TOC - G3: Genes | Genomes | Genetics

Contents
December 2014
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VOLUME 4
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ISSUE 12
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www.g3journal.org
INVESTIGATIONS
2297–2306
Natural Variation at sympathy for the ligule Controls Penetrance of the Semidominant
Liguleless narrow-R Mutation in Zea mays
Elizabeth M. Buescher, Jihyun Moon, Anne Runkel, Sarah Hake, and Brian P. Dilkes
Buescher et al. describe a novel genetic pathway affecting leaf development in maize. These genes were
identified as natural genetic variants that suppressed the Liguleless narrow-R (Lgn-R) mutation. By
crossing mutants to a mapping population, two loci, sympathy for the ligule (sol) and lucifer, modified
the expression of Lgn-R in the F1. This resulted from a three-way genetic interaction. The environment
determined the strength of the interaction between lucifer and sol. Identifying genes responsible for
leaf angle in grasses elucidates the mechanisms for plant adaptations for light harvesting and has
potential application in improving yield and plant density for agriculture.
2307–2315
Population- and Sex-Biased Gene Expression in the Excretion Organs of Drosophila melanogaster
Ann Kathrin Huylmans and John Parsch
Using high-throughput RNA sequencing, Hulmans and Parsch investigated gene expression variation in
the Drosophila melanogaster Malpighian tubules, which have a function analogous to the human kidney.
They identified thousands of genes that differ in expression between males and females and between
flies from an African and a European population. Thus, there is extensive sexual dimorphism and
intraspecific variation of gene expression in this somatic tissue. The genes expressed differentially
between populations may reflect gene regulatory adaptation to environmental conditions, such as the
presence of chemical toxins, that differ between habitats.
2317–2328
Influence of Outliers on Accuracy Estimation in Genomic Prediction in Plant Breeding
Sidi Boubacar Ould Estaghvirou, Joseph O. Ogutu, and Hans-Peter Piepho
Outliers are often a problem in analyses of data in plant breeding, but their influence on the performance
of methods for estimating predictive accuracy in genomic prediction studies has not yet been evaluated.
Ould Estaghvirou et al. evaluate the influence of outliers on the performance of seven methods for
accuracy estimation using simulated phenotypic data in which an outlier was added to one observation.
Simulation scenarios were defined by number of genotypes, marker effect variance, and outliers. Outliers
adversely influenced accuracy estimation in five of the seven methods, more so at smaller genetic
variance or number of genotypes.
2329–2343
An RNAi-Based Suppressor Screen Identifies Interactors of the Myt1 Ortholog of
Caenorhabditis elegans
Anna K. Allen, Jessica E. Nesmith, and Andy Golden
Allen et al. report an RNAi suppression screen in which they identified a number of new players in
the regulation of WEE-1.3, an extremely well-conserved inhibitory kinase of the cell cycle and
oocyte maturation in C. elegans. The Wee/Myt family of inhibitory kinases are universal
regulators of the meiotic cell cycle, acting in species from mouse to worms to humans. In addition,
they demonstrate that depletion of WEE-1.3 in C. elegans results in both premature oocyte-toembryo transition and early gene activation (EGA) occurring within the WEE-1.3-depleted
oocytes.
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2345–2351
Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the
Drosophila melanogaster Group
Rebekah L. Rogers, Ling Shao, Jaleal S. Sanjak, Peter Andolfatto, and Kevin R. Thornton
Rogers et al. provide RNA-seq based gene models for D. yakuba, D. ananassae, and the D. simulans
w501 reference. These revised gene models include UTR sequences as well as intron-exon boundaries
that are guided with empirical RNA-seq data. Additionally, they provide ortholog calls for each of these
species and D. melanogaster that can be used for comparative genomics and evolutionary molecular
genetics. Finally, the authors perform differential expression testing as a first step toward capturing the
evolution of gene expression across taxa and the nature of tissue-specific expression across species.
2353–2363
High-Resolution Genetic Mapping in the Diversity Outbred Mouse Population Identifies Apobec1 as
a Candidate Gene for Atherosclerosis
Tangi L. Smallwood, Daniel M. Gatti, Pamela Quizon, George M. Weinstock, Kuo-Chen Jung,
Liyang Zhao, Kunjie Hua, Daniel Pomp, and Brian J. Bennett
Smallwood et al. report high-resolution genetic mapping of atherosclerosis and related traits in the
Diversity Outbred (DO) mouse population. The authors focus on a high-resolution locus identified
for atherosclerosis on Chr 6, containing a high probability candidate, Apobec1. They characterize
expression differences in liver tissue from progenitor strains of the DO and identify eQTL for 2 isoforms
of Apobec1 in liver tissue from the DO population.
