Review
Biochemistry & Molecular Biology
Andrei P. Kozlov
Summary: A theory called the carcino-evo-devo theory is being developed to explain the evolutionary role of hereditary tumors. The theory proposes that hereditary tumors played a role in the evolution of multicellular organisms by providing additional cell masses for the expression of novel genes. It has made several nontrivial predictions that have been confirmed in laboratory experiments and offers explanations for previously unexplained biological phenomena. By considering individual development, evolutionary development, and neoplastic development within one framework, the carcino-evo-devo theory has the potential to become a unifying biological theory.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Xiangyu Pan, Yudong Cai, Zongjun Li, Xianqing Chen, Rasmus Heller, Nini Wang, Yu Wang, Chen Zhao, Yong Wang, Han Xu, Songhai Li, Ming Li, Cunyuan Li, Shengwei Hu, Hui Li, Kun Wang, Lei Chen, Bin Wei, Zhuqing Zheng, Weiwei Fu, Yue Yang, Tingting Zhang, Zhuoting Hou, Yueyang Yan, Xiaoyang Lv, Wei Sun, Xinyu Li, Shisheng Huang, Lixiang Liu, Shengyong Mao, Wenqing Liu, Jinlian Hua, Zhipeng Li, Guojie Zhang, Yulin Chen, Xihong Wang, Qiang Qiu, Brian P. Dalrymple, Wen Wang, Yu Jiang
Summary: The study identified genetic changes underlying rumen functional innovations, including coding mutations, newly evolved genes, and changes of regulatory elements. It was validated that the key ketogenesis gene HMGCS2 is under positive selection and exhibits higher synthesis activity in ruminants. Two newly evolved genes, LYZ1 and DEFB1, may regulate microbial community equilibrium by resisting Gram-positive bacteria.
SCIENCE CHINA-LIFE SCIENCES
(2021)
Review
Plant Sciences
Siyu Li, Hokuto Nakayama, Neelima R. Sinha
Summary: Comparative transcriptomics is a powerful method for understanding the genetic basis of organ morphogenesis and its diversification during evolution. However, studying plant morphological diversity using comparative transcriptomics faces challenges such as identifying homologous gene pairs, selecting appropriate developmental stages for comparison, and extracting biologically meaningful networks. Methods like phylostratigraphy, clustering, and gene co-expression networks are used to address these challenges and provide a comprehensive understanding of morphological evolution.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Cecilia Zumajo-Cardona, Natalia Pabon-Mora, Barbara A. Ambrose
Summary: The study reveals that the euAP2 gene plays a crucial role in vascular plants, initially contributing to spore and sporangium development and later being recruited for ovule, fruit, and floral organ development. The protein sequences of euAP2 are highly conserved, with changes in their function during development likely attributed to alterations in regulatory regions.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Cell Biology
Jan Stundl, Vladimir Soukup, Roman Franek, Anna Pospisilova, Viktorie Psutkova, Martin Psenicka, Robert Cerny, Marianne E. Bronner, Daniel Meulemans Medeiros, David Jandzik
Summary: In the last decade, CRISPR/Cas9 has been proven to be an effective and efficient method for targeted mutagenesis in genetic model systems. Its high efficiency allows the immediate generation of near-null mosaic mutants, making it valuable for organisms with life histories that preclude the establishment of purebred genetic lines. In the study, the successful use of CRISPR/Cas9 mutagenesis in a non-teleost fish, sterlet Acipenser ruthenus, was reported, indicating the potential for applying this technology to other long-lived, slow-maturing aquatic vertebrates.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Sebastian S. James, Mackenzie Englund, Riley Bottom, Roberto Perez, Kathleen E. Connor, Kelly J. Huffman, Stuart P. Wilson, Leah A. Krubitzer
Summary: Advances in sequencing techniques have allowed for comparative studies of gene expression, but spatial expression has remained limited due to a lack of robust methodology. In this study, methods and software tools were developed to quantify and compare tissue-wide spatial patterns of gene expression within and between species. The expression patterns of RZR beta and Id2 mRNA in the cortex were compared across early postnatal development in mice and voles. The results showed that RZR beta expression patterns were highly conserved between species, while Id2 expression patterns emerged in a consistent manner across layers in both species. These differences in neocortical patterning development were suggested to reflect the independent evolution of brains, bodies, and sensory systems since their common ancestor 35 million years ago.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Plant Sciences
Stuart F. McDaniel
Summary: The author suggests that certain terminology commonly used in plant systematics may lead to misunderstandings in interpreting phylogenetic trees, and advocates for utilizing a clear framework, such as tree thinking, to enhance understanding of phylogenies across different sub-disciplines of biology.
