Article
Plant Sciences
Zhiyan Gao, Xingyu Yang, Jinming Chen, Mark D. Rausher, Tao Shi
Summary: Cis- and trans-regulatory variations play distinct roles in lotus flower color evolution, with trans-regulatory mutations having a stronger impact on expression differences between species. In F1 hybrids, genes under cis-only and trans-only regulatory effects show different modes of inheritance, with additive and dominant inheritance respectively. The relative abundance of genes in different categories of regulatory divergence is associated with expression level and breadth constraints.
Article
Plant Sciences
Shuai Nie, Xue-Chan Tian, Lei Kong, Shi-Wei Zhao, Zhao-Yang Chen, Si-Qian Jiao, Yousry A. El-Kassaby, Ilga Porth, Fu-Sheng Yang, Wei Zhao, Jian-Feng Mao
Summary: This study reveals the origin and evolutionary history of Ericales, uncovering its ancient complex allopolyploid origin and detecting extensive gene loss following polyploidization. This finding provides a new explanation for genetic variation and adaptive diversity in Ericales.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Cell Biology
Umer Farooq, Dimple Notani
Summary: 9p21 locus is a highly reproducible region in genome-wide association studies (GWAS) and is associated with various diseases and cancers. The genes within this region, including CDKN2A/B genes, play critical roles in cell cycle regulation and are linked to cellular regeneration, stemness, aging, and cancers. Understanding the regulation of these genes through promoter-driven and distal mechanisms could provide insights for targeting this locus in pathologies and aging.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biology
Zhenling Lv, Zijuan Li, Meiyue Wang, Fei Zhao, Wenjie Zhang, Changping Li, Lei Gong, Yijng Zhang, Annaliese S. Mason, Bao Liu
Summary: The majority of homoeologous triad genes in the A and B subgenomes of polyploid wheat showed highly conserved histone modification patterns during domestication and ploidy transitions, while a subset of functionally relevant genes were trans-regulated by the D genome in hexaploid wheat. The overall histone modification levels were stable in most genes, but certain genes displayed differential modification and enrichment for specific gene ontology terms, indicating a complex regulatory network during evolution and domestication.
Article
Biochemistry & Molecular Biology
Petra Vande Zande, Patricia J. Wittkopp
Summary: This study uses expression and fitness data from Saccharomyces cerevisiae gene deletion strains to show that cis-acting mutations tend to have lower pleiotropy and trans-acting mutations are more deleterious. These findings provide strong support for the role of pleiotropy in the preferential fixation of cis-regulatory alleles over evolutionary time.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemical Research Methods
Fan Yang, Kevin J. Gleason, Jiebiao Wang, Jubao Duan, Xin He, Brandon L. Pierce, Lin S. Chen
Summary: The study introduces a new analysis method CCmed to detect replicable cis-mediated trans-associations in relevant conditions/studies by integrating statistics from multiple tissues/studies. Analyses of data from 13 brain tissues in the GTEx project revealed multiple cross-tissue trans-associations mediated by cis-gene expression, with evidence of replication in two studies. Additionally, trans-genes associated with schizophrenia loci in at least two brain tissues were identified.
Article
Horticulture
Kun Ning, Wangxiang Zhang, Donglin Zhang, Yousry A. El-Kassaby, Ting Zhou
Summary: This study identified 341 MIKCC-type genes among 13 species in the Malus lineage based on the conserved domains of the MADS-box gene family. Phylogenetic analysis revealed three different groups of genes, including an ancestral MIKCC-type gene cluster from lower moss to higher flowering plants. Comparative analysis with Arabidopsis thaliana demonstrated a similar evolutionary relationship. This study provides insights into the evolutionary history and expansion mechanism of the MIKCC-type MADS-box gene family in plants and its implications for flower development in the Malus lineage.
Article
Plant Sciences
Yafang Xiao, Mengdi Li, Jianbo Wang
Summary: This study evaluates the number, structure, phylogeny, and expression of MBD genes in Brassica napus and its diploid ancestors, providing a deeper understanding of MBD genes in allopolyploids and serving as a reference for future analyses of allopolyploidization.
Article
Genetics & Heredity
Gemma Puixeu, Ariana Macon, Beatriz Vicoso
Summary: The study focuses on the regulatory architecture of gene expression in Drosophila, revealing differences between sexes and tissues. The researchers find that the regulatory architecture in female and male heads, as well as ovaries, is similar, while the testes display distinct cis-regulatory effects. They also observe variations in cis-regulation in genes with different levels of sex bias in gonads and heads. Furthermore, they highlight the importance of using diverse genetic backgrounds to infer generalizable patterns.