2365–2379
Functional Multi-Locus QTL Mapping of Temporal Trends in Scots Pine Wood Traits
Zitong Li, Henrik R. Hallingbäck, Sara Abrahamsson, Anders Fries, Bengt Andersson Gull,
Mikko J. Sillanpää, and M. Rosario García-Gil
Quantitative trait loci (QTL) mapping of wood properties in conifers has hitherto not accounted for
within-tree trends. Li et al. performed a functional QTL analysis for wood properties in Scots pine. Two
multi-locus functional QTL analysis approaches were proposed, multilevel LASSO analysis and
Bayesian linear mixed model, and several different hypothesis tests were compared. Both methods
detected similar sets of QTLs given a dataset that comprised a large number of individuals. Five and
four significant QTLs were observed for intercept and slope traits, respectively. Four of those QTLs were
represented by genes, thus providing promising targets for future studies.
2381–2387
Fast and Efficient Drosophila melanogaster Gene Knock-Ins Using MiMIC Transposons
Sven Vilain, Roeland Vanhauwaert, Ine Maes, Nils Schoovaerts, Lujia Zhou, Sandra Soukup,
Raquel da Cunha, Elsa Lauwers, Mark Fiers, and Patrik Verstreken
Genome editing is a powerful method to study gene function. In this work, Vilain and Vanhauwaert
et al. present a novel genome editing methodology for fruit flies based on MiMIC transposons that are
present throughout the genome. The methodology enables the engineering of almost every gene in the
genome with high efficiency but is different from molecular-scissor-technology (CRISPR/Cas9, TALEN,
or Zn Fingers) as it does not require the creation of locus-specific scissors, and there is no need for
inefficient donor-dependent homologous recombination. MiMIC-based gene targeting is therefore an
attractive alternative to the currently available genome editing tools.
2389–2402
Genetic Differentiation and Evolutionary Adaptation in Cryptomeria japonica
Yoshihiko Tsumura, Kentaro Uchiyama, Yoshinari Moriguchi, Megumi K. Kimura, Saneyoshi Ueno,
and Tokuko Ujino-Ihara
The genetic structure of 14 natural populations of Cryptomeria japonica was investigated using 3930
SNPs markers. In total, 208 outlier-loci were detected, of which 43 were associated with environmental
variables. Four clumped regions of outlier-loci were detected in the genome by linkage analysis. Linkage
disequilibrium (LD) was quite high in these clumps of outlier-loci, which were found in linkage groups
(LGs) 2, 7, 10, and 11, especially between populations of two varieties, and when inter-chromosomal LD
was also detected. The detected LD may provide strong evidence for selection between varieties.
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2403–2408
The Role of Transcription in the Activation of a Drosophila Amplification Origin
Brian L. Hua, Sharon Li, and Terry L. Orr-Weaver
Proper regulation of replication initiation is crucial in maintaining gene copy number and genome
stability. How metazoan replication initiation is regulated, especially by transcription, remains poorly
understood. Hua et al. investigated the role of transcription at a Drosophila amplification origin that is
uniquely dependent on transcription for activation. Surprisingly, the authors found that transcription
was not required in cis for activation of this origin. They propose a mechanism in which a trans-acting
factor can act in a temporal manner to regulate this specific origin. This illustrates that a diversity of
mechanisms can be employed in the regulation of metazoan DNA replication initiation.
2409–2418
A Versatile Two-Step CRISPR- and RMCE-Based Strategy for Efficient Genome Engineering
in Drosophila
Xu Zhang, Wouter H. Koolhaas, and Frank Schnorrer
The development of CRISPR/Cas technologies promises a quantum leap in genome engineering.
However, an efficient standard protocol has not yet emerged. Zhang et al. developed a two-step strategy
to flexibly engineer the Drosophila genome by combining CRISPR with recombinase-mediated cassette
exchange (RMCE). In the first step, they use a Act5C-Cas9, Ligase4 stock to integrate a 3xP3dsRed
reporter by homology directed recombination. In the second step, the eye marker is replaced with the
DNA sequence of choice using RMCE, enabling entirely flexible gene modification. The authors applied
this strategy to engineer four genomic locations, suggesting that any fly lab can engineer their favorite
gene within about three months.
2419–2424
Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder,
Paralichthys olivaceus
Wenji Wang, Jing Wang, Feng You, Liman Ma, Xiao Yang, Jinning Gao, Yan He, Jie Qi,
Haiyang Yu, Zhigang Wang, Xubo Wang, Zhihao Wu, and Quanqi Zhang
Double haploids have two sets of identical chromosomes which make them useful for genetic research.
