Article
Biochemistry & Molecular Biology
Peng Liu, Jessica Ewald, Jose Hector Galvez, Jessica Head, Doug Crump, Guillaume Bourque, Niladri Basu, Jianguo Xia
Summary: Seq2Fun is a fast and efficient tool for RNA-seq data analysis, capable of performing functional quantification directly without transcriptome de novo assembly. It can quickly process large numbers of reads and generate various informative output results.
Article
Biochemical Research Methods
Erin H. Wilson, Joseph D. Groom, M. Claire Sarfatis, Stephanie M. Ford, Mary E. Lidstrom, David A. C. Beck
Summary: This study developed a computational framework to identify constitutively, strongly expressed genes and predict strong promoter signals using standard RNA-seq data sets. The framework was applied to methanotroph Methylotuvimicrobium buryatense 5GB1, identifying 25 genes with high expression levels across diverse experimental conditions. The predicted promoter motifs were experimentally validated and found to be biologically meaningful for engineering diverse microorganisms for biomolecule production.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Biochemical Research Methods
Ray Westenberg, Pamela Peralta-Yahya
Summary: Decarboxylation reduces the carbon yield of bioproduced chemicals. Implementing CO2 release can increase carbon yields for certain intermediates. Nonmodel hosts offer greater opportunities for implementing CCNs due to their ability to assimilate a wider range of feedstocks and unique biosynthetic pathways.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)
Article
Ecology
Yara A. Alshwairikh, Shayla L. Kroeze, Jenny Olsson, Steve A. Stephens-Cardenas, William L. Swain, Lisette P. Waits, Rebekah L. Horn, Shawn R. Narum, Travis Seaborn
Summary: By conducting genome-environment association studies, it was found that the environmental variation experienced throughout migration corridors had a greater impact on selection for Chinook salmon than the environmental conditions at spawning sites.
ECOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Shuang Ren, Guangqi Lyu, David M. Irwin, Xin Liu, Chunyu Feng, Runhong Luo, Junpeng Zhang, Yongfeng Sun, Songyang Shang, Shuyi Zhang, Zhe Wang
Summary: This study identified genes that potentially regulate feather color in geese through whole-genome resequencing, revealing molecular mechanisms underlying the change in feather color during the domestication of geese. The results expand the catalog of potential feather color regulators in geese, providing a basis for further research.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Guangqi Lyu, Chunyu Feng, Shiyu Zhu, Shuang Ren, Wanyi Dang, David M. Irwin, Zhe Wang, Shuyi Zhang
Summary: The difference in body size in Shiba Inu breeds may be related to candidate genes and specific sites, with 8 new genes requiring further study.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Juan Li, Liangfa Wang, Jiong Wan, Kuntai Dang, Yuan Lin, Shujun Meng, Xiaoqian Qiu, Qiyue Wang, Jiawen Zhao, Liqin Mu, Hongbing Luo, Dong Ding, Zehui Chen, Jihua Tang
Summary: This study found that seed coat heterosis in maize hybrids might be the result of the coordination between cell number and cell size. RNA-seq results showed significant changes in nonadditive genes between 0 day and 15 days, while the expression of additive genes did not differ significantly. Gene ontology and pathway enrichment analysis indicated that genes related to DNA replication, cell cycle regulation, circadian rhythms, and metabolite accumulation played a significant role in hybrid seed coat heterosis. These findings provide evidence for genes involved in hybrid seed coat heterosis.
Article
Multidisciplinary Sciences
Yusuke Oizumi, Takuto Kaji, Sanki Tashiro, Yumiko Takeshita, Yuko Date, Junko Kanoh
Summary: The complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe were reported, revealing highly polymorphic and hot spots for genome variation features. These subtelomeric regions may contribute to genome diversity and potentially lead to various diseases.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Floriane Coulmance, Derya Akkaynak, Yann Le Poul, Marc P. Hoeppner, W. Owen McMillan, Oscar Puebla
Summary: Coral reefs are known for their high species diversity, especially the vibrant color patterns displayed by reef fishes. This study focuses on hamlets as a model system to analyze the complex trait of color pattern using a custom underwater camera system and whole-genome sequencing. The results suggest that the diversity of color patterns in hamlets is determined by a modular genomic and phenotypic architecture.
