From animal domestication to human genome variation, from loblolly genomes to lager genomes, from wild zebrafish sex to untangled metagenomes, last year brought plenty of high points for the GSA journals. So gathering a small selection of those high points into the 2014 Spotlight booklets was a challenging, but rewarding task for the editors of GENETICS and G3. Each Spotlight is a showcase of the excellent research and scholarship published over the course of the year, along with a selection of striking images submitted by our authors.

Enjoy the 2014 Spotlights at the linked images below. Full text of the articles featured in Spotlight are also available below. You can also browse the 2013 GENETICS Spotlight and the 2013 G3 Spotlight.


GENETICS Spotlight cover:
In 2014, Zimin et al. and Wegrzyn et al. reported the 23-Gb reference sequence of the loblolly pine, the largest genome sequenced and assembled to date.
Image courtesy of Ron Billings, Texas A&M Forest Service.


G3 Spotlight Cover:
In 1883, Emil Christian Hansen isolated the first pure lager yeast strain, Saccharomyces carlsbergensis. In 2014, Walther et al. assembled the genome of S. carlsbergensis. This artwork shows Hansen, his signature, and Circos presentations of the genome. Image courtesy of Andrea Walther.

 

GENETICS SPOTLIGHT CITATIONS:

CELLULAR GENETICS

Menzel J., M.E. Malo, C. Chan, M. Prusinkiewicz, T. G. Arnason & T. A. A. Harkness (2014). The Anaphase Promoting Complex Regulates Yeast Lifespan and rDNA Stability by Targeting Fob1 for Degradation, Genetics, 196 (3) 693-709. DOI: 10.1534/genetics.113.158949 http://www.genetics.org/content/196/3/693.full

COMPLEX TRAITS

Li Y., R. Cheng, K. A. Spokas, A. A. Palmer & J. O. Borevitz (2014). Genetic Variation for Life History Sensitivity to Seasonal Warming in Arabidopsis thaliana, Genetics, 196 (2) 569-577. DOI: 10.1534/genetics.113.157628 http://www.genetics.org/content/196/2/569.full

DEVELOPMENTAL & BEHAVIORAL GENETICS

Hoover C.M., S.L. Edwards, S.-c. Yu, M. Kittelmann, J. E. Richmond, S. Eimer, R. M. Yorks & K. G. Miller (2014). A Novel CaM Kinase II Pathway Controls the Location of Neuropeptide Release from Caenorhabditis elegans Motor Neurons, Genetics, 196 (3) 745-765. DOI: 10.1534/genetics.113.158568 http://www.genetics.org/content/196/3/745.full

COMMENTARY

Nurrish S. (2014). Dense Core Vesicle Release: Controlling the Where as Well as the When, Genetics, 196 (3) 601-604. DOI: 10.1534/genetics.113.159905 http://www.genetics.org/content/196/3/601.full

GENE EXPRESSION

Wang G., E. Yang, C. L. Brinkmeyer-Langford & J. J. Cai (2014). Additive, Epistatic, and Environmental Effects Through the Lens of Expression Variability QTL in a Twin Cohort, Genetics, 196 (2) 413-425. DOI: 10.1534/genetics.113.157503 http://www.genetics.org/content/196/2/413.full

GENETICS OF SEX

Wilson C.A., S.K. High, B. M. McCluskey, A. Amores, Y.-l. Yan, T. A. Titus, J. L. Anderson, P. Batzel, M. J. Carvan, M. Schartl & J. H. Postlethwait (2014). Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains, Genetics, 198 (3) 1291-1308. DOI: 10.1534/genetics.114.169284 http://www.genetics.org/content/198/3/1291.full

GENOME & SYSTEMS BIOLOGY

Reed L.K., K. Lee, Z. Zhang, L. Rashid, A. Poe, B. Hsieh, N. Deighton, N. Glassbrook, R. Bodmer & G. Gibson (2014). Systems Genomics of Metabolic Phenotypes in Wild-Type Drosophila melanogaster, Genetics, 197 (2) 781-793. DOI: 10.1534/genetics.114.163857 http://www.genetics.org/content/197/2/781.full

GENOME INTEGRITY & TRANSMISSION

Bauerly E., S. E. Hughes, D. R. Vietti, D. E. Miller, W. McDowell & R. S. Hawley (2014). Discovery of Supernumerary B Chromosomes in Drosophila melanogaster, Genetics, 196 (4) 1007-1016. DOI: 10.1534/genetics.113.160556 http://www.genetics.org/content/196/4/1007.full