Article
Biology
Marco La Fortezza, Gregory J. Velicer
Summary: Aggregative multicellular development involves complex forms of cooperation among unicellular organisms and the cellular environment during development shapes morphological evolution. In an experiment with Myxococcus xanthus, it was found that partner genotype and social character play a role in fruiting body morphology diversification, with antagonistic partners selecting for greater fruiting body formation. Even small genetic differences between distinct cheater partners can drive morphological divergence, highlighting the impact of genetic divergence on multicellular body evolution.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Developmental Biology
Victoria M. R. Spencer, Lucy Bentall, C. Jill Harrison
Summary: Diverse branching forms have evolved multiple times in the tree of life. In vascular plants, the ancestral pattern of branching involves dichotomy, which is regulated by PIN-mediated auxin transport. In Selaginella, angle shoot development is also regulated by long-range auxin transport and a transitory drop in PIN expression. This study highlights the importance of PIN-mediated auxin transport in vascular plant branching and its independent recruitment in Selaginella angle shoot development and seed plant axillary branching.
Article
Biology
Jason Cheok Kuan Leong, Masahiro Uesaka, Naoki Irie
Summary: The concept of evolutionary conservation is used to explain ancestral features and traits, but it has been misused to evaluate derivedness. Distinguishing these two concepts can help understand phenotypic and organismal evolution. Conservation focuses on common genes or traits, while derivedness covers novel or lost traits and genes to evaluate changes from a common ancestor. Conservation-oriented methods are effective in identifying ancestral features, but may underestimate overall changes. A new method, the transcriptomic derivedness index, uses whole-embryonic transcriptome as a phenotype to estimate phenotypic derivedness.
Article
Cell Biology
Jason Cheok Kuan Leong, Yongxin Li, Masahiro Uesaka, Yui Uchida, Akihito Omori, Meng Hao, Wenting Wan, Yang Dong, Yandong Ren, Si Zhang, Tao Zeng, Fayou Wang, Luonan Chen, Gary Wessel, Brian T. Livingston, Cynthia Bradham, Wen Wang, Naoki Irie
Summary: The article introduces a new method, "derivedness index", to quantify the degree of derivedness in species. Unlike traditional qualitative enumeration based on conservative traits, this method also considers genes that may have been lost or duplicated during evolution. The study identified new gene expression profile characteristics and proposed technical improvements for the method.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Plant Sciences
Facundo Romani, Jorge R. Flores, Juan Ignacio Tolopka, Guillermo Suarez, Xiaolan He, Javier E. Moreno
Summary: This review discusses the recent advances in understanding the origin, development, and function of oil bodies in liverworts, emphasizing their importance in physiological processes and adaptation. The review also highlights the need for further research on the molecular mechanisms underlying the morphological and chemical diversity of secretory structures in land plants.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Review
Plant Sciences
Zheng Li, Michael T. W. McKibben, Geoffrey S. Finch, Paul D. Blischak, Brittany L. Sutherland, Michael S. Barker
Summary: This review discusses the impact of polyploidy on chromosome pairing behavior in land plants, as well as the two major processes of diploidization: cytological diploidization and genic diploidization/fractionation. It also compares gene fractionation variation across land plants and highlights differences in diploidization between plants and animals.
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 72, 2021
(2021)
Article
Biochemistry & Molecular Biology
Shuting Wang, Dequn Teng, Xueyan Li, Peiwen Yang, Wa Da, Yiming Zhang, Yubo Zhang, Guichun Liu, Xinshuang Zhang, Wenting Wan, Zhiwei Dong, Donghui Wang, Shun Huang, Zhisheng Jiang, Qingyi Wang, David J. Lohman, Yongjie Wu, Linlin Zhang, Fenghai Jia, Erica Westerman, Li Zhang, Wen Wang, Wei Zhang
Summary: Oakleaf butterflies in the genus Kallima have a polymorphic wing phenotype that enables them to mimic dead leaves. By analyzing multi-omic data and conducting functional validation, we inferred the evolutionary history of Kallima species and identified the genetic basis of their variable wing patterns. We found that Kallima butterflies diversified in the eastern Himalayas and that the wing patterning gene cortex controls leaf wing polymorphism.
