Review
Biochemistry & Molecular Biology
Bethan Clark, Muktai Kuwalekar, Bettina Fischer, Joost Woltering, Jakob Biran, Scott Juntti, Claudius F. Kratochwil, M. Emilia Santos, Miguel Vasconcelos Almeida
Summary: African cichlid fishes are important for aquaculture and research. However, the lack of genetic tools has hindered the study of genetic variation in these fish. A recent workshop on genome editing discussed advances in the field and proposed new avenues for research.
Article
Biochemistry & Molecular Biology
Sarah Khalil, Erik D. Enbody, Carolina Frankl-Vilches, Joseph F. Welklin, Rebecca E. Koch, Matthew B. Toomey, Simon Yung Wa Sin, Scott Edwards, Manfred Gahr, Hubert Schwabl, Michael S. Webster, Jordan Karubian
Summary: Carotenoid pigments play a crucial role in mate choice among vertebrates by producing red, orange, and yellow visual signals. However, the processes involved in carotenoid-based trait production remain largely unknown. In this study, we induced the production of a carotenoid-based red plumage patch in male red-backed fairywrens through testosterone elevation. We compared gene expression in the liver and feather follicles of unornamented males, testosterone-implanted males, and naturally ornamented males. Our findings suggest that testosterone regulates the expression of carotenoid-associated genes and coordinaes the complex processes underlying the production of carotenoid-based traits.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Lei Yang, Yang Chen, Min Wang, Huifang Hou, Shuang Li, Ling Guan, Haijian Yang, Wu Wang, Lin Hong
Summary: In this study, the phenotypic, metabolomic, and transcriptomic profiles of the lido blood orange cultivar grafted onto two rootstocks were investigated. The results showed that the Trifoliate orange rootstock had the best impact on fruit quality and flesh color. Metabolomics revealed significant differences in the accumulation patterns of metabolites, while transcriptome profiling identified differentially expressed genes associated with flavonoids and anthocyanins. The study also identified key transcription factors and genes involved in the anthocyanin synthesis pathway as modulators of anthocyanin content in lido blood orange. These findings provide valuable insights for improving the quality of blood orange varieties.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Tarang K. Mehta, Christopher Koch, Will Nash, Sara A. Knaack, Padhmanand Sudhakar, Marton Olbei, Sarah Bastkowski, Luca Penso-Dolfin, Tamas Korcsmaros, Wilfried Haerty, Sushmita Roy, Federica Di-Palma
Summary: This study developed a novel computational pipeline to predict regulators in co-expressed modules across cichlid species, revealing network rewiring in the visual system. Mutations in regulatory regions of visual opsin genes were found to disrupt regulatory edges across species, segregating according to phylogeny and ecology, indicating GRN rewiring in radiating cichlids.
Article
Marine & Freshwater Biology
Tetsumi Takahashi
Summary: This study examined changes in brood size during mouthbrooding in two open-water spawning cichlids from Lake Tanganyika, and found that the average egg and larval numbers decreased during the mouthbrooding process. Future studies should compare these species with bottom-spawning mouthbrooders to assess the efficacy of mouthbrooding behavior in different aquatic environments.
Article
Biotechnology & Applied Microbiology
Derek E. Kelly, Shweta Ramdas, Rong Ma, Renata A. Rawlings-Goss, Gregory R. Grant, Alessia Ranciaro, Jibril B. Hirbo, William Beggs, Meredith Yeager, Stephen Chanock, Thomas B. Nyambo, Sabah A. Omar, Dawit Woldemeskel, Gurja Belay, Hongzhe Li, Christopher D. Brown, Sarah A. Tishkoff
Summary: By mapping expression and splicing QTLs in a diverse cohort of 162 Africans, we found that the gene regulatory architecture is broadly shared between African and non-African populations, but individual loci show significant variation across populations. QTL mapping in Africans improves the detection and fine-mapping of expression QTLs compared to European Americans. Integrating QTL scans with signatures of natural selection revealed genes related to immunity, metabolism, and pigmentation that are highly differentiated between Africans and non-Africans.