Vrooman L.A., S.I. Nagaoka, T. J. Hassold & P. A. Hunt (2014). Evidence for Paternal Age-Related Alterations in Meiotic Chromosome Dynamics in the Mouse, Genetics, 196 (2) 385-396. DOI: 10.1534/genetics.113.158782 http://www.genetics.org/content/196/2/385.full

METHODS, TECHNOLOGY, & RESOURCES

Raj A., M. Stephens & J. K. Pritchard (2014). fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets, Genetics, 197 (2) 573-589. DOI: 10.1534/genetics.114.164350 http://www.genetics.org/content/197/2/573.full

PERSPECTIVES

Wilkins A.S., R.W. Wrangham & W. T. Fitch (2014). The “Domestication Syndrome” in Mammals: A Unified Explanation Based on Neural Crest Cell Behavior and Genetics, Genetics, 197 (3) 795-808. DOI: 10.1534/genetics.114.165423 http://www.genetics.org/content/197/3/795.full

POPULATION & EVOLUTIONARY GENETICS

de Vladar H.P. & N. Barton (2014). Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation, Genetics, 197 (2) 749-767. DOI: 10.1534/genetics.113.159111 http://www.genetics.org/content/197/2/749.full

Frenkel E.M., B.H. Good & M. M. Desai (2014). The Fates of Mutant Lineages and the Distribution of Fitness Effects of Beneficial Mutations in Laboratory Budding Yeast Populations, Genetics, 196 (4) 1217-1226. DOI: 10.1534/genetics.113.160069 http://www.genetics.org/content/196/4/1217.full

PRIMERS

Duina A.A., M.E. Miller & J. B. Keeney (2014). Budding Yeast for Budding Geneticists: A Primer on the Saccharomyces cerevisiae Model System, Genetics, 197 (1) 33-48. DOI: 10.1534/genetics.114.163188 http://www.genetics.org/content/197/1/33.full

STATISTICAL GENETICS & GENOMICS

Hormozdiari F., E. Kostem, E. Y. Kang, B. Pasaniuc & E. Eskin (2014). Identifying Causal Variants at Loci with Multiple Signals of Association, Genetics, 198 (2) 497-508. DOI: 10.1534/genetics.114.167908 http://www.genetics.org/content/198/2/497.full

METHODS, TECHNOLOGY, & RESOURCES: CRISPR

Gratz S.J., F.P. Ukken, C. D. Rubinstein, G. Thiede, L. K. Donohue, A. M. Cummings & K. M. O’Connor-Giles (2014). Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair in Drosophila, Genetics, 196 (4) 961-971. DOI: 10.1534/genetics.113.160713 http://www.genetics.org/content/196/4/961.full

Li M., H. Yang, J. Zhao, L. Fang, H. Shi, M. Li, Y. Sun, X. Zhang, D. Jiang, L. Zhou & D. Wang & (2014). Efficient and Heritable Gene Targeting in Tilapia by CRISPR/Cas9, Genetics, 197 (2) 591-599. DOI: 10.1534/genetics.114.163667 http://www.genetics.org/content/197/2/591.full

Kim H., T. Ishidate, K. S. Ghanta, M. Seth, D. Conte, M. Shirayama & C. C. Mello (2014). A Co-CRISPR Strategy for Efficient Genome Editing in Caenorhabditis elegans, Genetics, 197 (4) 1069-1080. DOI: 10.1534/genetics.114.166389 http://www.genetics.org/content/197/4/1069.full

Arribere J.A., R.T. Bell, B. X. H. Fu, K. L. Artiles, P. S. Hartman & A. Z. Fire (2014). Efficient Marker-Free Recovery of Custom Genetic Modifications with CRISPR/Cas9 in Caenorhabditis elegans, Genetics, 198 (3) 837-846. DOI: 10.1534/genetics.114.169730 http://www.genetics.org/content/198/3/837.full

Paix A., Y. Wang, H. E. Smith, C.-Y. S. Lee, D. Calidas, T. Lu, J. Smith, H. Schmidt, M. W. Krause & G. Seydoux (2014). Scalable and Versatile Genome Editing Using Linear DNAs with Microhomology to Cas9 Sites in Caenorhabditis elegans, Genetics, 198 (4) 1347-1356. DOI: 10.1534/genetics.114.170423 http://www.genetics.org/content/198/4/1347.full

