Contents December 2014 • VOLUME 4 • ISSUE 12 • 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. Volume 4 | December 2014 | ii 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. iii | Contents 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. Volume 4 | December 2014 | iv 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. v | Contents 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 Volume 4 | December 2014 | vi
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