Article
Biology
Shahar Avin, Adrian Currie, Stephen H. Montgomery
Summary: Vertebrate brain structure shows both consistent scaling between components and divergence from general trends. Different hypotheses explain these patterns, emphasizing external processes such as selection or internal processes like developmental coupling. The study introduces an agent-based model to simulate brain evolution and examines the relationships between variables shaping brain evolution.
Article
Plant Sciences
Heleen Coenen, Tom Viaene, Michiel Vandenbussche, Koen Geuten
Article
Genetics & Heredity
Olivier Raymond, Jerome Gouzy, Jeremy Just, Helene Badouin, Marion Verdenaud, Arnaud Lemainque, Philippe Vergne, Sandrine Moja, Nathalie Choisne, Caroline Pont, Sebastien Carrere, Jean-Claude Caissard, Arnaud Couloux, Ludovic Cottret, Jean-Marc Aury, Judit Szecsi, David Latrasse, Mohammed-Amin Madoui, Lea Francois, Xiaopeng Fu, Shu-Hua Yang, Annick Dubois, Florence Piola, Antoine Larrieu, Magali Perez, Karine Labadie, Lauriane Perrier, Benjamin Govetto, Yoan Labrousse, Priscilla Villand, Claudia Bardoux, Veronique Boltz, Celine Lopez-Roques, Pascal Heitzler, Teva Vernoux, Michiel Vandenbussche, Hadi Quesneville, Adnane Boualem, Abdelhafid Bendahmane, Chang Liu, Manuel Le Bris, Jerome Salse, Sylvie Baudino, Moussa Benhamed, Patrick Wincker, Mohammed Bendahmane
Article
Multidisciplinary Sciences
Lea Francois, Marion Verdenaud, Xiaopeng Fu, Darcy Ruleman, Annick Dubois, Michiel Vandenbussche, Abdelhafid Bendahmane, Olivier Raymond, Jeremy Just, Mohammed Bendahmane
SCIENTIFIC REPORTS
(2018)
Article
Biochemistry & Molecular Biology
Steve de Bossoreille, Patrice Morel, Christophe Trehin, Ioan Negrutiu
Review
Plant Sciences
Marie Monniaux, Michiel Vandenbussche
FRONTIERS IN PLANT SCIENCE
(2018)
Article
Biochemistry & Molecular Biology
Patrice Morel, Pierre Chambrier, Veronique Boltz, Sophy Chamot, Frederique Rozier, Suzanne Rodrigues Bento, Christophe Trehin, Marie Monniaux, Jan Zethof, Michiel Vandenbussche
Article
Biochemistry & Molecular Biology
Ariane Girardin, Tongming Wang, Yi Ding, Jean Keller, Luis Buendia, Megane Gaston, Camille Ribeyre, Virginie Gasciolli, Marie-Christine Auriac, Tatiana Vernie, Abdelhafid Bendahmane, Martina Katharina Ried, Martin Parniske, Patrice Morel, Michiel Vandenbussche, Martine Schorderet, Didier Reinhardt, Pierre-Marc Delaux, Jean-Jacques Bono, Benoit Lefebvre
Article
Multidisciplinary Sciences
Guowei Liu, Marina Stirnemann, Christian Gubeli, Susanne Egloff, Pierre-Emmanuel Courty, Sylvain Aubry, Michiel Vandenbussche, Patrice Morel, Didier Reinhardt, Enrico Martinoia, Lorenzo Borghi
Article
Cell Biology
Shuangjiang Li, Martina Cerri, Pamela Strazzer, Yanbang Li, Cornelis Spelt, Mattijs Bliek, Michiel Vandenbussche, Enric Martinez-Calvo, Biao Lai, Lara Reale, Ronald Koes, Francesca M. Quattrocchio
Summary: The study demonstrates that RAB5a protein in plants regulates trafficking to the central vacuole, with evolutionarily and functionally distinct features from other types of RAB5 proteins. Loss of RAB5a reduces cell height and abolishes vacuolino formation, while overexpression of RAB5a promotes vacuolino fusion, resulting in oversized vacuoles.
Article
Biochemistry & Molecular Biology
Patrice Morel, Klaas Heijmans, Kai Ament, Mathilde Chopy, Christophe Trehin, Pierre Chambrier, Suzanne Rodrigues Bento, Andrea Bimbo, Michiel Vandenbussche