Article
Biology
Giovanni Annona, Iori Sato, Juan Pascual-Anaya, David Osca, Ingo Braasch, Randal Voss, Jan Stundl, Vladimir Soukup, Allyse Ferrara, Quenton Fontenot, Shigeru Kuratani, John H. Postlethwait, Salvatore D'Aniello
Summary: Nitric oxide (NO) is a crucial signaling molecule in biological systems, playing important roles in cardiovascular, neurological, and immune functions. Understanding the evolution of NO synthases (Nos) genes, which produce NO in vivo, is still a puzzle, especially in fish compared to tetrapods. Recent studies have found the presence of nos3 gene, previously considered lost, in spotted gar, changing our perspective on the origin of nos genes. This study explored nos gene evolution in different vertebrate species and revealed lineage-specific gene duplications and losses, independent losses of nos3 in teleost lineages, and the expression of nos genes in the gills of certain gnathostome species. These findings provide insights into the roles and evolutionary history of nos genes.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Juan C. Opazo, Michael W. Vandewege, Federico G. Hoffmann, Kattina Zavala, Catalina Melendez, Charlotte Luchsinger, Viviana A. Cavieres, Luis Vargas-Chacoff, Francisco J. Morera, Patricia Burgos, Cheril Tapia-Rojas, Gonzalo A. Mardones
Summary: Studying the evolutionary history of gene families is important for understanding gene origin, evolution, and their implications for functional studies. The sirtuin gene family, involved in aging-related functions, has a complex duplicative history, but our results provide a well-resolved phylogeny and shed light on the repertoire of sirtuin genes among vertebrates. We identified a new member (SIRT3.2) that was lost in amniotes but retained in other jawed vertebrates, and its experimental analysis revealed its mitochondrial location and deacetylase activity similar to mammalian SIRT3.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Review
Endocrinology & Metabolism
Yorgui Santiago-Andres, Matan Golan, Tatiana Fiordelisio
Summary: The pituitary gland, a master endocrine gland in vertebrates, has recently been found to consist of tightly wired large-scale networks of cells that communicate with each other in homo and heterotypic manners, optimizing hormone pulse generation in response to changing physiological demands. The development of 3D imaging methods and transgenic models has allowed for further research into functional pituitary networks across different vertebrate classes.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Environmental Sciences
Binhao Liu, Pengcheng Dong, Xinzhe Zhang, Zhihang Feng, Zhugui Wen, Liang Shi, Yan Xia, Chen Chen, Zhenguo Shen, Chunlan Lian, Yahua Chen
Summary: This study aimed to establish a comprehensive inventory of MT genes from the ECM fungus Laccaria bicolor. Cloning 8 MT genes, the research found that expression levels of 4 MTs significantly increased during symbiosis stages. Functional analysis showed that all LbMT proteins provided similar levels of Cu(II) or Cd(II) tolerance, but were not affected by H2O2.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Nicolas Leurs, Camille Martinand-Mari, Sylvain Marcellini, Melanie Debiais-Thibaud
Summary: A scpp gene present in elasmobranchs (sharks and rays) is remarkably similar to the osteichthyan scpp members, but originated independently. In catsharks, this gene is coexpressed with sparc-L and fam20 degrees C, supporting a single origin for the hypermineralized outer odontode layer.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Lin Zhang, Xinxin Zhu, Yiyong Zhao, Jing Guo, Taikui Zhang, Weichen Huang, Jie Huang, Yi Hu, Chien-Hsun Huang, Hong Ma
Summary: The adaptation of Pooideae to cool climates has been influenced by gene duplications and regulatory mechanisms. Pooideae originated in the late Cretaceous and underwent divergences under cooling conditions. During the Eocene-Oligocene transition, Pooideae species experienced significant gene duplications and regulatory changes, promoting their adaptation to cold habitats.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Aurele Toussaint, Sebastien Brosse, C. Guillermo Bueno, Meelis Partel, Riin Tamme, Carlos P. Carmona
Summary: The projected losses of functional diversity among land and freshwater vertebrates are unevenly distributed across the world, with different taxonomic groups and realms experiencing varying effects of extinctions. The Indo-Malay and Palearctic realms are particularly inclined to experience a drastic loss of functional diversity.
