Spotlight

A showcase of research and scholarship

in selected articles from 2015

2015/16
Editorial Board
EDITOR-IN-CHIEF

Brenda J. Andrews
University of Toronto
DEPUTY EDITOR,
COMPLEX TRAITS

ASSOCIATE EDITORS

Eduard Akhunov
Kansas State
University
Danika L. Bannasch
University of California,
Davis

Dirk Jan de Koning

Swedish University of
Agricultural Sciences

Arash Bashirullah
University of
Wisconsin-Madison

DEPUTY EDITOR,
HUMAN GENETICS

Judith Berman
University of
Minnesota & Tel Aviv
University

Stephen W. Scherer
The Hospital for Sick
Children & University
of Toronto
EXECUTIVE EDITOR

Tracey DePellegrin
ASSISTANT EDITOR

Cristy Gelling
MANAGING EDITOR

Ruth Isaacson
SENIOR EDITORS

Katrien M. Devos
University of Georgia
Susan L. Forsburg
University of Southern
California
R. Scott Hawley
Stowers Institute for
Medical Research

James A. Birchler
University of Missouri
Charles Boone
University of Toronto
Michael Boutros
DKFZ & University of
Heidelberg
Rachel Brem
Buck Institute for
Research on Aging
Julie Brill
The Hospital for Sick
Children
David T. Burke
University of Michigan
Medical School
Rita M. Cantor
University of California,
Los Angeles

Howard D. Lipshitz
University of Toronto

Susan Celniker
Lawrence Berkeley
National Laboratory

Stephen I. Wright
Senior Editor
Population Genetics &
Genomics
University of Toronto

Aravinda Chakravarti
Johns Hopkins
University School of
Medicine
J. Michael Cherry
Stanford University
Timothy J. Close
University of California,
Riverside
Barak A. Cohen
Washington University
School of Medicine
Josep M. Comeron
University of Iowa

William S. Davidson
Simon Fraser
University

Tanja Slotte
University of
Stockholm

Ira M. Hall
University of Virginia

Kim S. McKim
Rutgers University

Jay R. Hesselberth
University of Colorado
School of Medicine

Donald G. Moerman
University of British
Columbia

Gustavo A. de los
Campos
Michigan State
University

Charles S. Hoffman
Boston College

Chad L. Myers
University of
Minnesota

Lars M. Steinmetz
European Molecular
Biology Laboratory &
Stanford University

Job Dekker
University of
Massachusetts
Medical School

State University

University of British
Columbia

Hidenori Tachida
Kyushu University

Brian Oliver
Institutes of Health

Kevin Thornton
University of California,
Irvine

Andrew H. Paterson
University of Georgia

David W. Threadgill
Texas A&M University

Peter Pfaffelhuber
University of Freiburg

Sarah A. Tishkoff
University of
Pennsylvania

Kelly Dawe
University of Georgia

Fred S. Dietrich
Duke University
Medical Center
Rebecca W. Doerge
Purdue University
Aime M. Dudley
Diabetes Research
Institute
Jay C. Dunlap
Dartmouth Medical
School
Mark Estelle
University of California,
San Diego
Justin D. Faris
USDA-ARS Cereal
Crops Research Unit
David S. Fay
University of Wyoming
Justin C. Fay
Washington University
in St. Louis
Audrey Gasch
University of
Wisconsin-Madison
Cayetano Gonzalez
IRB Barcelona
Brian D. Gregory
University of
Pennsylvania
David J. Gresham
Erich Grotewold
The Ohio State
University
David J. Grunwald
The University of Utah
Kris Gunsalus

James B. Holland

Ross Houston
The Roslin Institute
Emma Huang
Janssen Pharma R & D
Timothy R. Hughes
University of Toronto
Scott A. Jackson
University of Georgia
Mattias Jakobsson
Uppsala University

Patrick C. Phillips
University of Oregon

Sue L. Jaspersen
Stowers Institute for
Medical Research

Eric M. Phizicky
University of
Rochester Medical
Center

Stephen L. Johnson
Washington University
School of Medicine

Craig S. Pikaard
Indiana University

Duke University
Cynthia Kenyon
University of California,
San Francisco
John K. Kim
Johns Hopkins
University
Ewha Womans
University
Rob J. Kulathinal
Temple University
Siu Sylvia Lee
Cornell University

David D. Pollock
University of Colorado
School of Medicine
Jasper Rine
University of California,
Berkeley
Antonis Rokas
Vanderbilt University
Jeffrey Ross-Ibarra
University of California,
Davis
Fritz P. Roth
University of Toronto
Matthew S. Sachs
Texas A&M University