SPOTLIGHT IMAGES

Zimin A., K.A. Stevens, M. W. Crepeau, A. Holtz-Morris, M. Koriabine, G. Marcais, D. Puiu, M. Roberts, J. L. Wegrzyn, P. J. de Jong, D. B. Neale, S.L. Salzberg, J.A. Yorke & C.H. Langley (2014). Sequencing and Assembly of the 22-Gb Loblolly Pine Genome, Genetics, 196 (3) 875-890. DOI: 10.1534/genetics.113.159715 http://www.genetics.org/content/196/3/875.full

Wegrzyn J.L., J.D. Liechty, K. A. Stevens, L.-S. Wu, C. A. Loopstra, H. A. Vasquez-Gross, W. M. Dougherty, B. Y. Lin, J. J. Zieve, P. J. Martínez-García, C. Holt, M. Yandell, A.V. Zimin, J.A. Yorke, M.W. Crepeau, D. Puiu, S.L. Salzberg, P.J. de Jong, K. Mockaitis, D. Main, C.H. Langley & D.B. Neale (2014). Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation, Genetics, 196 (3) 891-909. DOI: 10.1534/genetics.113.159996 http://www.genetics.org/content/196/3/891.full

Stronach B., A.L. Lennox & R. A. Garlena (2014). Domain Specificity of MAP3K Family Members, MLK and Tak1, for JNK Signaling in Drosophila, Genetics, 197 (2) 497-513. DOI: 10.1534/genetics.113.160937 http://www.genetics.org/content/197/2/497.full

Wilkening S., G. Lin, E. S. Fritsch, M. M. Tekkedil, S. Anders, R. Kuehn, M. Nguyen, R. S. Aiyar, M. Proctor, N. A. Sakhanenko, D. J. Galas, J. Gagneur, A. Deutschbauer & L.M. Steinmetz (2014). An Evaluation of High-Throughput Approaches to QTL Mapping in Saccharomyces cerevisiae, Genetics, 196 (3) 853-865. DOI: 10.1534/genetics.113.160291 http://www.genetics.org/content/196/3/853.full

Bannister S., O. Antonova, A. Polo, C. Lohs, N. Hallay, A. Valinciute, F. Raible & K. Tessmar-Raible (2014). TALENs Mediate Efficient and Heritable Mutation of Endogenous Genes in the Marine Annelid Platynereis dumerilii, Genetics, 197 (1) 77-89. DOI: 10.1534/genetics.113.161091 http://www.genetics.org/content/197/1/77.full

Zantke J., S. Bannister, V. B. V. Rajan, F. Raible & K. Tessmar-Raible (2014). Genetic and Genomic Tools for the Marine Annelid Platynereis dumerilii, Genetics, 197 (1) 19-31. DOI: 10.1534/genetics.112.148254 http://www.genetics.org/content/197/1/19.full

LaFave M.C., G.K. Varshney, M. Vemulapalli, J. C. Mullikin & S. M. Burgess (2014). A Defined Zebrafish Line for High-Throughput Genetics and Genomics: NHGRI-1, Genetics, 198 (1) 167-170. DOI: 10.1534/genetics.114.166769 http://www.genetics.org/content/198/1/167.full

Brooks S.S., A.L. Wall, C. Golzio, D. W. Reid, A. Kondyles, J. R. Willer, C. Botti, C. V. Nicchitta, N. Katsanis & E. E. Davis (2014). A Novel Ribosomopathy Caused by Dysfunction of RPL10 Disrupts Neurodevelopment and Causes X-Linked Microcephaly in Humans, Genetics, 198 (2) 723-733. DOI: 10.1534/genetics.114.168211 http://www.genetics.org/content/198/2/723.full

 

G3 SPOTLIGHT CITATIONS: 

INVESTIGATIONS

Burton J.N., I. Liachko, M. J. Dunham & J. Shendure (2014). Species-Level Deconvolution of Metagenome Assemblies with Hi-C-Based Contact Probability Maps, G3, 4 (7) 1339-1346. DOI: 10.1534/g3.114.011825 http://www.g3journal.org/content/4/7/1339.full

Atencio D., C. Barnes, T. M. Duncan, I. M. Willis & S. D. Hanes (2014). The Yeast Ess1 Prolyl Isomerase Controls Swi6 and Whi5 Nuclear Localization, G3, 4 (3) 523-537. DOI: 10.1534/g3.113.008763 http://www.g3journal.org/content/4/3/523.full