G3-GENES GENOMES GENETICS
(2023)
Article
Biology
Hao Song, Ximing Guo, Lina Sun, Qianghui Wang, Fengming Han, Haiyan Wang, Gregory A. Wray, Phillip Davidson, Qing Wang, Zhi Hu, Cong Zhou, Zhenglin Yu, Meijie Yang, Jie Feng, Pu Shi, Yi Zhou, Libin Zhang, Tao Zhang
Summary: The study reveals a significant expansion and diversification of the IAP gene family in hard clams, indicating its crucial role in evolutionary success in coping with environmental stresses.
Article
Entomology
Yan-Yan Zhou, Yue Jin, Shuai-Qi Liu, Shi-Liang Xu, Yu-Xin Huang, Yu-Song Xu, Lian-Gen Shi, Hua-Bing Wang
Summary: This study identified a lineage-specific expansion of lipocalin genes in lepidopteran insects, particularly in butterflies. Tandem duplication events played a role in this expansion, and some lipocalin genes involved in insect coloration underwent further expansion through tandem duplication. The study also revealed both conservation and divergence in the protein structures of lipocalins in lepidopteran insects. Expression analysis showed dynamic changes in tissue preference of lipocalin paralogs in Bombyx mori. Subcellular localization experiments demonstrated the localization of lipocalins in the cytoplasm, nuclear membrane, or nucleus in BmN cells. Furthermore, several lipocalin genes exhibited different responses to abiotic and biotic stresses.
Article
Genetics & Heredity
Shuang Liu, Hyejung Won, Declan Clarke, Nana Matoba, Saniya Khullar, Yudi Mu, Daifeng Wang, Mark Gerstein
Summary: This study investigates the transcriptional regulatory structure of the human brain, revealing the coordination of both cis- and trans-regulatory variants. By analyzing large datasets, the researchers identified candidate trans-eQTLs that influence the expression of target genes and found overlap with known cis-eQTLs. Through colocalization and mediation analyses, they identified mediators in trans-regulation and linked trans-eQTLs to schizophrenia risk genes. The findings demonstrate the importance of trans-regulatory mechanisms in understanding psychiatric disorders.
Article
Genetics & Heredity
Stijn van de Sompele, Kent W. Small, Munevver Burcu Cicekdal, Victor Lopez Soriano, Eva D'haene, Fadi S. Shaya, Steven Agemy, Thijs van der Snickt, Alfredo Duenas Rey, Toon Rosseel, Mattias Van Heetvelde, Sarah Vergult, Irina Balikova, Arthur A. Bergen, Camiel J. F. Boon, Julie De Zaeytijd, Chris F. Inglehearn, Bohdan Kousal, Bart P. Leroy, Carlo Rivolta, Veronika Vaclavik, Jenneke van den Ende, Mary J. van Schooneveld, Jose Luis Gomez-Skarmeta, Juan J. Tena, Juan R. Martinez-Morales, Petra Liskova, Kris Vleminckx, Elfride De Baere
Summary: This study elucidates the cis-regulatory mechanisms of NCMD and supports the view that this condition is a retinal enhanceropathy.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Chunlei Yang, Binna Zhu, Shijie Ye, Zhengwei Fu, Jinjun Li
Summary: The study found that trans-10,cis-12-CLA had better anti-inflammatory effects compared to cis-9,trans-11-CLA by downregulating genes related to inflammation, cell proliferation, and migration in RECs. Additionally, trans-10,cis-12-CLA significantly suppressed biological signals in response to LPS in RECs. Furthermore, pretreatment with trans-10,cis-12-CLA reduced the expression of lipogenic genes and biosynthesis of unsaturated fatty acids in RECs, indicating distinct isomer differences in regulating inflammatory responses and adipocytokine signaling.
Review
Plant Sciences
Linying Du, Zhenbing Ma, Hude Mao
Summary: Gene duplication is a common phenomenon in biology that impacts genomic variation and diversity, particularly in plant evolution and genetic engineering. Duplicated genes contribute to the emergence of novel functionality and adaptability to abiotic stress. Understanding the effects and mechanisms of gene duplication is crucial for future crop research and the development of high-performance, stress-resistant wheat lines.