Marcus B. Smolka
Cornell University

Olga Troyanskaya
Princeton University
Mike Tyers
Universit de Montral
Veronica J. Vieland
Hospital
Marian Walhout
University of
Massachusetts
Medical School
Marilyn Warburton
USDA-ARS Corn
Host Plant Resistance
Research Unit
Mick Watson
University of Edinburgh
Jonathan F. Wendel
Iowa State University
University of
Wisconsin-Madison

Jianxin Ma
Purdue University

Helen K. Salz
Case Western Reserve
University

University of California,
Riverside

Christian R. Marshall
The Hospital for Sick
Children

Michael J. Scanlon
Cornell University

University of Minnesota

David S. Schneider
Stanford University

Dani Zamir
The Hebrew University
of Jerusalem

Robert A. Sclafani
University of Colorado
School of Medicine

Monique Zetka
McGill University

Andrew S. McCallion
Johns Hopkins
University School of
Medicine
John H. McCusker
Duke University
Medical Center

I was really impressed at the speed of the whole process.

Useful and very speedy reviews, and very fast turn-around
all the way through.
Hamish G. Spencer
University of Otago

The G3 publication process was straightforward, fast and

transparent. I especially appreciated the ability to submit
reformatted LaTeX pdfs for initial review. I also appreciated
that within days of acceptance, the manuscript was published
online ahead of print.
Rob Unckless
Cornell University

The GSA blog post about our G3 paper was the most accurate
and well-thought-out summary of our research that one
could envision. It nailed the essence of what we were after with
the project, and we were excited to see our work reframed for
a broad audience so eloquently!
Seth Tomchik
The Scripps Research Institute

ON THE COVER The mosquito Aedes aegypti and its relative A. albopictus are responsible
for the spread of Zika, Chikungunya, and yellow fever viruses, among others, and A. aegypti
transmits as many as 528 million dengue infections per year. Evans et al. developed an
A. aegypti 50,000 SNP genotyping chip, which enables high-throughput genome-scale study
of this important disease vector. G3 5:711718. Image shows a 1905 illustration of A. aegypti
from Goeldis Os Mosquitos No Par reflected in the new chip. Photo: Benjamin Evans.

G3: Genes | Genomes | Genetics

Get Published, Get Discovered.
With so many publishing choices, why consider G3?
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including genome maps, single allele studies, GWAS
and QTL studies, population genetics, human genetics,
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Your work wont get lost in a sea of articles. Your
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We hope you enjoy this Spotlight, which features a
selection of excellent papers that illustrate the breadth
of work published in G3.

Editor-in-Chief,
G3: Genes | Genomes | Genetics

A Genetic Screen for Saccharomyces cerevisiae

Mutants That Fail to Enter Quiescence
Lihong Li, Shawna Miles, and Linda L. Breeden
G3: Genes | Genomes | Genetics August 2015 5:17831795
EDITORS NOTE Mutant Screen Reports in G3 present the results of mutant
screens in a peer-reviewed format designed to make it fast and easy for
authors to submit, for reviewers to rapidly assess, and for readers to easily
make useful data available to the community as quickly as possible.
Li et al. took advantage of morphological changes in yeast quiescent cells to
identify genes required for transitioning from the cell cycle into quiescence.
contributions from genes involved in cell wall integrity, stress tolerance,
autophagy, DNA replication, and many other cellular pathways.

ABSTRACT Budding yeast begin the transition to quiescence by prolonging

G1 and accumulating limited nutrients. They undergo asymmetric cell
construct elaborate cell walls. These morphologic changes give rise to
quiescent (Q) cells, which can be distinguished from three other cell types in
to screen for genes that are required to obtain the quiescent cell fraction.

host innate immune response are common. These may be new targets for
antifungal drugs. Acquired thermotolerance is also a common property,
and we show that the stress-response transcription factors Msn2 and Msn4
promote quiescence. Many other pathways also contribute, including a
subset of genes involved in autophagy, ubiquitin-mediated proteolysis, DNA
replication, bud site selection, and cytokinesis.

EMBRYONIC MIGRATIONS Cross-sections of Drosophila embryos

in wild-type and mutant backgrounds from an ectopic expression
screen to identify factors supporting mesoderm migration. Brown and
black depicts the migrating mesoderm (anti-Twist staining) or dualphosphorylated form of ERK (anti-dpERK), and blue depicts gene
expression of either HSPGs Trol or Syndecan. Image: Nathanie Trisnadi.

