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Biochemistry & Molecular Biology
Xavier Farre, Ruben Molina, Fabio Barteri, Paul R. H. J. Timmers, Peter K. Joshi, Baldomero Oliva, Sandra Acosta, Borja Esteve-Altava, Arcadi Navarro, Gerard Muntane
Summary: The study identified amino acid changes and genes related to longevity in mammals, with pathways involved in regulating lifespan. It also found that certain genes explain a larger fraction of human lifespan heritability than expected, with longevity-associated proteins being significantly more stable. Overall, the research demonstrates the potential of comparative genomics in enhancing understanding of human genome-wide association studies.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Gabrielle A. Hartley, Mariam Okhovat, Rachel J. O'Neill, Lucia Carbone
Summary: The study reveals dynamic shifts in the repeat content that define gibbon centromeres, with the presence of retroelements dominating the centromeric repeat sequences across gibbon genera. Hoolock centromeres show an independent evolutionary trajectory compared to other genera, with the presence of retroelement-derived macrosatellite SST1. Additionally, transcripts originating from gibbon centromeres recapitulate the species-specific TE composition, indicating evolutionary divergence within the gibbon lineage.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Siqian Chen, Shuli Liu, Shaolei Shi, Yifan Jiang, Mingyue Cao, Yongjie Tang, Wenlong Li, Jianfeng Liu, Lingzhao Fang, Ying Yu, Shengli Zhang
Summary: In this study, the researchers systematically analyzed functional genomic regulatory elements (REs) in the liver across six mammals and demonstrated their associations with gene expression, evolutionary conservation, and complex traits. By integrating large-scale GWAS and eQTLs data, they found that REs with different degrees of evolutionary conservation showed enrichment for GWAS signals of complex traits. This study is of great importance for understanding the genetic basis of complex traits in livestock and humans.
Article
Biochemistry & Molecular Biology
Jiankai Wei, Penghui Liu, Fuyun Liu, An Jiang, Jinghan Qiao, Zhongqi Pu, Bingrou Wang, Jin Zhang, Dongning Jia, Yuli Li, Shi Wang, Bo Dong
Summary: Evolutionary developmental biology (evo-devo) is an interdisciplinary field that aims to understand the origin and evolution of developmental processes in different animals. EDomics is a comparative multi-omics database that provides comprehensive genomic, transcriptomic, and single-cell data for 40 representative species. It offers valuable resources and customized datasets for evo-devo research, allowing researchers to decipher the history of developmental evolution across the tree of life.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Severin Uebbing, Jake Gockley, Steven K. Reilly, Acadia A. Kocher, Evan Geller, Neeru Gandotra, Curt Scharfe, Justin Cotney, James P. Noonan
Summary: Massively parallel enhancer assays in neural stem cells were used to quantify the functional impact of >32,000 human-specific substitutions in >4,300 human accelerated regions (HARs) and human gain enhancers (HGEs). Over 30% of active HARs and HGEs showed differential activity between human and chimpanzee, with human-specific substitutions interacting in additive and nonadditive ways to modify enhancer function. Substitutions in HARs, which are highly constrained compared to HGEs, had smaller effects on enhancer activity, indicating buffering of the impact of human-specific substitutions in enhancers with constrained ancestral functions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Emily R. Hager, Olivia S. Harringmeyer, T. Brock Wooldridge, Shunn Theingi, Jacob T. Gable, Sade McFadden, Beverly Neugeboren, Kyle M. Turner, Jeffrey D. Jensen, Hopi E. Hoekstra
Summary: This study characterized the genetic basis of trait variation in different ecotypes of deer mice and identified a chromosomal inversion linked to tail length and coat color. The frequency of the inversion was high in the forest ecotype, decreased across a habitat transition, and was absent in the prairie ecotype. Divergent selection was implicated in maintaining the inversion at observed frequencies despite high levels of gene flow, and the study explored the fitness benefits arising from suppressed recombination within the inversion.