RNA-Seq reads of double haploids are easy to assemble as they don't contain allelic variations. The
authors performed transcriptome sequencing using a doubled haploid Japanese flounder (Paralichthys
olivaceus) individual. Efficient assembly and annotation identified lots of functional genes. The authors
detected gene alternative splicing, some of which were randomly selected and validated. By taking
advantage of double haploids, the authors also detected duplicated genes in the P. olivaceus genome.
2425–2432
Statistical Inference of Selection and Divergence of the Rice Blast Resistance Gene Pi-ta
Amei Amei, Seonghee Lee, Kirankumar S. Mysore, and Yulin Jia
The disease resistance gene Pi-ta has been effectively used to control rice blast disease worldwide. A few recent
studies have described the evolution of Pi-ta in rice. However, the evolutionary statistics used for the studies
were too limited to understand time of selection of Pi-ta during domestication. Amei et al. applied a timedependent Poisson random field model to examine the evolution of the Pi-ta gene in rice. The data suggest
that the Pi-ta gene may have more recently introgressed into cultivated rice and U.S. weedy rice. These results
provide a valuable analytical tool for understanding the evolution of resistance genes in crop plants.
2433–2449
Evidence for Stabilizing Selection on Codon Usage in Chromosomal Rearrangements of
Drosophila pseudoobscura
Zachary L. Fuller, Gwilym D. Haynes, Dianhui Zhu, Matthew Batterton, Hsu Chao, Shannon Dugan,
Mehwish Javaid, Joy C. Jayaseelan, Sandra Lee, Mingmei Li, Fiona Ongeri, Sulan Qi, Yi Han,
Harshavardhan Doddapaneni, Stephen Richards, and Stephen W. Schaeffer
The maintenance of codon bias has traditionally been explained through a balance of mutation,
genetic drift and weak purifying selection. However, recent studies have failed to detect the expected
association between the recombination rate and intensity of selection acting at synonymous sites
predicted under these models in several species, including Drosophila pseudoobscura. The authors use
the full genomic sequences of 47 D. pseudoobscura individuals and the third chromosome inversion
polymorphism system to directly analyze codon usage and selection in regions of suppressed
recombination. They provide evidence for stabilizing selection acting on synonymous codon usage on
the third chromosome.
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2451–2460
A Screen for F1 Hybrid Male Rescue Reveals No Major-Effect Hybrid Lethality Loci in the
Drosophila melanogaster Autosomal Genome
Tawny N. Cuykendall, P. Satyaki, Shuqing Ji, Derek M. Clay, Nathaniel B. Edelman, Alexandra Kimchy,
Ling-Hei Li, Erin A. Nuzzo, Neil Parekh, Suna Park, and Daniel A. Barbash
Hybrid incompatibility (HI) maintains species boundaries by decreasing the fitness of interspecific
hybrids. Hybrid males from Drosophila melanogaster females and D. simulans males are lethal. Two
genes have been identified as causing this lethality but several experiments indicate that additional HI
factors must exist. Cuykendall et al. use the Bloomington Deficiency Kit to screen for suppressors of
hybrid male lethality. The authors find no major-effect HI loci on the D. melanogaster major autosomes,
but show that additional HI factor(s) on the D. melanogaster X chromosome are likely to exist.
2461–2471
Prevalence, Evolution, and cis-Regulation of Diel Transcription in Chlamydomonas reinhardtii
Nicholas Panchy, Guangxi Wu, Linsey Newton, Chia-Hong Tsai, Jin Chen, Christoph Benning,
Eva M. Farré, and Shin-Han Shiu
Light-dark cycles are known to entrain gene expression. The authors found that in the green alga
Chlamydomonas reinhardtii almost half of the transcriptome exhibits a cyclic pattern of expression in
response to alternating periods of light and dark. The timing of this cyclic expression pattern is highly
correlated with gene function as well as major biological processes such as DNA replication and cell division.
Additionally, the authors found that duplicate cycling genes preferentially retain the same or similar timing
of cyclic expression and that this timing may be controlled, in part, by putative cis-regulatory elements.
2473–2481
Association Mapping of Disease Resistance Traits in Rainbow Trout Using Restriction
Site Associated DNA Sequencing
Nathan R. Campbell, Scott E. LaPatra, Ken Overturf, Richard Towner, and Shawn R. Narum
This study utilizes the RAD sequencing technique to identify thousands of SNP loci within an
aquaculture strain of rainbow trout. Genotypes collected at these loci were then used to test for
association with resistance to IHN virus and bacterial cold water disease. The study identifies 31 RAD
markers associated with disease resistance.