Genes Affecting Drosophila Mesoderm Development Including

the HSPG Trol
Nathanie Trisnadi and Angelike Stathopoulos
G3: Genes | Genomes | Genetics February 2015 5:301313

Systematic Evaluation of Drosophila CRISPR

Tools Reveals Safe and Robust Alternatives to
Autonomous Gene Drives in Basic Research
Fillip Port, Nadine Muschalik, and Simon L. Bullock
G3: Genes | Genomes | Genetics
EDITORS NOTE
genome engineering. Port et al. systematically compared Cas9-expressing
Drosophila
success rates varied substantially between different protocols. The authors
use the results to suggest safer alternatives to CRISPR-based gene drive
technology, which has previously been proposed for ecosystem management
and pest control.

ABSTRACT The Clustered Regularly Interspaced Short Palindromic Repeat/

studies in Drosophila melanogaster have used various CRISPR/Cas tools

about how to put this technology into practice. Moreover, it is unclear what
we address these issues by systematically evaluating available CRISPR/Cas
reagents and methods in Drosophila
choices of Cas9 sources and strategies for generating knock-in alleles. We
perform gene editing at a large number of target sites using a highly active
Cas9 line and a collection of transgenic gRNA strains. The vast majority of
We contrast our method to recently developed autonomous gene drive
technology for somatic and germline genome engineering and conclude that
and does not represent a biosafety risk.

Global Diversity Lines: A Five-Continent

Reference Panel of Sequenced Drosophila
melanogaster Strains
Jennifer K. Grenier, J. Roman Arguello, Margarida Cardoso Moreira,
Srikanth Gottipati, Jaaved Mohammed, Sean R. Hackett, Rachel Boughton,
Anthony J. Greenberg, and Andrew G. Clark
G3: Genes | Genomes | Genetics April 2015 5:593603
EDITORS NOTE Grenier et al. present a unique resource for complex trait
genetics, systems biology, and evolutionary biology. The Global Diversity Lines
capture an exceptionally large amount of genetic variation from wild Drosophila
melanogaster populations in 84 stable inbred lines. As with all resources
published in G3 and GENETICS, the lines and data are freely available.

ABSTRACT Reference collections of multiple Drosophila lines with

accumulating collections of omics data have proven especially valuable for
a description of a resource collection of 84 strains of Drosophila melanogaster
whose genome sequences were obtained after 12 generations of full-sib
inbreeding. The initial rationale for this resource was to foster development
of a systems biology platform for modeling metabolic regulation by the
use of natural polymorphisms as perturbations. As reference lines, they
are amenable to repeated phenotypic measurements, and already a large
collection of metabolic traits have been assayed. Another key feature of these
strains is their widespread geographic origin, coming from Beijing, Ithaca,
Netherlands, Tasmania, and Zimbabwe. After obtaining 12.5 coverage of
paired-end Illumina sequence reads, SNP and indel calls were made with the
GATK platform. Thorough quality control was enabled by deep sequencing
one line to >100, and single-nucleotide polymorphisms and indels were
validated using ddRAD-sequencing as an orthogonal platform. In addition,
a series of preliminary population genetic tests were performed with these
single-nucleotide polymorphism data for assessment of data quality. We
found 83 segregating inversions among the lines, and as expected these were
especially abundant in the African sample. We anticipate that this will make
a useful addition to the set of reference D. melanogaster strains, thanks to its
geographic structuring and unusually high level of genetic diversity.

A Genomic Selection Index Applied to

Simulated and Real Data
J. Jesus Ceron-Rojas, Jos Crossa, Vivi N. Arief, Kaye Basford, Jessica Rutkoski,
Diego Jarqun, Gregorio Alvarado, Yoseph Beyene, Kassa Semagn, and Ian DeLacy
G3: Genes | Genomes | Genetics October 2015 5:21552164
EDITORS NOTE Genomic selection makes use of genomic data to select
individuals for breeding. A genomic selection index (GSI) combines estimated
breeding values of individuals and is used to optimally choose parents for
which there is genotype information, but no phenotype data. Ceron-Rojas et
al.