NATURE COMMUNICATIONS
(2021)
Review
Genetics & Heredity
Md. Sifatul Islam, Ajit Ghosh
Summary: Aldehyde dehydrogenases (ALDHs) play an important role in plants by serving as scavengers for reactive aldehydes and responding to stress. Both animals and plants have multiple ALDH families, with plants having 14 families. The expansion of ALDH isoforms in plants allows for diverse functions. Studies have shown that ALDH is crucial for plant development and environmental stress adaptability.
Article
Endocrinology & Metabolism
Daniel Ocampo Daza, Christina A. Bergqvist, Dan Larhammar
Summary: This study provides a parsimonious explanation for the origin of the OTR/VTR gene family, based on phylogenetic and chromosomal conserved synteny analyses. The findings suggest a chromosome quadruplication event associated with whole-genome duplications early in vertebrate evolution, prior to the radiation of jawed vertebrates. The evolution of the OTR/VTR gene family can be explained by two whole-genome duplications followed by differential gene losses of VTR2 genes in different lineages.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Editorial Material
Multidisciplinary Sciences
Matt Friedman
Summary: Scarce evidence suggests that important evolutionary developments for jawed vertebrates may have taken place during or prior to the Silurian period. Fossil discoveries unveil insights into this particular interval.
Review
Ecology
Diego Safian, Geert F. Wiegertjes, Bart J. A. Pollux
Summary: Fish are an interesting model for studying regeneration, with the Poeciliidae family proposed as a new model system to investigate the evolution of fin regeneration. Current research has focused on the mechanisms and evolutionary pressures of fin regeneration, introducing three new theories for the evolution of this capacity.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Colin J. Shew, Paulina Carmona-Mora, Daniela C. Soto, Mira Mastoras, Elizabeth Roberts, Joseph Rosas, Dhriti Jagannathan, Gulhan Kaya, Henriette O'Geen, Megan Y. Dennis
Summary: Evidence shows that in humans, paralogous segmental duplication genes exhibit different expression patterns, possibly due to relaxed selection or neofunctionalization. While ancestral paralogs show greater expression conservation with chimpanzee orthologs, certain derived paralogs may retain or supplant ancestral functions.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Entomology
Jia-Bao Lu, Peng-Peng Ren, Qiao Li, Fang He, Zhong-Tian Xu, Sai-Nan Wang, Jian-Ping Chen, Jun-Min Li, Chuan-Xi Zhang
Summary: This study identified 10 ApoD-like genes in Nilaparvata lugens (BPH) and found that NlApoD2 is essential for BPH development and survival. NlApoD4/5 are highly expressed in testes and may play a role in reproduction. Additionally, NlApoD3-5/9, NlApoD3-5, and NlApoD9 were up-regulated after treatment with lipopolysaccharide, H2O2, and ultraviolet-C, respectively, suggesting their potential roles in stress resistance.
Article
Biochemistry & Molecular Biology
Yang Mao, Feng Shao, Qingyuan Zhao, Zuogang Peng
Summary: This study investigates the evolutionary history of the clock gene family in a diverse set of vertebrates based on 102 vertebrate genomes, revealing insights into the evolution of clock genes, especially in ray-finned fishes. Analysis shows that most teleosts possess three clock genes while osteoglossomorph fishes have two clock2 genes. Protein sequence comparisons indicate changes in CLOCK protein at specific regions among vertebrates, and dN/dS analysis suggests distinct fates for duplicated clock genes between different fish clades.
JOURNAL OF MOLECULAR EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Peilin Cheng, Yu Huang, Yunyun Lv, Hao Du, Zhiqiang Ruan, Chuangju Li, Huan Ye, Hui Zhang, Jinming Wu, Chengyou Wang, Rui Ruan, Yanping Li, Chao Bian, Xinxin You, Chengcheng Shi, Kai Han, Junming Xu, Qiong Shi, Qiwei Wei
Summary: This study generated the first high-quality genome assembly of the American paddlefish, revealing a recent species-specific whole-genome duplication event and extensive chromosomal changes. The flourishing period of SCPP members in the paddlefish occurred at least before the split between Acipenseriformes and teleosts.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Nair Vilas-Arrondo, Andre Gomes-dos-Santos, Montse Perez, Francisco Baldo, Ana Verissimo, Diana Catarino, Andre M. Machado, Esther Roman-Marcote, Rafael Banon, Elsa Froufe, L. Filipe C. Castro
Summary: This study sequenced and characterized the complete mitogenome of the opal chimera using long-read sequencing technology. The results placed the opal chimera within the Chimaeridae family and reinforced previous findings that the genus Chimera is paraphyletic.
