSURYLGHVHYLGHQFHIRUWKHRSHUDWLRQRI6$='LQWKHPRGHODrosophila simulans.
ABSTRACT*HQRPLFFRQLFWRFFXUVZKHQDJHQRPLFFRPSRQHQWJDLQVDUHSURGXFWLYHDGYDQWDJHDWWKHH[SHQVHRIWKHRUJDQLVPDVDZKROH;OLQNHGVHJUHJDWLRQGLVWRUWHUVNLOORULQFDSDFLWDWH
17
MUTANT SCREEN REPORT
A Genetic Screen Based on in Vivo RNA Imaging Reveals Centrosome-Independent Mechanisms for Localizing gurken Transcripts in Drosophila 1HOODH'@X@RGH2,@QJ6@HMVQHFGS2NOGHD)+HCCDKK2GDDM@,/HMBGHM
2ST@QS'NQRVDKK@MC#@UHC(RG'NQNVHBY
G3: Genes | Genomes | Genetics April 2014 4:749760
EDITORS NOTE Transport of gurken mRNA along microtubules establishes WKHPDMRUERG\D[HVRIWKHGHYHORSLQJDrosophila oocyte. This Mutant Screen Report describes a screen for maternal mutations that disrupt localization of XRUHVFHQWO\ODEHOHGgurkenDQGSURYLGHVHYLGHQFHRIORFDOL]DWLRQPHFKDQLVPVindependent of the centrosome.
7KHVHDUWLFOHVSUHVHQWWKHUHVXOWVRIPXWDQWVFUHHQVLQDSHHUUHYLHZHGIRUPDWGHVLJQHGWRPDNHLWIDVWDQGHDV\IRUDXWKRUVWRVXEPLWIRUUHYLHZHUVto rapidly assess, and for readers to easily understand the screen and its UHVXOWV7KH5HSRUWVIXOOORQHRI*pVJRDOVWRPDNHXVHIXOGDWDDYDLODEOHWRWKHFRPPXQLW\DVTXLFNO\DVSRVVLEOH
ABSTRACT:HKDYHVFUHHQHGFKURPRVRPHDUP/IRUHWK\OPHWKDQHVXOIRQDWHLQGXFHGPXWDWLRQVWKDWGLVUXSWORFDOL]DWLRQRIXRUHVFHQWO\ODEHOHGgurken (grk) messenger (m)RNA, whose transport along microtubules establishes both major ERG\D[HVRIWKHGHYHORSLQJDrosophilaRRF\WH5DSLGLGHQWLFDWLRQRIFDXVDWLYHPXWDWLRQVE\VLQJOHQXFOHRWLGHSRO\PRUSKLVPUHFRPELQDWLRQDOPDSSLQJDQGZKROHJHQRPLFVHTXHQFLQJDOORZHGXVWRGHQHQLQHFRPSOHPHQWDWLRQJURXSVaffecting grk mRNA localization and other aspects of oogenesis, including alleles of elg1, scaf6, quemao, nudE, Tsc2/gigas, rasp, and Chd5/WrbDQGVHYHUDOQXOOalleles of the armitage3LZLSDWKZD\JHQH$QDO\VLVRIDQHZO\LQGXFHGkinesin light chainDOOHOHVKRZVWKDWNLQHVLQPRWRUDFWLYLW\LVUHTXLUHGIRUERWKHIFLHQWgrk mRNA localization and oocyte centrosome integrity. We also show that initiation of the dorsoanterior localization of grk mRNA precedes centrosome localization, VXJJHVWLQJWKDWPLFURWXEXOHVHOIRUJDQL]DWLRQFRQWULEXWHVWREUHDNLQJD[LDOV\PPHWU\WRJHQHUDWHDXQLTXHGRUVRYHQWUDOD[LV
18
INVESTIGATIONS
Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster Group 1DADJ@G+1NFDQR+HMF2G@N)@KD@K22@MI@J/DSDQ MCNKE@SSN@MC*DUHM13GNQMSNM
G3: Genes | Genomes | Genetics December 2014 4:23452351
EDITORS NOTE DrosophilaVSHFLHVSURYLGHH[FHOOHQWPRGHOVIRUFRPSDUDWLYHJHQRPLFVEXWDVLGHIURPD. melanogaster, genome annotations DUHQRW\HWFRPSUHKHQVLYHRIWHQODFNLQJLQIRUPDWLRQRQOLQHDJHVSHFLFJHQHVDOWHUQDWLYHLVRIRUPVDQGXQWUDQVODWHGUHJLRQV5RJHUVet al. used WLVVXHDQGVH[VSHFLF51$VHTXHQFLQJGDWDWRVLJQLFDQWO\LPSURYHJHQHPRGHOVIRUVHYHUDONH\Drosophila reference genomes.