ABSTRACT A genomic selection index (GSI) is a linear combination of

genomic estimated breeding values that uses genomic markers to predict
the net genetic merit and select parents from a non-phenotyped testing
population. Some authors have proposed a GSI; however, they have not used
simulated or real data to validate the GSI theory and have not explained how
to estimate the GSI selection response and the GSI expected genetic gain per
information about the genetic gains in each subsequent selection cycle. In
this paper, we develop the theory of a GSI and apply it to two simulated and
with that of the phenotypic selection index (PSI) by using the ratio of the GSI
response over the PSI response, and the PSI and GSI expected genetic
gain per selection cycle for observed and unobserved traits, respectively. In

Fingerprinting Soybean Germplasm and Its

Utility in Genomic Research
Qijian Song, David L. Hyten, Gaofeng Jia, Charles V. Quigley, Edward W. Fickus,
Randall L. Nelson, and Perry B. Cregan
G3: Genes | Genomes | Genetics October 2015 5:19992006
EDITORS NOTE This paper describes genome-wide genotyping and
analysis of more than 19,000 accessions in the USDA Soybean Germplasm
Collection. Song et al. detected a dramatic reduction of genetic diversity
associated with domestication, along with the genome regions involved.
crucial for identifying genes by association mapping. These important data
are already in wide use across the globe.

ABSTRACT The United States Department of Agriculture, Soybean

Germplasm Collection includes 18,480 domesticated soybean and 1168
wild soybean accessions introduced from 84 countries or developed in the
United States. This collection was genotyped with the SoySNP50K BeadChip
containing greater than 50K single-nucleotide polymorphisms. Redundant
of soybean from different geographic origins were observed that could be a
unique resource for soybean genetic improvement. We detected a dramatic
reduction of genetic diversity based on linkage disequilibrium and haplotype
structure analyses of the wild, landrace, and North American cultivar

soybean haplotype block maps in the wild, landrace, and North American
cultivar populations and observed that most recombination events occurred
in the regions between haplotype blocks. These haplotype maps are crucial
of economic importance. A case-control association test delimited potential
genomic regions along seven chromosomes that most likely contain genes
controlling seed weight in domesticated soybean. The resulting dataset will
traits, and will accelerate the creation of soybean varieties with improved seed
yield and quality.

High-Resolution Linkage Map and

Chromosome-Scale Genome Assembly for
Cassava (Manihot esculenta Crantz) from
10 Populations
International Cassava Genetic Map Consortium (ICGMC)
G3: Genes | Genomes | Genetics
EDITORS NOTE Though crucial for the survival of hundreds of millions
of people, cassava is vulnerable to the rapid spread of disease, and most
farmer-preferred varieties are nutrient-poor and deteriorate rapidly after
harvest. This paper presents crucial tools for future efforts at improving
the crop: a genetic map built by combining data from 10 cassava mapping
populations, and a chromosome-scale genome assembly.

ABSTRACT Cassava (Manihot esculenta Crantz) is a major staple crop in

Africa, Asia, and South America, and its starchy roots provide nourishment
for 800 million people worldwide. Although native to South America, cassava
was brought to Africa 400500 years ago and is now widely cultivated across
sub-Saharan Africa, but it is subject to biotic and abiotic stresses. To assist
and to accelerate breeding programs, we generated a framework map for
M. esculenta Crantz from reduced representation sequencing [genotypingby-sequencing (GBS)]. The composite 2412-cM map integrates 10 biparental
maps (comprising 3480 meioses) and organizes 22,403 genetic markers on 18
chromosomes, in agreement with the observed karyotype. We used the map
to anchor 71.9% of the draft genome assembly and 90.7% of the predicted
protein-coding genes. The chromosome-anchored genome sequence will
markers linked to important traits, and in providing a framework for genomic
selection-enhanced breeding of this important crop.

10

CASSAVA CROP Manihot esculenta from Khlers Medizinal-Pflanzen, 1896.

11

Identification of New Players in Cell Division,

DNA Damage Response, and Morphogenesis
Through Construction of Schizosaccharomyces
pombe Deletion Strains
Jun-Song Chen, Janel R. Beckley, Nathan A. McDonald, Liping Ren,
MariaSanta Mangione, Sylvia J. Jang, Zachary C. Elmore, Nicole Rachfall,
Anna Feoktistova, Christine M. Jones, Alaina H. Willet, Rodrigo Guillen,
Danny A. Bitton, Jrg Bhler, Michael A. Jensen, Nick Rhind, and Kathleen L. Gould
G3: Genes | Genomes | Genetics March 2015 5:361370
EDITORS NOTE To expand the toolkits for Schizosaccharomyces pombe
genetic screens, Chen et al. constructed deletion strains of 281 genes not
included in the widely-used Bioneer Corporation haploid strain collection.
The authors assayed growth of the new strains under a battery of conditions
to identify new players in cell division, DNA damage response, and
morphogenesis.

ABSTRACT Many fundamental biological processes are studied using the

Schizosaccharomyces pombe
of a set of 281 haploid gene deletion strains covering many previously
uncharacterized genes. This collection of strains was tested for growth under
DNA metabolism, completion of the cell cycle, and morphogenesis. This
subset of nonessential gene deletions will add to the toolkits available for the
study of biological processes in S. pombe.