MITOCHONDRIAL DNA PART B-RESOURCES
(2022)
Article
Fisheries
M. Nande, O. Monroig, A. M. Machado, L. F. C. Castro, M. Lopes-Marques, A. Capitao, J. C. Navarro
Summary: The common octopus, Octopus vulgaris, has high growth rates and commercial value in marine aquaculture. However, elevated mortalities during the planktonic stage due to nutritional deficiencies hinder the development of efficient rearing protocols. This study investigated the effects of different diets on the growth and development of paralarvae and found distinct fatty acid compositions and gene expression patterns in different body compartments. The results suggest that dietary treatments have a significant impact on paralarvae's FA profiles and gene expressions, and these findings provide important insights into the nutritional requirements and adaptation mechanisms of paralarvae.
Article
Physiology
Oana Birceanu, Patricia Ferreira, James Neal, Julia Sunga, Shaun Anthony, Shannon M. Davidson, Susan L. Edwards, Jonathan M. Wilson, John H. Youson, Mathilakath M. Vijayan, Michael P. Wilkie
Summary: This study investigates the handling and excretion of nitrogenous waste (N waste) during the life cycle of the sea lamprey. The study finds that the excretion rates of ammonia and urea decrease during metamorphosis but significantly increase after metamorphosis. The sea lampreys rely on different excretion pathways for ammonia and urea, with ammonia primarily excreted via the gills and urea predominantly excreted via extrabranchial routes and urine.
PHYSIOLOGICAL AND BIOCHEMICAL ZOOLOGY
(2022)
Article
Biochemistry & Molecular Biology
M. T. Nash, A. R. Quijada-Rodriguez, G. J. P. Allen, J. M. Wilson, D. Weihrauch
Summary: This study identified three different aquaporins in the intertidal crustacean C. maenas, which are expressed in the gills and antennal glands. These aquaporins play a role in osmoregulation and may be involved in the production of diluted urine.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY
(2022)
Article
Biology
Shuang Liu, Jonathan M. Wilson, Eric B. Taylor, Jeffrey G. Richards
Summary: Phenotypic divergence is a key characteristic of adaptive radiation. This study examined the differentiation in ion regulation characteristics among populations of prickly sculpin (Cottus asper) from different habitat types and explored the relationship between environmental water chemistry and physiological characteristics. The results suggest that habitat variation may play an important role in driving differences in gill Na+/K+-ATPase and H+-ATPase activity across populations, and the combined effect of water Na+ and pH may have contributed to physiological adaptation during freshwater colonization and dispersal of C. asper after the last glacial period.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2022)
Article
Biology
Bing Sun, Yuwei Huang, L. Filipe C. Castro, Su Yang, Songqian Huang, Wu Jin, He Zhou, Shigeho Ijiri, Yi Luo, Jian Gao, Xiaojuan Cao
Summary: This study provides insights into the genetic basis of the loach's adaptation to adverse environments. The fos gene is positively selected and associated with the loach's mud-dwelling behavior. Two key genes involved in intestinal air-breathing are identified. The expansion of the fmo5 gene and its differential expression in a drug stress trial indicate its importance to the loach's adaptation to noxious mud.
Article
Genetics & Heredity
Catarina Serrano, Monica Lopes-Marques, Antonio Amorim, Maria Joao Prata, Luisa Azevedo
Summary: Gene duplication plays a significant role in evolution. This study identified and explored a partial duplication of an X-linked region in the Macaca genus. Genomic comparisons revealed that the duplication involved important genes encoding ornithine transcarbamylase (OTC) and retinitis pigmentosa GTPase regulator (RPGR). Selective pressure analysis showed no significant differences, indicating no selective pressures were acting during the evolutionary process. Although rare, further study of partial duplications of functionally important genes is valuable in understanding their impact.