ABSTRACT+HUHZHSURYLGHUHYLVHGJHQHPRGHOVIRUD. ananassae, D. yakuba, and D. simulans, which include untranslated regions and empirically YHULHGLQWURQH[RQERXQGDULHVDVZHOODVRUWKRORJJURXSVLGHQWLHGXVLQJDIX]]\UHFLSURFDOEHVWKLWEODVWFRPSDULVRQ8VLQJWKHVHUHYLVHGDQQRWDWLRQVZHSHUIRUPGLIIHUHQWLDOH[SUHVVLRQWHVWLQJXVLQJWKHFXILQNVVXLWHWRSURYLGHDEURDGRYHUYLHZRIGLIIHUHQWLDOH[SUHVVLRQEHWZHHQUHSURGXFWLYHWLVVXHVDQGthe carcass. We identify thousands of genes that are differentially expressed across tissues in D. yakuba and D. simulans, with roughly 60% agreement in expression patterns of orthologs in D. yakuba and D. simulans. We identify VHYHUDOFDVHVRISXWDWLYHSRO\FLVWURQLFWUDQVFULSWVSRLQWLQJWRDFRPELQDWLRQRIWUDQVFULSWLRQDOUHDGWKURXJKLQWKHJHQRPHDVZHOODVSXWDWLYHJHQHIXVLRQDQGVVLRQHYHQWVDFURVVWD[D:HIXUWKHUPRUHLGHQWLI\KXQGUHGVRIOLQHDJHVSHFLFJHQHVLQHDFKVSHFLHVZLWKQREODVWKLWVDPRQJWUDQVFULSWVRIDQ\RWKHUDrosophila species, which are candidates for neofunctionalized proteins and a SRWHQWLDOVRXUFHRIJHQHWLFQRYHOW\
19
INVESTIGATIONS
Performance of High-Throughput Sequencing in Complete Size-Spectrum Genetic Variation Discovery MCX6HMF"GTM/@MF)DEEQDX1,@B#NM@KC1X@M*"8TDM5@MDRR@,'@XDR
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G3: Genes | Genomes | Genetics January 2014 4:6365
EDITORS NOTE+LJKWKURXJKSXWQH[WJHQHUDWLRQVHTXHQFLQJLVLQFUHDVLQJO\used to identify mutations in disease studies. But can the short reads generated by these methods and existing annotation tools detect the full spectrum of KXPDQJHQRPLFYDULDWLRQ"3DQJet al.V\VWHPDWLFDOO\FRPSDUHGKXPDQKLJKWKURXJKSXWVHTXHQFLQJGDWDWRD6DQJHUVHTXHQFHGUHIHUHQFHDQGIRXQGWKDWPDQ\LQGHOVDQGFRS\QXPEHUYDULDQWVZHUHPLVVHGE\FXUUHQWPHWKRGV
ABSTRACT:HREVHUYHGWKDWFXUUHQWKLJKWKURXJKSXWVHTXHQFLQJDSSURDFKHVRQO\GHWHFWHGDIUDFWLRQRIWKHIXOOVL]HVSHFWUXPRILQVHUWLRQVGHOHWLRQVDQGFRS\QXPEHUYDULDQWVFRPSDUHGZLWKDSUHYLRXVO\SXEOLVKHG6DQJHUVHTXHQFHGKXPDQJHQRPH7KHVHQVLWLYLW\IRUGHWHFWLRQZDVWKHORZHVWLQWKHWRESVL]HUDQJHDQGDW'1$UHSHDWVZLWKFRS\number gains harder to delineate than losses. We discuss strategies for GLVFRYHULQJWKHIXOOVSHFWUXPRIJHQHWLFYDULDWLRQQHFHVVDU\IRUGLVHDVHassociation studies.