Article
Biochemistry & Molecular Biology
Caroline M. S. Cauret, Marie-Theres Gansauge, Andrew S. Tupper, Benjamin L. S. Furman, Martin Knytl, Xue-Ying Song, Eli Greenbaum, Matthias Meyer, Ben J. Evans
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Neurosciences
Darcy B. Kelley, Irene H. Ballagh, Charlotte L. Barkan, Andres Bendesky, Taffeta M. Elliott, Ben J. Evans, Ian C. Hall, Young Mi Kwon, Ursula Kwong-Brown, Elizabeth C. Leininger, Emilie C. Perez, Heather J. Rhodes, Avelyne Villain, Ayako Yamaguchi, Erik Zornik
JOURNAL OF NEUROSCIENCE
(2020)
Article
Anthropology
Ben J. Evans, Marie-Theres Gansauge, Matthew W. Tocheri, Michael A. Schillaci, Thomas Sutikna, Jatmiko, E. Wahyu Saptomo, Amy Klegarth, Anthony J. Tosi, Don J. Melnick, Matthias Meyer
JOURNAL OF HUMAN EVOLUTION
(2020)
Article
Biology
Xue-Ying Song, Benjamin L. S. Furman, Tharindu Premachandra, Martin Knytl, Caroline M. S. Cauret, Domnick Victor Wasonga, John Measey, Ian Dworkin, Ben J. Evans
Summary: Research on the evolution of sex chromosomes in Xenopus species revealed a large region of sex-linked genes with sex-biased expression in X. borealis, suggesting a degenerate ancestral Y-chromosome transitioned into its contemporary Z-chromosome in this species. This study provides insights into how evolutionary transformations of ancestral sex chromosomes affect the function of new sex chromosomes.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Review
Biology
Matthias Stoeck, Lukas Kratochvil, Heiner Kuhl, Michail Rovatsos, Ben J. Evans, Alexander Suh, Nicole Valenzuela, Frederic Veyrunes, Qi Zhou, Tony Gamble, Blanche Capel, Manfred Schartl, Yann Guiguen
Summary: The article reviews the evolution of sex in vertebrates, covering sex determination mechanisms, sexual development, and reproductive modes across different clades. With the latest research data, it demonstrates the diversity and complexity of vertebrate sex genomes, as well as the research prospects for the evolution of sex determination.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biology
Ben J. Evans, Benjamin M. Peter, Don J. Melnick, Noviar Andayani, Jatna Supriatna, Jianlong Zhu, Anthony J. Tosi
Summary: In most macaques, females are philopatric while males migrate, leading to divergence of mitochondrial genomes. Analysis revealed evidence of natural selection associated with mitonuclear interactions and gender differences in gene flow shaping genome evolution.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Ecology
Laurie S. Stevison, Nick P. Bailey, Zachary A. Szpiech, Taylor E. Novak, Don J. Melnick, Ben J. Evans, Jeffrey D. Wall
Summary: Genital divergence plays an important role in reproductive isolation by establishing a lock-and-key mechanism for reproductive compatibility. The bear macaque, Macaca arctoides, has unique male and female genital morphology compared to its close relatives. Through whole-genome sequence analysis, it was found that M. arctoides shares more genomic regions with the sinica species group than the fascicularis species group. The bear macaque genome also shows evidence of extensive introgression between these two species groups.
ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Shun Hayashi, Kosuke Suda, Fuga Fujimura, Makoto Fujikawa, Kei Tamura, Daisuke Tsukamoto, Ben J. Evans, Nobuhiko Takamatsu, Michihiko Ito
Summary: This study investigated the origin and function of an exon (Ex4) in the sex-determining gene dm-W in African clawed frogs. The researchers found that Ex4 is derived from a noncoding portion of a DNA transposon. Analysis of transposons and Ex4 sequences from other species indicated that Ex4 was generated before the diversification of xenopus species. Further experiments showed that the amino acid sequence of Ex4 increased the DNA-binding ability and transrepression activity of dm-W. These findings provide insights into the origin and functional evolution of chimerical genes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Ecology
Ben J. Evans, Austin B. Mudd, Jessen Bredeson, Benjamin L. S. Furman, Domnick Victor Wasonga, Jessica B. Lyons, Richard M. Harland, Dan S. Rokhsar
Summary: In this study, we investigated the polymorphic sex chromosomes of the Marsabit clawed frog using genomic data. We found that the sex chromosomes of this species have undergone changes between different populations, with a region that is sex-linked in the east population but not in the west population. Our simulations support a model where some sex-linked regions from the east population acquired autosomal segregation in the west population. These findings highlight the complex evolutionary dynamics of the sex chromosomes in the Marsabit clawed frog and provide a foundation for further research on sex-determining genes in this species.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2022)
Article
Genetics & Heredity
Tharindu Premachandra, Caroline M. S. Cauret, Werner Conradie, John Measey, Ben J. Evans
Summary: Allotetraploid genomes consist of two subgenomes derived from separate diploid ancestral species. The study found that there is no significant difference in subgenome population structure and gene flow. However, the population structure in both the nuclear genome and the mitochondrial genome roughly correspond with seasonal rainfall variation and the topography of southern Africa.