Article
Biochemistry & Molecular Biology
Jinxi Li, James D. Glover, Haiguo Zhang, Meifang Peng, Jingze Tan, Chandana Basu Mallick, Dan Hou, Yajun Yang, Sijie Wu, Yu Liu, Qianqian Peng, Shijie C. Zheng, Edie Crosse, Alexander Medvinsky, Richard A. Anderson, Helen Brown, Ziyu Yuan, Shen Zhou, Yanqing Xu, John P. Kemp, Yvonne Y. W. Ho, Danuta Z. Loesch, Lizhong Wang, Yingxiang Li, Senwei Tang, Xiaoli Wu, Robin G. Walters, Kuang Lin, Ruogu Meng, Jun Lv, Jonathan M. Chernus, Katherine Neiswanger, Eleanor Feingold, David M. Evans, Sarah E. Medland, Nicholas G. Martin, Seth M. Weinberg, Mary L. Marazita, Gang Chen, Zhengming Chen, Yong Zhou, Michael Cheeseman, Lan Wang, Li Jin, Denis J. Headon, Sijia Wang
Summary: This study conducted genome-wide scans in Han Chinese cohorts and identified 18 loci associated with fingerprint type, as well as a genetic basis for the recognized pattern-block correlations. Additionally, a variant near EVI1 was found to alter regulatory activity and play a role in dermatoglyph patterning. Trans-ethnic meta-analysis identified 43 fingerprint-associated loci and revealed a genetic correlation between fingerprint patterns and hand proportions. These findings highlight the importance of limb development genes in shaping fingerprint patterning.
Article
Plant Sciences
Najla Ksouri, Jaime A. Castro-Mondragon, Francesc Montardit-Tarda, Jacques van Helden, Bruno Contreras-Moreira, Yolanda Gogorcena
Summary: This study presents a bottom-up approach for de novo motif discovery using peach as an example, revealing a large number of transcription factor families and some unknown motifs. The method was validated on different plant species by testing two different clustering algorithms, demonstrating its applicability across a range of plant species.
Article
Ecology
Arianna Passarotto, Emilio Rodriguez-Caballero, Angel Cruz-Miralles, Jesus M. Aviles
Summary: The study revealed that global patterns of color variation in owls do not fit the thermal melanism hypothesis but support Gloger's rule. It also emphasized that various alternative selective forces may explain climatic effects on coloration over large geographical scales.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Timothy E. Saunders, Anto Prime Nia Monteiro
Summary: New research on five lizard species shows that reaction-diffusion models can accurately predict future adult skin patterns, even without knowing the molecular details. This has implications for understanding the evolution of complex patterns.
Article
Biochemistry & Molecular Biology
Kelly Cochran, Divyanshi Srivastava, Avanti Shrikumar, Akshay Balsubramani, Ross C. Hardison, Anshul Kundaje, Shaun Mahony
Summary: The DNA sequence preferences and cooperative partners of transcription factors (TFs) are conserved across species. However, predicting TF binding in one species based on sequence models of a closely related species is challenging due to species-specific repeats. To address this challenge, researchers used neural networks to predict TF binding across species and found that the predictive performance was worse than within-species predictions. By using an augmented network architecture, they were able to correct for prediction errors caused by species-specific repeats and improve the overall cross-species model performance.
Article
Biochemistry & Molecular Biology
Yoshifumi Araki, Teiji Sota
Summary: The study on the geotrupid dung beetles in Japan reveals geographic color variations due to genetic clusters and specific gene loci affecting the expression of different color ranges. The transition zones between different colored forms suggest barriers to gene flow and regionally specific selection, allowing for the maintenance of color diversity within the species.