12

The Nature, Extent, and Consequences of

Genetic Variation in the opa Repeats of Notch
in Drosophila
Clinton Rice, Danielle Beekman, Liping Liu, and Albert Erives
G3: Genes | Genomes | Genetics November 2015 5:24052419
EDITORS NOTE The conserved Drosophila regulatory protein Notch
carries polyglutamine tracts. Polyglutamine tracts in regulatory proteins may
mediate protein interactions, and variation in tract length is implicated in
et al. report an extraordinary
range of Notch alleles that are invisible to current short-read sequencing
methods. Alleles with either very short or very long polyglutamine tracts were
associated with developmental defects, which can be suppressed in many

ABSTRACT Polyglutamine (pQ) tracts are abundant in proteins co-interacting

on DNA. The lengths of these pQ tracts can modulate their interaction

of variation in the pQ-encoding opa repeats of Notch in Drosophila

melanogaster. We use Sanger sequencing to genotype opa sequences
(5'-CAX repeats), which have resisted assembly using short sequence reads.
While most sampled lines carry the major allele opa31 encoding Q13 17 or
the opa32 allele encoding Q13 18, many lines carry rare alleles encoding pQ
tracts >32 residues: opa33a (Q14 18), opa33b (Q15 17), opa34 (Q16 17),
opa35a1/opa35a2 (Q13 21), opa36 (Q13 22), and opa37 (Q13 23). Only
one rare allele encodes a tract <31 residues: opa23 (Q13Q10). This opa23
allele shortens the pQ tract while simultaneously eliminating the interrupting
histidine. We introgressed these opa variant alleles into common backgrounds
and measured the frequency of Notch
for the short and long opa alleles have defects in embryonic survival and
sensory bristle organ patterning, and sometimes show wing notching.
Consistent with functional differences between Notch opa
that a scute inversion carrying the rare opa33b allele suppresses the bristle
patterning defect caused by achaete/scute
scute inversion carrying opa31 manifests the patterning defect. Our results
demonstrate the existence of potent pQ variants of Notch and the need for long
read genotyping of key repeat variables underlying gene regulatory networks.

13

Quantitative Genetics of Migration-Related

Traits in Rainbow and Steelhead Trout
Benjamin C. Hecht, Jeffrey J. Hard, Frank P. Thrower, and Krista M. Nichols
G3: Genes | Genomes | Genetics May 2015 5:873889
EDITORS NOTE Before rainbow trout migrate from their birthplace to the
shiny silver morphs adapted for ocean journeys. But not all populations
migrate or undergo this remarkable change. To better understand the
evolution and genetics of the complex life history that moves animals over
et al. explore the heritability and genetic correlation of
migration-related traits in trout, showing that growth and body shape have a
strong genetic correlation with the propensity to remain resident, or undergo
the complex physiological change promoting a migratory life history.

ABSTRACT Rainbow trout (Oncorhynchus mykiss) exhibit remarkable life

history diversity throughout their native range, and among the most evident is
variation in migratory propensity. Although some populations and ecotypes
will remain resident in freshwater habitats throughout their life history, others
have the ability to undertake tremendous marine migrations. Those that
migrate undergo a suite of behavioral, morphological, and physiological
genetic analysis of 22 growth, size, and morphological traits in addition to

of migratory and resident rainbow trout derived from a wild population, which
genetic variance and covariance among the suite of traits that make up a
component of the migratory syndrome in this species. Additionally, we identify
strong negative genetic correlation between the migratory and resident life
history trajectories. Given the large heritability estimates of all of the traits
that segregate between migratory and resident rainbow trout, we conclude
genetic correlation between these traits, they do not evolve in isolation, but
rather as a suite of coordinated characters in a predictable manner.

14

Analysis of Circadian Rhythms in the Basal

Filamentous Ascomycete Pyronema confluens
Stefanie Traeger and Minou Nowrousian
G3: Genes | Genomes | Genetics October 2015 5:20612071
EDITORS NOTE Circadian clocks enable organisms to anticipate daily
changes in the environment. Traeger and Nowrousian demonstrate that a
key component of the circadian system was present in fungi many millions
of years earlier than previously thought, and this gene shows some of the
properties of a functioning circadian clock. This suggests that other taxa
may have lost their clock or switched to clocks based on different molecular
components over the course of evolution.