G3-GENES GENOMES GENETICS
(2023)
Article
Evolutionary Biology
Jianlong Zhu, Ben J. Evans
Summary: In most eukaryotes, aerobic respiration requires interactions between autosomally encoded genes (N-interact genes) and mitochondrial DNA, RNA, and protein. In species where females are philopatric, contrasting distributions of genetic variation in mitochondrial and nuclear genomes create variation in mitonuclear interactions that may be subject to natural selection. Our study on macaque monkeys suggests that natural selection on mitonuclear interactions could have influenced several aspects of macaque societies including species diversity, ecological breadth, female-biased adult sex ratio and demography, sexual dimorphism, and mitonuclear phylogenomics.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Stephen Rong, Christopher R. Neil, Anastasia Welch, Chaorui Duan, Samantha Maguire, Ijeoma C. Meremikwu, Malcolm Meyerson, Ben J. Evans, William G. Fairbrother
Summary: Humans coexisted and interbred with other hominins which later became extinct. By engineering Neanderthal and Denisovan sequences into artificial genes, researchers reconstructed the pre-mRNA processing patterns of these extinct populations. They found genetic differences in exon recognition between extant and extinct hominins and identified splicing variants associated with purifying selection in modern humans and positive selection following introgression. Additionally, they discovered unique alternative splicing variants in genes related to immunity and sperm maturation, as well as variants that may contribute to variation in areas such as bilirubin levels, balding, hemoglobin levels, and lung capacity among modern humans. The findings provide insights into natural selection in human evolution and the role of splicing in gene regulation and phenotype differences.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Evolutionary Biology
Jimmy A. Mcguire, Xiaoting Huang, Sean B. Reilly, Djoko T. Iskandar, Cynthia Y. Wang-Claypool, Sarah Werning, Rebecca A. Chong, Shobi Z. S. Lawalata, Alexander L. Stubbs, Jeffrey H. Frederick, Rafe M. Brown, Ben J. Evans, Umilaela Arifin, Awal Riyanto, Amir Hamidy, Evy Arida, Michelle S. Koo, Jatna Supriatna, Noviar Andayani, Robert Hall
Summary: The biota of Sulawesi is known for its unique species and diversification. In this study, the diversification history of Sulawesi flying lizards, an endemic group to Sulawesi, was explored using a geological framework. The analysis revealed that there are more Draco species in Sulawesi than previously thought, with cryptic and arrested speciation events and ancient hybridization affecting the phylogenetic analyses. The colonization of Sulawesi by the common ancestor of the Draco lineatus Group occurred around 11 million years ago, followed by radiations and dynamic species interactions.
SYSTEMATIC BIOLOGY
(2023)
Article
Ecology
Nicola R. Fornaini, Barbora Bergelova, Vaclav Gvozdik, Halina Cernohorska, Vladimir Krylov, Svatava Kubickova, Eric B. Fokam, Gabriel Badjedjea, Ben J. Evans, Martin Knytl
Summary: Using fluorescence in situ hybridization and genomic data, we mapped repetitive elements in six species of African clawed frogs and found that polyploidization and divergence play important roles in the evolution of repetitive elements. We also observed conserved loci number and position in one of the subgenus species, while the number of signals varied in other species derived from different polyploidization events.
EUROPEAN JOURNAL OF WILDLIFE RESEARCH
(2023)
Article
Genetics & Heredity
Benjamin L. S. Furman, Caroline M. S. Cauret, Martin Knytl, Xue-Ying Song, Tharindu Premachandra, Caleb Ofori-Boateng, Danielle C. Jordan, Marko E. Horb, Ben J. Evans