Article
Microbiology
Daniel Castillo, Valentina L. Donati, Johanna Jorgensen, Krister Sundell, Inger Dalsgaard, Lone Madsen, Tom Wiklund, Mathias Middelboe
Summary: This study analyzed whole-genome sequences of 25 F. psychrophilum isolates from Baltic Sea countries and found a conserved population across these countries, with no clear association between genomic information and virulence traits. Analysis of four isolates at the whole-genome level revealed genetic variances in certain proteins and gene regions, providing insights into the genetic variation and potential role in modulating F. psychrophilum virulence.
Editorial Material
Multidisciplinary Sciences
Chris Amemiya
Summary: Genome sequencing and analysis of genomic interactions have revealed new insights into the evolution of the wing shapes in skates and rays, dating back over 200 million years.
Article
Multidisciplinary Sciences
Maya Wardeh, Marcus S. C. Blagrove, Kieran J. Sharkey, Matthew Baylis
Summary: By using a divide-and-conquer approach, researchers predicted over 20,000 unknown associations between known viruses and susceptible mammalian species, revealing a significant underestimation of associations in wild and semi-domesticated mammals by a factor of 4.3 and the potential mammalian host-range of viruses by a factor of 3.2. The study highlights a critical knowledge gap in the wild reservoirs of important zoonotic and domesticated mammals' viruses.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Jun Chen, Yu Zang, Shuo Liang, Song Xue, Shuai Shang, Meiling Zhu, Ying Wang, Xuexi Tang
Summary: This study sequenced and compared the mitochondrial genomes of Zostera japonica and Phyllospadix iwatensis, providing new evidence of genome size reduction, gene loss, and adaptive evolution in seagrasses. It found a large number of repeat sequences and extensive loss of ribosomal protein genes in seagrass species. Additionally, it identified positive selection genes associated with seagrass adaptation to the marine environment.
Article
Microbiology
Michela Ruinelli, Jochen Blom, Theo H. M. Smits, Joeel F. Pothier
Summary: A comparative genomics approach identified genes significantly associated with strains isolated from Prunus spp., with the HopAY gene predicted to encode a C58 cysteine protease being highly related to these strains, supporting co-evolution and host adaptation patterns.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Cell Biology
Renate L. M. Jansen, Carlos Santana-Molina, Marco van den Noort, Damien P. Devos, Ida J. van der Klei
Summary: PEX genes encode proteins involved in peroxisome biogenesis and proliferation. A comparative genomics approach was used to clarify the evolutionary relationships between the 37 known PEX proteins in a representative set of eukaryotes, defining the core set of PEX proteins required for peroxisome formation. The molecular processes in peroxisome biogenesis in different organisms were analyzed, showing that peroxisomes are not static organelles in eukaryotic evolution.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Nicole A. Fusco, Bradley J. Cosentino, James P. Gibbs, Maximilian L. Allen, Alexander J. Blumenfeld, George H. Boettner, Elizabeth J. Carlen, Merri Collins, Catherine Dennison, Devin Digiacopo, Andre-Philippe Drapeau Picard, Jonathan Edmonson, M. Caitlin Fisher-Reid, Rebecca Fyffe, Travis Gallo, Alannah Grant, William Harbold, Stephen B. Heard, Diana J. R. Lafferty, Richard M. Lehtinen, Shealyn Marino, John E. Mcdonald, Alessio Mortelliti, Maureen Murray, Amy Newman, Krista N. Oswald, Caitlin Ott-Conn, Jonathan L. Richardson, Rebecca Rimbach, Paul Salaman, Michael Steele, Mason R. Stothart, Mark C. Urban, Kurt Vandegrift, John P. Vanek, Sean N. Vanderluit, Lucie Vezina, Adalgisa Caccone
Summary: Urbanization influences genetic connectivity of eastern grey squirrels, but connected populations are still maintained in forested areas.