2483–2492
Characterization of the Mutagenic Spectrum of 4-Nitroquinoline 1-Oxide (4-NQO) in Aspergillus
nidulans by Whole Genome Sequencing
Damien J. Downes, Mark Chonofsky, Kaeling Tan, Brandon T. Pfannenstiel, Samara L. Reck-Peterson,
and Richard B. Todd
The potent mutagen 4-nitroquinoline 1-oxide (4-NQO) is used to generate mutants for genetic screens.
Whole genome sequencing of Aspergillus nidulans mutant strains was used to reveal the full spectrum of
effects of 4-NQO mutagenesis. The number of mutations in surviving strains was not affected by dose,
and 4-NQO mutations were not biased by genome location or flanking sequence. 4-NQO induced all six
transitions and transversions with a 19-fold preference for mutation of guanine over adenine. Using
these data, the authors predict that gene saturation in A. nidulans genetic screens is readily attainable.
2493–2503
A Shigella flexneri Virulence Plasmid Encoded Factor Controls Production of Outer
Membrane Vesicles
Saima Sidik, Haila Kottwitz, Jeremy Benjamin, Julie Ryu, Ameer Jarrar,
Rafael Garduno, and John R. Rohde
Shigella flexneri is the causative agent of bacillary dysentery, also referred to as shigellosis. Virulence for
S. flexneri is mediated by genes coded on extra-chromosomal DNA known as the virulence plasmid
pWR100. pWR100 encodes many genes whose functions are unknown or partially characterized. The
authors constructed a collection of precise mutants for the genes on the virulence plasmid and validated
their collection, using it to ascribe new functions for virK. This collection will allow for a systematic
analysis of phenotypes associated with S. flexneri virulence.
2505–2518
Spatial Localization of Recent Ancestors for Admixed Individuals
Wen-Yun Yang, Alexander Platt, Charleston Wen-Kai Chiang, Eleazar Eskin, John Novembre,
and Bogdan Pasaniuc
Ancestry analysis from genetic data plays a critical role in studies of human disease and evolution.
Yang et al. introduce methods that model admixture between ancestors from multiple sources across
a geographic continuum. The authors devise efficient algorithms based on hidden Markov models to
localize on a map the recent ancestors (e.g. grandparents) of admixed individuals, joint with assigning
ancestry at each locus in the genome.
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2519–2533
Quantitative Trait Locus Mapping of Melanization in the Plant Pathogenic Fungus
Zymoseptoria tritici
Mark H. Lendenmann, Daniel Croll, Ethan L. Stewart, and Bruce A. McDonald
Lendenmann et al. characterized the genetic architecture of melanization in two crosses of the wheat
pathogenic fungus Zymoseptoria tritici and identified 15 significant quantitative trait loci. Comparison
of complete genome sequences led the authors to identify 16 candidate genes likely to affect
melanization. One of these was PKS1, the polyketide synthase enzyme catalyzing the first step of DHN
melanin synthesis. A candidate polymorphism was identified in the nucleotide sequence of PKS1. Most
of the remaining candidate genes were not previously associated with melanization, suggesting novel
genes affecting melanin synthesis in fungi.
2535–2543
Regulation of Synaptic Transmission at the Caenorhabditis elegans M4 Neuromuscular Junction
by an Antagonistic Relationship Between Two Calcium Channels
Mark Steciuk, Mi Cheong, Christopher Waite, Young-Jai You, and Leon Avery
To identify genes that negatively regulate synaptic transmission, Steciuk et al. looked for C. elegans
mutants that enhance communication from motor neuron M4 to pharyngeal muscle. To the authors'
surprise, these suppressors included null mutations in NPQR-type calcium channel subunit genes unc-2
and unc-36. These results are consistent with the hypothesis that Ca2+ entry through the NPQR-type
channel inhibits synaptic transmission by activating the calcium-activated K+ channel SLO-1, thus
antagonizing the EGL-19 L-type calcium channel.
2545–2552
Correcting for Sequencing Error in Maximum Likelihood Phylogeny Inference
Mary K. Kuhner and James McGill
Felsenstein proposed a correction for DNA sequencing error in maximum likelihood phylogeny
estimation, but it has not been widely used. Researchers may fear that an inaccurate estimate of
sequencing error is worse than nothing. Kuhner and McGill use simulated data to show that the
correction improves recovery of times in the inferred tree—critical for accurate dating of evolutionary
events—even if the assumed sequencing error rate is up to two times too high. The authors recommend
that researchers measure their sequencing error rates and use an appropriate correction rather than
ignoring the issue.
2553
2555–2557
CORRIGENDUM
REVIEWER INDEX
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