Mezmouk S. & J. Ross-Ibarra (2014). The Pattern and Distribution of Deleterious Mutations in Maize, G3, 4 (1) 163-171. DOI: 10.1534/g3.113.008870 http://www.g3journal.org/content/4/1/163.full

Spivakov M., T.O. Auer, R. Peravali, I. Dunham, D. Dolle, A. Fujiyama, A. Toyoda, T. Aizu, Y. Minakuchi, F. Loosli & K. Naruse, E. Birney & J. Wittbrodt (2014). Genomic and Phenotypic Characterization of a Wild Medaka Population: Towards the Establishment of an Isogenic Population Genetic Resource in Fish, G3, 4 (3) 433-445. DOI: 10.1534/g3.113.008722 http://www.g3journal.org/content/4/3/433.full

Glater E.E., M.V. Rockman & C. I. Bargmann (2014). Multigenic Natural Variation Underlies Caenorhabditis elegans Olfactory Preference for the Bacterial Pathogen Serratia marcescens, G3, 4 (2) 265-276. DOI: 10.1534/g3.113.008649 http://www.g3journal.org/content/4/2/265.full

Hahn M.W., S.V. Zhang & L. C. Moyle (2014). Sequencing, Assembling, and Correcting Draft Genomes Using Recombinant Populations, G3, 4 (4) 669-679. DOI: 10.1534/g3.114.010264 http://www.g3journal.org/content/4/4/669.full

Rajagopal N., J. Ernst, P. Ray, J. Wu, M. Zhang, M. Kellis & B. Ren (2014). Distinct and Predictive Histone Lysine Acetylation Patterns at Promoters, Enhancers, and Gene Bodies, G3, 4 (11) 2051-2063. DOI: 10.1534/g3.114.013565 http://www.g3journal.org/content/4/11/2051.full

Engel S.R., F.S. Dietrich, D. G. Fisk, G. Binkley, R. Balakrishnan, M. C. Costanzo, S. S. Dwight, B. C. Hitz, K. Karra, R. S. Nash, S. Weng, E.D. Wong, P. Lloyd, M.S. Skrzypek, S.R. Miyasato, M. Simison & J.M. Cherry (2014). The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now, G3, 4 (3) 389-398. DOI: 10.1534/g3.113.008995 http://www.g3journal.org/content/4/3/389.full

Rice W.R. (2014). An X-Linked Sex Ratio Distorter in Drosophila simulans That Kills or Incapacitates Both Noncarrier Sperm and Sons, G3, 4 (10) 1837-1848. DOI: 10.1534/g3.114.013292 http://www.g3journal.org/content/4/10/1837.full

Rogers R.L., L. Shao, J. S. Sanjak, P. Andolfatto & K. R. Thornton (2014). Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster Group, G3, 4 (12) 2345-2351. DOI: 10.1534/g3.114.013532 http://www.g3journal.org/content/4/12/2345.full

Pang A.W.C., J.R. MacDonald, R. K. C. Yuen, V. M. Hayes & S. W. Scherer (2014). Performance of High-Throughput Sequencing for the Discovery of Genetic Variation Across the Complete Size Spectrum, G3, 4 (1) 63-65. DOI: 10.1534/g3.113.008797 http://www.g3journal.org/content/4/1/63.full

Vaughn J.N., R.L. Nelson, Q. Song, P. B. Cregan & Z. Li (2014). The Genetic Architecture of Seed Composition in Soybean Is Refined by Genome-Wide Association Scans Across Multiple Populations, G3, 4 (11) 2283-2294. DOI: 10.1534/g3.114.013433 http://www.g3journal.org/content/4/11/2283.full

Walther A., A. Hesselbart & J. Wendland (2014). Genome Sequence of Saccharomyces carlsbergensis, the World’s First Pure Culture Lager Yeast, G3, 4 (5) 783-793. DOI: 10.1534/g3.113.010090 http://www.g3journal.org/content/4/5/783.full

MUTANT SCREEN REPORT

Hayashi R., S.M. Wainwright, S. J. Liddell, S. M. Pinchin, S. Horswell & D. Ish-Horowicz (2014). A Genetic Screen Based on in Vivo RNA Imaging Reveals Centrosome-Independent Mechanisms for Localizing gurken Transcripts in Drosophila, G3, 4 (4) 749-760. DOI: 10.1534/g3.114.010462 http://www.g3journal.org/content/4/4/749.full