ABSTRACT Many organisms use circadian clocks to adapt to daily

changes in the environment. Major insights into the molecular mechanisms
of circadian oscillators have been gained through studies of the model
organism Neurospora crassa; however, little is known about molecular
components of circadian clocks in other fungi. An important part of the
N. crassa circadian clock is the frequency (frq) gene, homologs of which can
be found in Sordariomycetes, Dothideomycetes, and Leotiomycetes, but not
frq homolog in Pyronema confluens,
ascomycetes. The P. confluens FRQ shares many conserved domains with
the N. crassa
showing overt circadian rhythmicity in P. confluens. To investigate whether
a molecular clock is present, we analyzed frq transcription in constant
darkness, and found circadian oscillation of frq with a peak in the subjective
morning. This rhythm was temperature compensated. To identify additional
clock-controlled genes, we performed RNA sequencing of two time points
(subjective morning and evening). Circadian expression of two morningchain reaction (RT-qPCR) over a full time course, whereas expression of
frq expression was synchronized, but not
entrained by light. In summary, we have found evidence for two of the three
main properties of circadian rhythms (free-running rhythm, temperature
compensation) in P. confluens, suggesting that a circadian clock with
rhythmically expressed frq

15

FLY CATWALK How animals regulate their size is crucial for understanding
both normal development and cancerous growth. In Drosophila, a popular
model for studying growth, time-consuming manual measurements limit the
number of individuals to be analyzed. Medici et al. developed the FlyCatwalk,
an automated system for measuring live Drosophila with similar accuracy to
manual processing, but four times greater throughput.

The FlyCatwalk: A High-Throughput Feature-Based Sorting

Drosophila
16

G3: Genes | Genomes | Genetics March 2015 5:317327

RNAseq Analysis Highlights Specific

Transcriptome Signatures of Yeast and Mycelial
Growth Phases in the Dutch Elm Disease
Fungus Ophiostoma novo-ulmi
Martha Nigg, Jrme Laroche, Christian R. Landry, and Louis Bernier
G3: Genes | Genomes | Genetics November 2015 5:24872495
EDITORS NOTE Some pathogenic fungi can live as either unicellular yeast
or as elongated mycelia. Because our understanding of this dimorphic
lifestyle is mostly limited to a few human pathogens, Nigg et al. propose the
wide analysis of both yeast and mycelial forms of this species, showing that
gene expression signatures of the two phases are poorly conserved with
classical dimorphic pathogen models.

ABSTRACT Fungal dimorphism is a complex trait and our understanding

of the ability of fungi to display different growth morphologies is limited to a
fungus, the ascomycete Ophiostoma novo-ulmi, which is a model in plant
pathology and the causal agent of Dutch elm disease. The two growth phases
that this fungus displays, i.e., a yeast phase and mycelial phase, are thought
to be involved in key steps of disease development. We used RNAseq to
with yeast and mycelial growth phases in vitro. Our results show a clear
molecular distinction between yeast and mycelial phase gene expression

phase. We compared O. novo-ulmi

model dimorphic fungi, Candida albicans and Histoplasma capsulatum. Few
orthologs showed similar expression regulation between the two growth
phases, which suggests that, globally, the genes associated with these two
life forms are poorly conserved. This poor conservation underscores the
distantly related to the classical ones. Taken together, our results provide
O. novo-ulmi
and offer a new perspective for understanding fungal dimorphism.

17

SMRT Sequencing for Parallel Analysis of

Multiple Targets and Accurate SNP Phasing
Xiaoge Guo, Kevin Lehner, Karen OConnell, Jenny Zhang, Sandeep S. Dave, and
Sue Jinks-Robertson
G3: Genes | Genomes | Genetics December 2015 5:28012808
EDITORS NOTE Guo et al. describe a simple protocol that provides a highthroughput alternative to Sanger sequencing for analyzing a small number of
targets in many independent samples. The method couples barcoding with
single-molecule real-time (SMRT or PacBio) sequencing to provide a time-

ABSTRACT Single-molecule real-time (SMRT) sequencing generates much

longer reads than other widely used next-generation (next-gen) sequencing
methods, but its application to whole genome/exome analysis has been limited.
simultaneously analyze one or a small number of genomic targets derived
from multiple sources. In the budding yeast system, SMRT sequencing was
used to analyze strand-exchange intermediates generated during mitotic
recombination and to analyze genetic changes in a forward mutation assay. The
general barcoding-SMRT approach was then extended to diffuse large B-cell
lymphoma primary tumors and cell lines, where detected changes agreed
with prior Illumina exome sequencing. A distinct advantage afforded by SMRT
sequencing over other next-gen methods is that it immediately provides the
linkage relationships between SNPs in the target segment sequenced. The
strength of our approach for mutation/recombination studies (as well as linkage
lack of reliance on sophisticated statistical analyses.