Article
Multidisciplinary Sciences
Nikolas L. Jorstad, Janet H. T. Song, David Exposito-Alonso, Hamsini Suresh, Nathan Castro-Pacheco, Fenna M. Krienen, Anna Marie Yanny, Jennie Close, Emily Gelfand, Brian Long, Stephanie C. Seeman, Kyle J. Travaglini, Soumyadeep Basu, Marc Beaudin, Darren Bertagnolli, Megan Crow, Song-Lin Ding, Jeroen Eggermont, Alexandra Glandon, Jeff Goldy, Katelyn Kiick, Thomas Kroes, Delissa Mcmillen, Trangthanh Pham, Christine Rimorin, Kimberly Siletti, Saroja Somasundaram, Michael Tieu, Amy Torkelson, Guoping Feng, William D. Hopkins, Thomas Hollt, C. Dirk Keene, Sten Linnarsson, Steven A. Mccarroll, Boudewijn P. Lelieveldt, Chet C. Sherwood, Kimberly Smith, Christopher A. Walsh, Alexander Dobin, Jesse Gillis, Ed S. Lein, Rebecca D. Hodge, Trygve E. Bakken
Summary: Our study used snRNA-seq to analyze the transcriptome of the cerebral cortex in humans and four nonhuman primate species. We found that cell types in the cerebral cortex are highly conserved among great apes, with marmosets showing some unique cell type proportions. Profiling gorillas allowed us to identify expression differences between humans and chimpanzees that are specialized in humans. We also discovered that neuronal gene expression has evolved faster on the human lineage, while glial expression changes have occurred rapidly in all species. Human-specific DEGs are enriched near adaptive genomic changes and may contribute to specialized cortical function.
Review
Plant Sciences
Kobra Yousefi, Siti Nor Akmar Abdullah, Muhammad Asyraf Md Hatta, Kong Lih Ling
Summary: Coconut is an economically important palm species that has been widely used by humans for a long time. Its unique nutritional and medicinal properties have gained renewed interest in recent years, however, the sustainable growth of the coconut industry has been hindered by a lack of good quality seedlings. Molecular biotechnological tools, such as molecular markers and next-generation sequencing, have the potential to accelerate genetic improvement efforts in coconut.
Editorial Material
Biochemistry & Molecular Biology
R. Sanders Williams, Samad Lotia, Alisha K. Holloway, Alexander R. Pico
Article
Biochemical Research Methods
Reuben Thomas, Sean Thomas, Alisha K. Holloway, Katherine S. Pollard
BRIEFINGS IN BIOINFORMATICS
(2017)
Article
Biochemistry & Molecular Biology
Luis Luna-Zurita, Christian U. Stirnimann, Sebastian Glatt, Bogac L. Kaynak, Sean Thomas, Florence Baudin, Md Abul Hassan Samee, Daniel He, Eric M. Small, Maria Mileikovsky, Andras Nagy, Alisha K. Holloway, Katherine S. Pollard, Christoph W. Mueller, Benoit G. Bruneau
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Biochemistry & Molecular Biology
Dennis Kostka, Alisha K. Holloway, Katherine S. Pollard
MOLECULAR BIOLOGY AND EVOLUTION
(2018)
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Genetics & Heredity
Jared C. Roach, Gustavo Glusman, Robert Hubley, Stephen Z. Montsaroff, Alisha K. Holloway, Denise E. Mauldin, Deepak Srivastava, Vidu Garg, Katherine S. Pollard, David J. Galas, Leroy Hood, Arian F. A. Smit
AMERICAN JOURNAL OF HUMAN GENETICS
(2011)
Article
Oncology
Erin E. Patterson, Alisha K. Holloway, Julie Weng, Tito Fojo, Electron Kebebew