20
INVESTIGATIONS
The Genetic Architecture of Seed Composition in Soybean Is Refined by Genome-Wide Association Scans Across Multiple Populations )TRSHM-5@TFGM1@MC@KK+-DKRNM0HIH@M2NMF/DQQX!"QDF@M@MC9DMFKT+H
G3: Genes | Genomes | Genetics1RYHPEHUt
EDITORS NOTE Soybean is recognized as a major contributor to worldwide IRRGSURGXFWLRQDQGDVLJQLFDQWVRXUFHRIELRGLHVHO7KHVHDXWKRUVXVHGKLJKGHQVLW\JHQRW\SLQJGDWDIURPWKH86'$6R\EHDQ*HUPSODVP&ROOHFWLRQVWRH[SORUHWKHXWLOLW\RIJHQRPHZLGHDVVRFLDWLRQVFDQVLQVR\EHDQDQGWRH[DPLQHWKHJHQHWLFDUFKLWHFWXUHDQGUHQH47/VIRUNH\HFRQRPLFWUDLWVVHHGSURWHLQDQGRLOOHYHOV
ABSTRACT6R\EHDQRLODQGPHDODUHPDMRUFRQWULEXWRUVWRZRUOGZLGHIRRGSURGXFWLRQ&RQVHTXHQWO\WKHJHQHWLFEDVLVIRUVR\EHDQVHHGFRPSRVLWLRQKDVEHHQLQWHQVHO\VWXGLHGXVLQJIDPLO\EDVHGPDSSLQJ3RSXODWLRQEDVHGPDSSLQJDSSURDFKHVLQWKHIRUPRIJHQRPHZLGHDVVRFLDWLRQ*:$VFDQVKDYHEHHQDEOHWRUHVROYHORFLFRQWUROOLQJPRGHUDWHO\FRPSOH[TXDQWLWDWLYHtraits (QTL) in numerous crop species. Yet, it is still unclear how soybeans XQLTXHSRSXODWLRQKLVWRU\ZLOODIIHFW*:$VFDQV8VLQJRQHRIWKHSRSXODWLRQVin this study, we simulated phenotypes resulting from a range of genetic architectures. We found that with a heritability of 0.5, ~100% and ~33% of the DQGVLPXODWHG47/FDQEHUHFRYHUHGUHVSHFWLYHO\ZLWKDIDOVHSRVLWLYHrate of less than ~610 per marker tested. Additionally, we demonstrated that FRPELQLQJLQIRUPDWLRQIURPPXOWLORFXVPL[HGPRGHOVDQGFRPSUHVVHGOLQHDUPL[HGPRGHOVLPSURYHV47/LGHQWLFDWLRQDQGLQWHUSUHWDWLRQ:HDSSOLHGWKHVHLQVLJKWVWRH[SORULQJVHHGFRPSRVLWLRQLQVR\EHDQUHQLQJWKHOLQNDJHJURXS,(chromosome 20) protein QTL and identifying additional oil QTL that may allow some decoupling of highly correlated oil and protein phenotypes. Because WKHYDOXHRISURWHLQPHDOLVFORVHO\UHODWHGWRLWVHVVHQWLDODPLQRDFLGSUROHwe attempted to identify QTL underlying methionine, threonine, cysteine, DQGO\VLQHFRQWHQW0XOWLSOH47/ZHUHIRXQGWKDWKDYHQRWEHHQREVHUYHGLQIDPLO\EDVHGPDSSLQJVWXGLHVDQGHDFKWUDLWH[KLELWHGDVVRFLDWLRQVDFURVVmultiple populations. Chromosomes 1 and 8 contain strong candidate alleles IRUHVVHQWLDODPLQRDFLGLQFUHDVHV2YHUDOOZHSUHVHQWWKHVHDQGDGGLWLRQDOdata that will be useful in determining breeding strategies for the continued LPSURYHPHQWRIVR\EHDQpVQXWULHQWSRUWIROLR
IMMUNE REPERTOIRE In 2014, the GSA journals launched a contest inviting image submissions related to genetics and genomics. The winning entry was created by Jian Han, of the HudsonAlpha Institute for Biotechnology. It depicts an imprint tree map, with each rectangle representing a unique gene combination of B or T cell receptors, and the ability to defend against a particular antigen. The larger the rectangle, the more expressed the gene combination. Imprints provide not only a quick graphical representation of the overall diversity of an individuals immune repertoire, but are also personalized artwork.