Article
Ecology
Aaron B. A. Shafer, Jochen B. W. Wolf, Paulo C. Alves, Linnea Bergstrom, Michael W. Bruford, Ioana Brannstrom, Guy Colling, Love Dalen, Luc De Meester, Robert Ekblom, Katie D. Fawcett, Simone Fior, Mehrdad Hajibabaei, Jason A. Hill, A. Rus Hoezel, Jacob Hoglund, Evelyn L. Jensen, Johannes Krause, Torsten N. Kristensen, Michael Kruetzen, John K. McKay, Anita J. Norman, Rob Ogden, E. Martin Osterling, N. Joop Ouborg, John Piccolo, Danijela Popovic, Craig R. Primmer, Floyd A. Reed, Marie Roumet, Jordi Salmona, Tamara Schenekar, Michael K. Schwartz, Gernot Segelbacher, Helen Senn, Jens Thaulow, Mia Valtonen, Andrew Veale, Philippine Vergeer, Nagarjun Vijay, Caries Vila, Matthias Weissensteiner, Lovisa Wennerstrom, Christopher W. Wheat, Piotr Zielinski
TRENDS IN ECOLOGY & EVOLUTION
(2015)
Article
Biochemistry & Molecular Biology
Naomi L. P. Keehnen, Jason Hill, Soeren Nylin, Christopher W. Wheat
Correction
Multidisciplinary Sciences
Camille Meslin, Tamara S. Cherwin, Melissa S. Plakke, Jason Hill, Brandon S. Small, Breanna J. Goetz, Christopher W. Wheat, Nathan I. Morehouse, Nathan L. Clark
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Biology
Christopher W. Wheat, Jason Hill
CURRENT OPINION IN INSECT SCIENCE
(2014)
Article
Ecology
Sumitha Nallu, Jason A. Hill, Kristine Don, Carlos Sahagun, Wei Zhang, Camille Meslin, Emilie Snell-Rood, Nathan L. Clark, Nathan I. Morehouse, Joy Bergelson, Christopher W. Wheat, Marcus R. Kronforst
NATURE ECOLOGY & EVOLUTION
(2018)
Article
Multidisciplinary Sciences
Jason Hill, Pasi Rastas, Emily A. Hornett, Ramprasad Neethiraj, Nathan Clark, Nathan Morehouse, Maria De La Paz Celorio-Mancera, Jofre Carnicer, Heinrich Dircksen, Camille Meslin, Naomi Keehnen, Peter Pruisscher, Kristin Sikkink, Maria Vives, Heiko Vogel, Christer Wiklund, Alyssa Woronik, Carol L. Boggs, Soren Nylin, Christopher W. Wheat
Article
Multidisciplinary Sciences
Jason Hill, Erik D. Enbody, Mats E. Pettersson, C. Grace Sprehn, Dorte Bekkevold, Arild Folkvord, Linda Laikre, Gunnar Kleinau, Patrick Scheerer, Leif Andersson
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Ecology
Sara Kurland, Christopher W. Wheat, Maria de la Paz Celorio Mancera, Verena E. Kutschera, Jason Hill, Anastasia Andersson, Carl-Johan Rubin, Leif Andersson, Nils Ryman, Linda Laikre
ECOLOGY AND EVOLUTION
(2019)
Article
Biochemistry & Molecular Biology
Mats E. Pettersson, Christina M. Rochus, Fan Han, Junfeng Chen, Jason Hill, Ola Wallerman, Guangyi Fan, Xiaoning Hong, Qiwu Xu, He Zhang, Shanshan Liu, Xin Liu, Leanne Haggerty, Toby Hunt, Fergal J. Martin, Paul Flicek, Ignas Bunikis, Arild Folkvord, Leif Andersson
Article
Multidisciplinary Sciences
Alyssa Woronik, Kalle Tunstrom, Michael W. Perry, Ramprasad Neethiraj, Constanti Stefanescu, Maria de la Paz Celorio-Mancera, Oskar Brattstrom, Jason Hill, Philipp Lehmann, Reijo Kakela, Christopher W. Wheat
NATURE COMMUNICATIONS
(2019)
Article
Multidisciplinary Sciences
Jason Hill, Mette Lillie, Mats E. Pettersson, Carl-Johan Rubin, B. Rosemary Grant, Peter R. Grant, Leif Andersson, Patric Jern
Summary: By studying Darwin's finches, researchers have discovered the genetic remnants of endogenous retroviruses (ERVs), shedding light on the historical interactions between retroviruses and their hosts. The study found significant variation in ERVs among different finch species, as well as variation across different islands, suggesting changes in gene flow and selection over time.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jason Hill, Erik D. Enbody, Huijuan Bi, Sangeet Lamichhaney, Weipan Lei, Juexin Chen, Chentao Wei, Yang Liu, Doreen Schwochow, Shady Younis, Fredrik Widemo, Leif Andersson
Summary: A paradox in evolutionary biology is how supergenes can maintain high fitness despite reduced effective population size, the suppression of recombination, and the expected accumulation of mutational load. The ruff supergene involves 2 rare inversion haplotypes (satellite and faeder). These are recessive lethals but with dominant effects on male mating strategies, plumage, and body size. Sequence divergence to the wild-type (independent) haplotype indicates that the inversion could be as old as 4 million years. Here, we have constructed a highly contiguous genome assembly of the inversion region for both the independent and satellite haplotypes. Based on the new data, we estimate that the recombination event(s) creating the satellite haplotype occurred only about 70,000 yr ago. Contrary to expectations for supergenes, we find no substantial expansion of repeats and only a modest mutation load on the satellite and faeder haplotypes despite high sequence divergence to the non-inverted haplotype (1.46%). The essential centromere protein N (CENPN) gene is disrupted by the inversion and is as well conserved on the inversion haplotypes as on the noninversion haplotype. These results suggest that the inversion may be much younger than previously thought. The low mutation load, despite recessive lethality, may be explained by the introgression of the inversion from a now extinct lineage.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)