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Biochemistry & Molecular Biology
Joseph A. Wamstad, Jeffrey M. Alexander, Rebecca M. Truty, Avanti Shrikumar, Fugen Li, Kirsten E. Eilertson, Huiming Ding, John N. Wylie, Alexander R. Pico, John A. Capra, Genevieve Erwin, Steven J. Kattman, Gordon M. Keller, Deepak Srivastava, Stuart S. Levine, Katherine S. Pollard, Alisha K. Holloway, Laurie A. Boyer, Benoit G. Bruneau
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Oncology
E. Patterson, R. Webb, A. Weisbrod, B. Bian, M. He, L. Zhang, A. K. Holloway, R. Krishna, N. Nilubol, K. Pacak, E. Kebebew
ENDOCRINE-RELATED CANCER
(2012)
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Genetics & Heredity
Charles H. Langley, Kristian Stevens, Charis Cardeno, Yuh Chwen G. Lee, Daniel R. Schrider, John E. Pool, Sasha A. Langley, Charlyn Suarez, Russell B. Corbett-Detig, Bryan Kolaczkowski, Shu Fang, Phillip M. Nista, Alisha K. Holloway, Andrew D. Kern, Colin N. Dewey, Yun S. Song, Matthew W. Hahn, David J. Begun
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Multidisciplinary Sciences
Kerstin Lindblad-Toh, Manuel Garber, Or Zuk, Michael F. Lin, Brian J. Parker, Stefan Washietl, Pouya Kheradpour, Jason Ernst, Gregory Jordan, Evan Mauceli, Lucas D. Ward, Craig B. Lowe, Alisha K. Holloway, Michele Clamp, Sante Gnerre, Jessica Alfoeldi, Kathryn Beal, Jean Chang, Hiram Clawson, James Cuff, Federica Di Palma, Stephen Fitzgerald, Paul Flicek, Mitchell Guttman, Melissa J. Hubisz, David B. Jaffe, Irwin Jungreis, W. James Kent, Dennis Kostka, Marcia Lara, Andre L. Martins, Tim Massingham, Ida Moltke, Brian J. Raney, Matthew D. Rasmussen, Jim Robinson, Alexander Stark, Albert J. Vilella, Jiayu Wen, Xiaohui Xie, Michael C. Zody, Kim C. Worley, Christie L. Kovar, Donna M. Muzny, Richard A. Gibbs, Wesley C. Warren, Elaine R. Mardis, George M. Weinstock, Richard K. Wilson, Ewan Birney, Elliott H. Margulies, Javier Herrero, Eric D. Green, David Haussler, Adam Siepel, Nick Goldman, Katherine S. Pollard, Jakob S. Pedersen, Eric S. Lander, Manolis Kellis
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Multidisciplinary Sciences
Nelle Lambert, Marie-Alexandra Lambot, Angeline Bilheu, Valerie Albert, Yvon Englert, Frederick Libert, Jean-Christophe Noel, Christos Sotiriou, Alisha K. Holloway, Katherine S. Pollard, Vincent Detours, Pierre Vanderhaeghen
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Multidisciplinary Sciences
Yin Xiong, Lisa Zhang, Alisha K. Holloway, Xiaolin Wu, Ling Su, Electron Kebebew
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Multidisciplinary Sciences
Sean Thomas, Jason G. Underwood, Elizabeth Tseng, Alisha K. Holloway
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Ecology
Abigail L. Lind, Yvonne Y. Y. Lai, Yulia Mostovoy, Alisha K. Holloway, Alessio Iannucci, Angel C. Y. Mak, Marco Fondi, Valerio Orlandini, Walter L. Eckalbar, Massimo Milan, Michail Rovatsos, Ilya G. Kichigin, Alex Makunin, Martina Johnson Pokorna, Marie Altmanova, Vladimir A. Trifonov, Elio Schijlen, Lukas Kratochvil, Renato Fani, Petr Velensky, Ivan Rehak, Tomaso Patarnello, Tim S. Jessop, James W. Hicks, Oliver A. Ryder, Joseph R. Mendelson, Claudio Ciofi, Pui-Yan Kwok, Katherine S. Pollard, Benoit G. Bruneau
NATURE ECOLOGY & EVOLUTION
(2019)