SPOTLIGHT IMAGES

Lehnert E.M., M.E. Mouchka, M. S. Burriesci, N. D. Gallo, J. A. Schwarz & J. R. Pringle (2014). Extensive Differences in Gene Expression Between Symbiotic and Aposymbiotic Cnidarians, G3, 4 (2) 277-295. DOI: 10.1534/g3.113.009084 http://www.g3journal.org/content/4/2/277.full

Jovelin R., J.S. Comstock, A. D. Cutter & P. C. Phillips (2014). A Recent Global Selective Sweep on the age-1 Phosphatidylinositol 3-OH Kinase Regulator of the Insulin-Like Signaling Pathway Within Caenorhabditis remanei, G3, 4 (6) 1123-1133. DOI: 10.1534/g3.114.010629 http://www.g3journal.org/content/4/6/1123.full

Sikkink K.L., R.M. Reynolds, C. M. Ituarte, W. A. Cresko & P. C. Phillips (2014). Rapid Evolution of Phenotypic Plasticity and Shifting Thresholds of Genetic Assimilation in the Nematode Caenorhabditis remanei, G3, 4 (6) 1103-1112. DOI: 10.1534/g3.114.010553 http://www.g3journal.org/content/4/6/1103.full

INVESTIGATIONS: CRISPR

Xue Z., M. Ren, M. Wu, J. Dai, Y. S. Rong & G. Gao (2014). Efficient Gene Knock-out and Knock-in with Transgenic Cas9 in Drosophila, G3, 4 (5) 925-929. DOI: 10.1534/g3.114.010496 http://www.g3journal.org/content/4/5/925.full

Lee J.S., S.-J. Kwak, J. Kim, A.-K. Kim, H. M. Noh, J.-S. Kim & K. Yu (2014). RNA-Guided Genome Editing in Drosophila with the Purified Cas9 Protein, G3, 4 (7) 1291-1295. DOI: 10.1534/g3.114.012179 http://www.g3journal.org/content/4/7/1291.full

Ren X., Z. Yang, D. Mao, Z. Chang, H.-H. Qiao, X. Wang, J. Sun, Q. Hu, Y. Cui, L.-P. Liu, J.-Y. Ji, J. Xu & J.-Q Ni (2014). Performance of the Cas9 Nickase System in Drosophila melanogaster, G3, 4 (10) 1955-1962. DOI: 10.1534/g3.114.013821 http://www.g3journal.org/content/4/10/1955.full

Xue Z., M. Wu, K. Wen, M. Ren, L. Long, X. Zhang & G. Gao (2014). CRISPR/Cas9 Mediates Efficient Conditional Mutagenesis in Drosophila, G3, 4 (11) 2167-2173. DOI: 10.1534/g3.114.014159 http://www.g3journal.org/content/4/11/2167.full

Gokcezade J., G. Sienski & P. Duchek (2014). Efficient CRISPR/Cas9 Plasmids for Rapid and Versatile Genome Editing in Drosophila, G3, 4 (11) 2279-2282. DOI: 10.1534/g3.114.014126 http://www.g3journal.org/content/4/11/2279.full

Upadhyay S.K., J. Kumar, A. Alok & R. Tuli (2014). RNA-Guided Genome Editing for Target Gene Mutations in Wheat, G3, 3 (12) 2233-2238. DOI: 10.1534/g3.113.008847 http://www.g3journal.org/content/3/12/2233.full

Vilain S., R. Vanhauwaert, Maes, N. Schoovaerts, L. Zhou, S. Soukup, R. da Cunha, E. Lauwers, M. Fiers & P. Verstreken (2014). Fast and Efficient Drosophila melanogaster Gene Knock-Ins Using MiMIC Transposons, G3, 4 (12) 2381-2387. DOI: 10.1534/g3.114.014803 http://www.g3journal.org/content/4/12/2381.full

Zhang X., W.H. Koolhaas & F. Schnorrer (2014). A Versatile Two-Step CRISPR- and RMCE-Based Strategy for Efficient Genome Engineering in Drosophila, G3, 4 (12) 2409-2418. DOI: 10.1534/g3.114.013979 http://www.g3journal.org/content/4/12/2409.full

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Cristy Gelling is a science writer, lapsed yeast geneticist, and former Communications Director at the GSA.

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