Article
Biochemistry & Molecular Biology
Tarang K. Mehta, Luca Penso-Dolfin, Will Nash, Sushmita Roy, Federica Di-Palma, Wilfried Haerty
Summary: The divergence of regulatory regions and gene regulatory network (GRN) rewiring is an important driver of cichlid phenotypic diversity. This study links miRNA-binding site turnover to GRN evolution across cichlids and identifies species-specific networks associated with cichlid phenotypic traits. The findings suggest that positive selection acting upon discrete mutations in regulatory regions plays a role in rewiring GRNs in rapidly radiating cichlids.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Elliott Scott, Duncan E. Edgley, Alan Smith, Domino A. Joyce, Martin J. Genner, Christos C. Ioannou, Sabine Hauert
Summary: We studied two morphologically divergent species of fish and their hybrids to investigate the association between lateral line morphology and collective behavior. Our results showed that individuals with larger canal pore sizes and fewer superficial neuromasts were associated with closer proximities to neighboring fish. Hydrodynamic modeling of an artificial lateral line sensor supported these findings by demonstrating that simulated canal-based neuromasts were less susceptible to saturation during unidirectional movement, while increasing the canal pore size of the simulated lateral line sensor elevated sensitivity to vortices shed by neighboring fish. Our study proposes a mechanism behind lateral line flow sensing during collective behavior in fishes.
ROYAL SOCIETY OPEN SCIENCE
(2023)
Article
Multidisciplinary Sciences
Thomas Schmitt, Werner Ulrich, Andjela Delic, Mike Teucher, Jan Christian Habel
Summary: Species community structures in East African drylands are highly sensitive to both natural and anthropogenic impacts, with seasonality playing a significant role in resource availability and species composition. Farmland and savannah support distinct butterfly communities, with human activities buffering the seasonal fluctuations in detectable species abundances. Strict habitat associations are weaker in the savannah region, suggesting a more generalized species distribution compared to the farmland area.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Silvia Medda, Maria Teresa Sanchez-Ballesta, Irene Romero, Leonarda Dessena, Maurizio Mulas
Summary: For the myrtle species, different genotypes produce dark-blue or white berries depending on peel color, with dark-blue cultivars showing increased anthocyanin content and specific flavonoid gene expression compared to white cultivars. The transcript levels of UFGT in dark-blue cultivars corresponded with anthocyanin accumulation, while gene expression for flavonols and flavan-3-ols were modulated differently during ripening.
Article
Dentistry, Oral Surgery & Medicine
L. Fan, Y. J. Ou, Y. X. Zhu, Y. D. Liang, Y. Zhou, Y. N. Wang
Summary: The study revealed the crucial role of LIF in tooth development, showing that Lif deficiency in mice resulted in whitened incisors, shorter length, decreased enamel surface hardness and acid resistance. Furthermore, Lif deficiency affected iron transportation in maturation-stage ameloblasts. The results indicated that Lif modulated the expression of iron-related proteins in enamel development through the Stat3 signaling pathway.
JOURNAL OF DENTAL RESEARCH
(2022)
Article
Microbiology
Paulina Fermani, Sebastian Metz, Vanessa Balague, Jean Pierre Descy, Cedric Morana, Ramiro Logares, Ramon Massana, Hugo Sarmento
Summary: The study revealed a high diversity of protists in the East African Great Lakes, with a large proportion of unknown species suggesting novel diversity. Environmental factors such as geography, depth, and water properties play significant roles in shaping the protistan community composition and distribution in these lakes.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Fisheries
Jidapa Yamkasem, Chutchai Piewbang, Somporn Techangamsuwan, Felipe Pierezan, Esteban Soto, Win Surachetpong
Summary: The results indicate that ornamental Malawi cichlid can be infected with Tilapia lake virus (TiLV), leading to severe symptoms and mortality. The infected fish show various clinical signs and histopathological changes, suggesting that ornamental African cichlids could be potential carriers for TiLV.
Article
Biotechnology & Applied Microbiology
Fan Ren, Quan Zhou, Yinglu Meng, Wenjie Guo, Qin Tang, Jie Mei
Summary: This study identified evaluation indicators for fish egg quality by combining the study of fertilization rate, hatching rate, embryo malformation rate and gene expression profile. A cluster of RNA-binding proteins were found to potentially regulate egg quality.