18

Dendrites often have an elaborate branched morphology important for receiving

information from other cells or the environment. Antonacci et al. performed a
genetic screen for RNA-binding proteins that regulate dendrite morphogenesis
in the multidendritic PVD sensory neuron (green) in Caenorhabditis elegans.
The authors identify 12 genes that code for RNA-binding proteins important
for dendrite development. Importantly, orthologs of these proteins have
previously been implicated in dendrite development in Drosophila, and
human orthologs are expressed in the brain, suggesting that they may regulate
dendrites in humans as well. Image: Eugenia Olesnicky.

Conserved RNA-Binding Proteins Required for Dendrite

Morphogenesis in Caenorhabditis elegans Sensory Neurons
Simona Antonacci, Daniel Forand, Margaret Wolf, Courtney Tyus,
Kristen L. Wells, Serena Younes, Nathan T. Mortimer,
G3: Genes | Genomes | Genetics April 2015 5:639653

19

Genetic Networks Required to Coordinate

Chromosome Replication by DNA Polymerases
, , and in Saccharomyces cerevisiae
Marion Dubarry, Conor Lawless, A. Peter Banks, Simon Cockell, and David Lydall
G3: Genes | Genomes | Genetics October 2015 5:21872197
EDITORS NOTE Eukaryotic DNA replication depends principally on three
DNA polymerase activities. Dubarry et al.
investigate DNA replication when each polymerase is defective. Because the
interaction networks for each polymerase are non-overlapping, these data
support biochemical evidence that the polymerases play distinct roles at
replication forks. The authors also developed two visualization tools to help
others engage with these data.

ABSTRACT Three major DNA polymerases replicate the linear eukaryotic

chromosomes. DNA polymerase -primase (Pol ) and DNA polymerase
(Pol ) replicate the lagging-strand and Pol and DNA polymerase (Pol ) the
leading-strand. To identify factors affecting coordination of DNA replication, we
cells containing defective polymerases. We combined temperature-sensitive
mutations affecting the three replicative polymerases, Pol , Pol , and Pol
with genome-wide collections of null and reduced function mutations. We
identify large numbers of genetic interactions that inform about the roles that
, Pol , and Pol function. Surprisingly, the
overlap between the genetic networks affecting the three DNA polymerases
our data support a model for division of labor between the different DNA
polymerases during DNA replication. For example, our genetic interaction data
are consistent with biochemical data showing that Pol is more important to
the Pre-Loading complex than either Pol or Pol . We also observed distinct
patterns of genetic interactions between leading- and lagging-strand DNA
polymerases, with particular genes being important for coupling proliferating
cell nuclear antigen loading/unloading (Ctf18, Elg1) with nucleosome assembly
reveal specialized genetic networks that affect different aspects of leading- and
lagging-strand DNA replication. To help others to engage with these data we

20

INVESTIG ATIONS

A Powerful New Quantitative Genetics

Platform, Combining Caenorhabditis elegans
High-Throughput Fitness Assays with a Large
Collection of Recombinant Strains
Erik C. Andersen, Tyler C. Shimko, Jonathan R. Crissman, Rajarshi Ghosh,
Joshua S. Bloom, Hannah S. Seidel, Justin P. Gerke, and Leonid Kruglyak
G3: Genes | Genomes | Genetics May 2015 5:911920
EDITORS NOTE To comprehensively identify alleles underlying complex
traits in Caenorhabditis elegans, the phenotypes of a large number of
independent strains need to be measured accurately. Andersen et al. present
an expanded collection of C. elegans recombinant inbred lines that avoid
genetic background problems inherent to existing resources, along with

ABSTRACT The genetic variants underlying complex traits are often elusive
even in powerful model organisms such as Caenorhabditis elegans with
controlled genetic backgrounds and environmental conditions. Two major
contributing factors are: (1) the lack of statistical power from measuring the
phenotypes of small numbers of individuals, and (2) the use of phenotyping
platforms that do not scale to hundreds of individuals and are prone to noisy
measurements. Here, we generated a new resource of 359 recombinant
inbred strains that augments the existing C. elegans N2xCB4856 recombinant
inbred advanced intercross line population. This new strain collection removes
variation in the neuropeptide receptor gene npr-1, known to have large
physiological and behavioral effects on C. elegans and mitigates the hybrid
strain incompatibility caused by zeel-1 and peel-1
quantitative trait loci that otherwise would have been masked by those effects.
Additionally, we optimized highly scalable and accurate high-throughput
assays of fecundity and body size using the COPAS BIOSORT large particle
involved in fecundity and growth under normal growth conditions and after
exposure to the herbicide paraquat, including independent genetic loci that
regulate different stages of larval growth. Our results offer a powerful platform
for the discovery of the genetic variants that control differences in responses to
drugs, other aqueous compounds, bacterial foods, and pathogenic stresses.

