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

4IN THEIR OWN WORDS

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SNHLOQNUDSGDRBHDMSHBPT@KHSXNESGDO@ODQRUWKHHIIRUWWRJLYHappropriate reasons if the article is rejected.

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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:

5

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

10

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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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

@MC2SDOGDM62BGDQDQ

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

6GNKD&DMNLD M@KXRHRNE,TKSHDMUHQNMLDMSNQ,TKSHSQ@HS03+HM, &(" Arunas P. Verbyla et al. G3: Genes | Genomes | Genetics September 2014 4:15691584

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

1@OHC(CDMSHB@SHNMNE,@INQ$EEDBS&DMDR4RHMFSGD"NKK@ANQ@SHUD"QNRR Ram et al. Genetics September 2014 198:7586

&DMDQ@K,NCDKHMF%Q@LDVNQJENQ&DMNLD MBDRSQ@K.QHFHMRHM,TKSHO@QDMS@K

/NOTK@SHNMR =KHQJet al. Genetics September 2014 198:87101

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F2@MC CU@MBDC(MSDQBQNRR,HBD Parker et al. Genetics September 2014 198:103116

"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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3Q@CD.EE4RHMFArabidopsis thaliana, &("+HMDR Gnan et al. Genetics December 2014 198:17511758

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6HMSDQ2NVM6GD@S"QD@SHNM/QNODQSHDR@MC5@KHC@SHNM Mackay et al. G3: Genes | Genomes | Genetics September 2014 4:16031610

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#XM@LHB&DMDSHB/@SSDQMRNE1DFTK@SHNM Wrschum et al. G3: Genes | Genomes | Genetics September 2014 4:15851591

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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

%HMD,@OOHMF-HBNSHMD1DRHRS@MBD+NBHHMDrosophila4RHMF@,TKSHO@QDMS CU@MBDC&DMDQ@SHNM(MSDQ"QNRR/NOTK@SHNM Marriage et al. Genetics September 2014 198:4557

25

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Within days of initial manuscript submission, we will let you know whether the manuscript will be sent for review. For reviewed manuscripts, the editors strive to reach a decision in less than 30 days. For revised papers, more than 90% are accepted without an additional round of reviews.

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Your manuscripts will be handled by practicing scientists like you, who understand IURPH[SHULHQFHZKDWLWWDNHVWRWHOODVLJQLFDQWVWRU\WRFUHDWHDXVHIXOPHWKRGor resource, or to extract meaning from large datasets. Rather than simply tally reviewer votes, your editor synthesizes the reviews into a single, clear decision letter that offers guidance and explains rationales for all decisions, helping to improve your papers impact.

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At least TWOEDITORS consult on every decision.

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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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