Article
Multidisciplinary Sciences
Fabien Guegan, K. Shanmugha Rajan, Fabio Bento, Daniel Pinto-Neves, Mariana Sequeira, Natalia Guminska, Seweryn Mroczek, Andrzej Dziembowski, Smadar Cohen-Chalamish, Tirza Doniger, Beathrice Galili, Antonio M. Estevez, Cedric Notredame, Shulamit Michaeli, Luisa M. Figueiredo
Summary: This study identified 1428 previously uncharacterized lncRNA genes in the T. brucei genome. The key regulator, grumpy lncRNA, was found to promote parasite differentiation into the quiescent stumpy form, with this function being promoted by the encoded small nucleolar RNA. Overexpression of grumpy reduced parasitemia in infected mice.
Article
Ecology
Athimed El Taher, Astrid Boehne, Nicolas Boileau, Fabrizia Ronco, Adrian Indermaur, Lukas Widmer, Walter Salzburger
Summary: The study focused on the evolution of gene expression in cichlid fishes from Lake Tanganyika, revealing variations in the rate of gene expression evolution among different organs, transcriptome parts, and subclades of the radiation. The study also found that noncoding parts of the transcriptome evolved more rapidly than coding parts, and that gonadal transcriptomes evolved faster than somatic ones. The rate of gene expression change was not constant and accelerated in the later phase of the radiation, with per-gene level evolution patterns dominated by stabilizing selection.
NATURE ECOLOGY & EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Vendula Slechtova, Zuzana Musilova, Heok Hui Tan, Maurice Kottelat, Jorg Bohlen
Summary: The study found that the current classification of Nemacheilus species is actually a polyphyletic assemblage with some undescribed new species. Three major clades were identified within the genus Nemacheilus, classified based on their pigmentation pattern, with origins mainly in mainland Southeast Asia. In contrast, the genus Pangio originated in Sundaland and extended northwards into Indochina and northern India.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Virginie Ricci, Fabrizia Ronco, Zuzana Musilova, Walter Salzburger
Summary: This study examined the diversity and sequence evolution of RH1 in the adaptive radiation of cichlid fishes in Lake Tanganyika, focusing on adaptations to the environmental light with respect to depth. The findings show that Tanganyikan cichlid genomes contain a single copy of RH1 and have several variable sites that may be functionally important in terms of depth-related adaptations. The study provides new insights into the evolution of RH1 in a freshwater environment.
Article
Environmental Sciences
Jaroslav Semerad, Petra Horka, Alena Filipova, Jaroslav Kukla, Katerina Holubova, Zuzana Musilova, Katerina Jandova, Jan Frouz, Tomas Cajthaml
Summary: This study assessed the geographical trends of fish contamination by per- and polyfluorinated alkyl substances (PFASs) in the Czech section of the Elbe River and its tributary. Long chain PFASs were found in higher concentrations, while short-chain PFASs and Gen-X were detected in lower quantities. The study also revealed that PFAS concentrations increased downstream and were positively correlated with δ N-15 and negatively correlated with δ C-13. Additionally, molecular mass and the number of fluorine substituents were found to play crucial roles in PFAS bioaccumulation.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Genetics & Heredity
Telma G. Laurentino, Nicolas Boileau, Fabrizia Ronco, Daniel Berner
Summary: This study identified a new candidate locus, EDAR, for lateral plate number in stickleback fish through genome-wide differentiation mapping. The study illustrates the power of pooled whole-genome sequencing and provides opportunities for exploring the population genetics and ecological significance of stickleback armor evolution.
G3-GENES GENOMES GENETICS
(2022)
Article
Evolutionary Biology
Viviana Astudillo-Clavijo, Melanie L. J. Stiassny, Katriina L. Ilves, Zuzana Musilova, Walter Salzburger, Hernan Lopez-Fernandez
Summary: African cichlids are highly diverse vertebrates and serve as a model system in evolutionary research. This study investigates the relationships of African cichlids and their close relatives using species tree and hybrid network analyses. The findings provide robust hypotheses for higher-level relationships and reveal widespread gene heterogeneity.
SYSTEMATIC BIOLOGY
(2023)
Article
Fisheries
Frederic D. B. Schedel, Zuzana Musilova, Adrian Indermaur, Arnold Roger Bitja-Nyom, Walter Salzburger, Ulrich K. Schliewen
Summary: This study provides the first molecular evidence for the phylogenetic position of the small cyprinid genus Prolabeops from Cameroon, revealing its close relationship with African Smiliogastrinae. The results also highlight the need for a taxonomic revision of the small African barbs in the genus Enteromius.