21
COVER ART CONTEST WINNER
22
INVESTIGATIONS
Genome Sequence of Saccharomyces carlsbergensis, the Worlds First Pure Culture Lager Yeast MCQD@6@KSGDQ M@'DRRDKA@QS@MC)QFDM6DMCK@MC
G3: Genes | Genomes | Genetics May 2014 4:783793
EDITORS NOTE Crisp lagers taste different from robust ales because they DUHEUHZHGZLWKDFROGDGDSWHGK\EULGWKHODJHU\HDVW7KLVDUWLFOHGHVFULEHGWKHJHQRPHDQGHYROXWLRQRISaccharomyces carlsbergensis, the strain that NLFNVWDUWHGWKHLQGXVWULDOVFDOHODJHUEXVLQHVVLQ
ABSTRACT/DJHU\HDVWEHHUSURGXFWLRQZDVUHYROXWLRQL]HGE\WKHLQWURGXFWLRQRISXUHFXOWXUHVWUDLQV7KHUVWHVWDEOLVKHGODJHU\HDVWVWUDLQLVknown as the bottom fermenting Saccharomyces carlsbergensis, which was originally termed Unterhefe No. 1 by Emil Chr. Hansen and has been used in production in since 1883. S. carlsbergensisEHORQJVWRJURXS,6DD]W\SHlager yeast strains and is better adapted to cold growth conditions than JURXS,,)URKEHUJW\SHODJHU\HDVWVe.g., the Weihenstephan strain WS34/70. +HUHZHVHTXHQFHGS. carlsbergensisXVLQJQH[WJHQHUDWLRQVHTXHQFLQJtechnologies. Lager yeasts are descendants from hybrids formed between a S. cerevisiae parent and a parent similar to S. eubayanus. Accordingly, the S. carlsbergensis0EJHQRPHLVVXEVWDQWLDOO\ODUJHUWKDQWKHMb S. cerevisiaeJHQRPH%DVHGRQWKHVHTXHQFHVFDIIROGVV\QWHQ\WRthe S. cerevisiae genome, and by using directed polymerase chain reaction for gap closure, we generated a chromosomal map of S. carlsbergensis FRQVLVWLQJRIXQLTXHFKURPRVRPHV:HSUHVHQWHYLGHQFHIRUJHQRPHDQGFKURPRVRPHHYROXWLRQZLWKLQS. carlsbergensisYLDFKURPRVRPHORVVDQGORVVRIKHWHUR]\JRVLW\VSHFLFDOO\RISDUWVGHULYHGIURPWKHS. cerevisiae SDUHQW%DVHGRQRXUVHTXHQFHGDWDDQGYLDXRUHVFHQFHDFWLYDWHGFHOOsorting analysis, we determined the ploidy of S. carlsbergensis. This inferred that this strain is basically triploid with a diploid S. eubayanus and haploid S. cerevisiae genome content. In contrast the Weihenstephan strain, ZKLFKZHUHVHTXHQFHGLVHVVHQWLDOO\WHWUDSORLGFRPSRVHGRIWZRGLSORLGS. cerevisiae and S. eubayanusJHQRPHV%DVHGRQFRQVHUYHGWUDQVORFDWLRQVbetween the parental genomes in S. carlsbergensis and the Weihenstephan VWUDLQZHSURSRVHDMRLQWHYROXWLRQDU\DQFHVWU\IRUODJHU\HDVWVWUDLQV
23
WORMS IN THE FIELD The nematode Caenorhabditis remanei is an obligate outcrosser with separate males (fanned tail) and females (pointed tail). In contrast to its primarily self-reproducing relative, C. elegans, natural populations of C. remanei display large amounts of genetic variation, providing an ideal model system for capitalizing on functional knowledge gained from C. elegans for use in studies of molecular population genetics. Image courtesy of Kristin Sikkink.
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Caenorhabditis remanei 5LFKDUG-RYHOLQ-HQQLIHU6&RPVWRFN$VKHU'&XWWHUDQG3DWULFN&3KLOOLSVG3: Genes | Genomes | Genetics June 2014 4:11231133
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&DMDSHB RRHLHK@SHNMHMSGD-DL@SNCDCaenorhabditis remanei Kristin L. Sikkink, Rose M. Reynolds, Catherine M. Ituarte, William A. Cresko, and Patrick C. PhillipsG3: Genes | Genomes | Genetics June 2014 4:11031112
24
MULTIPARENTAL POPULATIONS
In September 2014, the GSA journals launched an ongoing special collection featuring articles on QTL mapping in multiparental populations (MPPs). We continue to welcome submissions of both experimental and methodological FRQWULEXWLRQVLQDOOW\SHVRIRUJDQLVPV3XEOLVKLQJLQWKHFROOHFWLRQZLOOJLYHyour article greater exposure, both to prominent researchers working with MPPs and to the wider readership of GENETICS and G3.