Article
Chemistry, Analytical
Ines Pascoa, Rita Biltes, Joao Sousa, Marco Aurelio Correia Preto, Vitor Vasconcelos, Luis Filipe Castro, Raquel Ruivo, Isabel Cunha
Summary: Cyanobacteria produce secondary metabolites that can act as ligands for PPARs, making them a potential source of bioactive compounds. A cell-based PPAR transactivation activity biosensor was upgraded and used in a screening campaign for drug discovery.
Article
Fisheries
Arne M. Malzahn, Andrea Villena-Rodriguez, Oscar Monroig, Asmund Johansen, L. Filipe C. Castro, Juan C. Navarro, Andreas Hagemann
Summary: This study evaluated the effects of rearing temperature and mixtures of aquaculture and biogas side streams on the biomass production and fatty acid composition of the polychaete Hediste diversicolor. The results showed that temperature significantly affected the biomass production, with higher temperatures promoting higher growth rates but lower survival rates. The diet had a significant effect on the fatty acid composition of the polychaetes. Therefore, optimizing the production temperature can enhance the growth of H. diversicolor without compromising the fatty acid composition and quality.
Article
Biochemistry & Molecular Biology
Bernardo Pinto, Raul Valente, Filipe Caramelo, Raquel Ruivo, L. Filipe C. Castro
Summary: The mammalian skin has evolved a diverse array of adaptations, with the pilosebaceous unit being a prominent feature. Pangolins, belonging to the order Pholidota, have keratin-derived scales as iconic skin appendages. While they have hair on their abdomens, the presence of sebaceous and sweat glands is uncertain. By studying pangolin genomes, researchers have found evolutionary changes in genes related to skin physiology, such as wax monoester formation and triacylglycerol synthesis, as well as genes involved in skin defense and structural integrity. The findings shed light on the complex evolutionary history of mammalian skin.
JOURNAL OF MOLECULAR EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Andre Gomes-dos-Santos, Elsa Froufe, John M. Pfeiffer, Nathan A. Johnson, Chase H. Smith, Andre M. Machado, L. Filipe C. Castro, Van Tu Do, Akimasa Hattori, Nicole Garrison, Nathan V. Whelan, Ivan N. Bolotov, Ilya V. Vikhrev, Alexander V. Kondakov, Mohamed Ghamizi, Vincent Prie, Arthur E. Bogan, Manuel Lopes Lima
Summary: The proliferation of genomic sequencing approaches has greatly impacted the field of phylogenetics, and target capture approaches have become a cost-effective and fast strategy for non-model organism inference. However, existing pipelines for target capture processing are not capable of incorporating whole genome sequencing data. In this study, a new pipeline is developed to accurately capture and assemble targeted regions using whole genome re-sequencing reads, showing potential for users with limited resources and high-coverage sequencing requirements.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Marine & Freshwater Biology
Gonzalo Mucientes, Nair Vilas-Arrondo, Giulia Secci-Petretto, Uxia Vazquez, Xabier Pin, Alfredo Lopez, L. Filipe C. Castro, Elsa Froufe
Summary: The smalltooth sand tiger shark, O. ferox, has a widespread and fragmented distribution in tropical and warm-temperate oceans worldwide. A female O. ferox was caught and released by a fishing vessel in Ria de Arousa, Spain, and later stranded alive on the coast. This is the first confirmed record of O. ferox in Galician waters, contributing to our understanding of the species' occurrence in the Northeastern Atlantic.
Correction
Immunology
Fabiana Neves, Antonio Munoz-Merida, Andre M. Machado, Tereza Almeida, Arnaud Gaigher, Pedro J. Esteves, L. Filipe C. Castro, Ana Verissimo
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Andre Gomes-dos-Santos, Manuel Lopes-Lima, M. Andre Machado, Amilcar Teixeira, L. Filipe C. Castro, Elsa Froufe
Summary: Mussels of order Unionida, a group of freshwater bivalves, are highly threatened and show the highest record of extinction events. The first genome assembly of the dolphin freshwater mussel Unio delphinus is presented, which will aid in understanding its biology, evolutionary history, and conservation strategies.
Editorial Material
Biochemistry & Molecular Biology
Bernardo Pinto, Andre M. Machado, Salman Malakpour Kolbadinezhad, Elza Fonseca, Jose Pedro Andrade, Jorge Palma, Raquel Ruivo, Nuno Monteiro, Jonathan M. Wilson, L. Filipe C. Castro