JOURNAL OF FISH BIOLOGY
(2022)
Article
Biology
Nik Lupse, Monika Klodawska, Veronika Truhlarova, Prokop Kosatko, Vojtech Kaspar, Arnold Roger Bitja Nyom, Zuzana Musilova
Summary: Fish often change their habitat and trophic preferences during development, which also affects their sensory systems, including vision. This study investigates the gene expression profiles of photoreceptors in the retina during development using comparative transcriptomics on 63 fish species. The findings suggest general developmental patterns of opsin expression and reveal specific changes in selected species, providing molecular support for understanding the stage-specific visual features and shifts in fish.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Chemistry, Applied
Subham Mukherjee, Petr Hanak, Diliara Jilkova, Zuzana Musilova, Petra Horka, Zdenek Lerch, Kamila Zdenkova, Eliska Cermakova
Summary: Globalisation has led to increased trade and consumption of fish, increasing the likelihood of fish adulteration. Researchers have developed a real-time PCR assay that can simultaneously detect and quantify European anglerfish and black-bellied anglerfish, serving as a potential tool in preventing illegal species substitutions and food fraud.
JOURNAL OF FOOD COMPOSITION AND ANALYSIS
(2023)
Article
Multidisciplinary Sciences
Laura Baldo, Giacomo Tavecchia, Andreu Rotger, Jose Manuel Igual, Joan Lluis Riera
Summary: This study used the endemic Balearic wall lizard to investigate the interaction between host and microbial diversity. The research found that the major composition of the host's microbiota remained consistent across populations and exhibited unique microbial signatures at a finer taxonomic level. Seasonality had a significant impact on microbiota diversity, while the effects of sex and age were minimal. The study suggests a parallel diversification process between the host and associated gut microbes and highlights the importance of microbial plasticity in the lizard's adaptation to resource-constrained environments.
Article
Ecology
Petra Horka, Zuzana Musilova, Katerina Holubova, Katerina Jandova, Jaroslav Kukla, Jitka Rutkayova, John Iwan Jones
Summary: This study examined the effect of environmental factors on trophic interactions within river fish assemblages using stable isotope ratios. The results showed that nutrient loading significantly influenced the overall trophic niche and position of species, suggesting the importance of eutrophication for fish assemblages.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biodiversity Conservation
Katerina Holubova, Zuzana Musilova, Petra Horka
Summary: This study provides length-weight relationships (LWRs) data for 17 fish species from rivers Vltava and Elbe in the Czech Republic. The results show significant LWRs in riverine environments, which can be used for fisheries management and future research.
EUROPEAN JOURNAL OF ENVIRONMENTAL SCIENCES
(2022)
Article
Genetics & Heredity
Jessica Gomez-Garrido, Fernando Cruz, Tyler S. Alioto, Nathalie Feiner, Tobias Uller, Marta Gut, Ignacio Sanchez Escudero, Giacomo Tavecchia, Andreu Rotger, Katherin Eliana Otalora Acevedo, Laura Baldo
Summary: This study reports the first high-quality assembly and annotation of the P. lilfordi genome, along with its mitogenome, using a mixed sequencing strategy. The genome assembly is highly contiguous and complete, and the annotation reveals a large number of protein-coding genes. Comparison to a related species showed substantial similarity in genome size, annotation metrics, repeat content, and collinearity. This genome provides a critical resource for studying the molecular and evolutionary processes underlying the phenotypic diversity of this insular species, as well as for conservation genomics.
Article
Neurosciences
Zuzana Musilova, Fabio Cortesi
Summary: Vertebrates have evolved four visual cone opsin classes that allow sensitivity to different wavelengths of light. The RH2 opsin, which is sensitive to green light, has undergone gene duplications, losses, and conversions in the evolution of teleost fishes. By studying the genomes and retinal/eye transcriptomes of 132 teleost species, researchers found a varying number of RH2 gene copies per species and identified conserved gene clusters. The study also revealed a correlation between habitat depth and the presence of certain opsin genes in the visual system of teleost fishes.
Article
Multidisciplinary Sciences
Virginie Ricci, Fabrizia Ronco, Nicolas Boileau, Walter Salzburger
Summary: Through studying the retinal transcriptomes of cichlid fishes from Lake Tanganyika, we found that adaptive changes in gene expression at the macro-evolutionary and ecosystem level primarily occur through variation in the expression of a subset of cone opsin genes.