21

A Multifunctional Mutagenesis System for

Analysis of Gene Function in Zebrafish
Helen Ngoc Bao Quach, Shijie Tao, Pavle Vrljicak, Adita Joshi, Hua Ruan,
Rashmi Sukumaran, Gaurav K. Varshney, Matthew C. LaFave, The Ds Screen Team,
Shawn M. Burgess, Christoph Winkler, Alexander Emelyanov, Sergey Parinov, and
Karuna Sampath
G3: Genes | Genomes | Genetics
EDITORS NOTE Quach et al. report a system to simultaneously introduce
maize Ac/Ds transposon, this dual trap system not only provides expression
information, but also creates protein-disrupting mutants. The authors have
provided a searchable database of results from a collection of transgenic

ABSTRACT Since the sequencing of the human reference genome, many

the functions of all the genes in the genome remains a challenge. The
biological activities of these genes are usually investigated in model organisms
disruptive mutations are useful for identifying and understanding the activities
using the maize Ds transposon. Integration of the Ds transposable element
containing an mCherry reporter for protein trap events and an EGFP reporter for
enhancer trap events produced a collection of transgenic lines marking distinct
trapping and prematurely terminating endogenous protein coding sequences.

of reporter expression is available online (

genomic studies in this model of human development and disease.

22

). Our

Whole-Exome Sequencing and Targeted

Copy Number Analysis in Primary Ciliary
Dyskinesia
Christian R. Marshall, Stephen W. Scherer, Maimoona A. Zariwala, Lynette Lau,
Tara A. Paton, Tracy Stockley, Rebekah K. Jobling, Peter N. Ray, Michael R. Knowles,
FORGE Canada Consortium, David A. Hall, Sharon D. Dell, and Raymond H. Kim
G3: Genes | Genomes | Genetics August 2015 5:17751781
EDITORS NOTE People with primary ciliary dyskinesia (PCD) suffer from
chronic respiratory infections. To the frustration of the patient community, this
disorder is extremely challenging to diagnose. Marshall et al. demonstrate a
cost-effective method of genetic analysis using whole-exome sequencing,
complemented with assays of copy number variation. This approach allowed
cases than traditional methods.

ABSTRACT Primary ciliary dyskinesia (PCD) is an autosomal-recessive

disorder resulting from loss of normal ciliary function. Symptoms include
neonatal respiratory distress, chronic sinusitis, bronchiectasis, situs inversus,
and infertility. Clinical features may be subtle and highly variable, making the
ultrastructure analysis and/or molecular genetic testing of 32 PCD-associated
molecular genetic testing is not considered the standard of care, and the most

We conducted targeted copy number variation (CNV) analysis and/or wholeexome sequencing on 20 families (22 patients) from a subset of 45 families
(52 patients) with a clinical diagnosis of PCD who did not have a molecular
genetic diagnosis after Sanger sequencing of 12 PCD-associated genes.

increased molecular genetic diagnostic rate of 55% (11/20). In patients with a

clinical diagnosis of PCD, whole-exome sequencing followed by targeted CNV
analysis results in an overall molecular genetic yield of 76% (34/45).

23

PLANT GENETIC ARCHAEOLOGY Salom and Weigel used whole

genome sequencing to uncover the unexpectedly complex origins of a classical
Arabidopsis trisomic line. They found evidence for inadvertent outcrossing
between accessions and detected a mutation in the GIGANTEA (GI) gene that
was identical to the original gi-1 allele isolated 50 years ago. The gi-1 mutation
explained the late-flowering phenotype that was originally assumed to be
caused by trisomy. Image shows the effect of modifiers on the gi mutation.
The top row represents the trisomic line; middle row is gi mutant; and
bottom row is wild-type. Image: Patrice Salom.

24

Plant Genetic Archaeology: Whole-Genome Sequencing

Reveals the Pedigree of a Classical Trisomic Line
Patrice A. Salom and Detlef Weigel
G3: Genes | Genomes | Genetics February 2015 5:253259

G3: Five years

and still growing!
New submissions by year
Percent change relative to 2011
400

300

200

100

2011

2012

2013

2014

2015

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