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,TKSHOKD0T@MSHS@SHUD3Q@HS M@KXRHR4RHMF!@XDRH@M-DSVNQJR Scutari et al. Genetics September 2014 198:129137
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0T@MSHS@SHUD3Q@HS+NBTR,@OOHMF,DSGNCRENQ#HUDQRHSX.TSAQDC,HBD Gatti et al. G3: Genes | Genomes | Genetics September 2014 4:16231633
4RDETKMDRRNE,TKSHO@QDMS@K/NOTK@SHNMRNE,@HYDZea mays+ENQ&DMNLD!@RDC/QDCHBSHNM Lehermeier et al. Genetics September 2014 198:316
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$RSHL@SDRHM,TKSHO@QDMS/NOTK@SHNMR Munger et al. Genetics September 2014 198:5973
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&DMDQ@K,NCDKHMF%Q@LDVNQJENQ&DMNLD [email protected],TKSHO@QDMS@K
/NOTK@SHNMR =KHQJet al. Genetics September 2014 198:87101
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"G@Q@BSDQHYHMF4MBDQS@HMSXHM'HFG#DMRHSX,@OREQNL,TKSHO@QDMS@K/NOTK@SHNMR Ahfock et al. Genetics September 2014 198:117128
!@XDRH@M,NCDKHMFNE'@OKNSXOD$EEDBSRHM,TKSHO@QDMS/NOTK@SHNMR =KDQJet al. Genetics September 2014 198:139156
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&QNTORNE,@HYD Giraud et al. Genetics December 2014 198:17171734
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[email protected] thaliana, &("+HMDR Gnan et al. Genetics December 2014 198:17511758
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(RNFDMHB2NQFGTL%@LHKHDR Higgins et al. G3: Genes | Genomes | Genetics September 2014 4:15931602
3GD&DMDSHB QBGHSDBSTQDNE,@HYDZea mays+*DQMDK6DHFGS#DSDQLHM@SHNM $OYDUH]3UDGRet al. G3: Genes | Genomes | Genetics September 2014 4:16111621
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&DMDSHB1DFTK@SHNMNEZfp30"7"+@MC-DTSQNOGHKHB(M@LL@SHNMHM,TQHMD+TMF Rutledge et al. Genetics October 2014 198:735745
(CDMSHB@SHNMNE@-NUDK&DMDENQ#H@ADSHB3Q@HSRHM1@SR,HBD@MC'TL@MR Tsaih et al. Genetics September 2014 198:1729
4RHMFDrosophila melanogaster3N(CDMSHEX"GDLNSGDQ@OX3NWHBHSX&DMDR King et al. Genetics September 2014 198:3143
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25
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Average time from submission to acceptance is LESSTHANWEEKS
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If you submit a manuscript to GENETICS that reports high-quality and XVHIXOQGLQJVuEXWODFNVWKHEURDGDSSHDOVLJQLFDQFHRUQRYHOW\RIa published GENETICS articleyou may be offered a transfer to G3. This seamless process either guarantees review at G3, or G3 editors will use the GENETICS reviews to offer a decision within days.
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Within days, manuscripts are published Early Online, indexed in PubMed, and available to colleagues. You may be selected for highlights in GENETICS, cover art, press releases, promotion on blogs, social media, and other outreach. We enhance discovery and use of your research, which in turn increases its impact.
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Our journals are run by and for scientists under the aegis of the Genetics Society of America. GSA represents us, advocates for us, convenes us, publicizes us, provides educational resources, and fosters our work.
GENETICS and G3 have long been committed to integrating with community resources. We recently partnered with Cold Spring Harbor Laboratories to enable seamless deposits of manuscripts from GENETICS and G3 submission systems straight into bioRxiv, and have for years supported arXiv deposits. Articles feature links to model organism databases like SGD, FlyBase, and WormBase. In 2015, were providing custom templates for authors who use LaTex, saving them time at submission.
Access to Data
Our data policy, instituted in 2009, requires that all primary data DQGVRXUFHFRGHDVVRFLDWHGZLWKWKHPDQXVFULSWpVQGLQJVPXVWEHpublicly available, either as supplemental information or in a public repository like Dryad, FigShare, and GenBank. Besides providing everything needed for replication, this policy allows your research to KDYHWKHJUHDWHVWSRVVLEOHLPSDFWDQGWRHQVXUHWKDW\RXUQGLQJVwill be used for years to come.
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