Article
Multidisciplinary Sciences
Thu Thi Minh Vo, Gianluca Amoroso, Tomer Ventura, Abigail Elizur
Summary: The increasing seawater temperatures in Tasmania during the summer period have led to thermal stress-induced starvation events in farmed Atlantic salmon, resulting in flesh pigment depletion. In this study, the effect of prolonged exposure to elevated water temperature on flesh pigmentation and muscle structural integrity was investigated using histological and transcriptomic analysis. The results showed that muscle degradation and atrophy were observed in fish with low flesh pigmentation, while genes related to metabolism and muscle integrity were differentially expressed in fish with high flesh pigmentation.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Marion Sinclair-Waters, Nikolai Piavchenko, Annukka Ruokolainen, Tutku Aykanat, Jaakko Erkinaro, Craig R. Primmer
Summary: Efforts to understand the genetic basis of phenotypic variation in molecular ecology are increasing. In Atlantic salmon, a study utilizing natural recombination between two candidate genes, vgll3 and akap11, found strong association between vgll3 single nucleotide polymorphisms (SNPs) and early maturation, while little or no association was found with akap11 SNPs. This suggests vgll3 as the primary candidate gene influencing early maturation.
Article
Horticulture
Hui Xia, Xiu Wang, Yuanjie Zhou, Wenyue Su, Liujing Jiang, Honghong Deng, Mingzhang Li, Qiguo Zhuang, Yue Xie, Dong Liang
Summary: The biochemical and molecular factors causing flesh-color variation between two yellow-flesh kiwifruit cultivars were identified by analyzing carotenoids, chlorophyll composition, and gene expression profile during fruit development. The brighter yellow flesh of 'Jinshi 1' was attributed to higher carotenoid/chlorophyll ratio and beta-cryptoxanthin proportion, along with differences in gene expression related to chlorophyll degradation and carotenoid formation.
SCIENTIA HORTICULTURAE
(2021)
Article
Biotechnology & Applied Microbiology
Thu Thi Minh Vo, Tuan Viet Nguyen, Gianluca Amoroso, Tomer Ventura, Abigail Elizur
Summary: The reduction in flesh pigmentation of farmed Atlantic salmon was investigated using RNA sequencing. Differential gene expression analysis between different flesh color phenotypes revealed associations with metal ion transport, oxidation-reduction processes, immune responses, and lipid metabolism. The study compared two library preparation methods and found similarities in the trend of differentially expressed genes validated by qPCR.
Article
Forestry
Weinan Li, Jiahang Che, Qile Lian, Cuiping Wang, Guoli Dai, Jinhuan Chen
Summary: Through analysis of the goji genome, 12 members of the CCO gene family were identified, including the discovery of the CCD3 gene. The gene structure and motif analysis revealed the conservation of the CCO gene family. The study also found that the CCD4-1 gene may dominate carotenoid degradation in goji fruits. These findings enhance our understanding of the functions and responses of CCOs in goji species.
Article
Plant Sciences
Muhammad Anees, Lei Gao, Muhammad Jawad Umer, Pingli Yuan, Hongju Zhu, Xuqiang Lu, Nan He, Chengsheng Gong, Mohamed Omar Kaseb, Shengjie Zhao, Wenge Liu
Summary: By utilizing weighted genes co-expression network analysis, researchers identified gene networks responsible for changes in flesh firmness of watermelon, uncovering key genes involved in cell wall biosynthesis and the ethylene signaling transduction pathway.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Jifang Zhang, Jian Zhao, Qunyun Tan, Xiaojun Qiu, Shiyong Mei
Summary: This study identified key genes and transcription factors related to anthocyanin biosynthesis in different colored radish accessions. The expression levels of anthocyanin biosynthetic genes were significantly upregulated in red- and purple-colored accessions, while downregulated or absent in white and black accessions. The correlation test revealed specific structural genes and transcription factors significantly correlated with flavonoids and metabolites in the skin and flesh of the radishes. These findings provide a foundation for future studies on genetic diversity and gene functions in radish pigmentation.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Wenwen Wang, Yujia Yang, Suxu Tan, Tao Zhou, Yang Liu, Changxu Tian, Lisui Bao, De Xing, Baofeng Su, Jinhai Wang, Yu Zhang, Shikai Liu, Huitong Shi, Dongya Gao, Rex Dunham, Zhanjiang Liu
Summary: The X and Y chromosomes of channel catfish have the same gene contents. The X-borne hydin-1 gene is silenced, while the Y-borne hydin-1 gene is expressed, resulting in monoallelic expression of hydin-1 responsible for sex determination, similar to genomic imprinting. Treatment with a methylation inhibitor, 5-aza-dC, erases the epigenetic marks and causes sex reversal.
Article
Green & Sustainable Science & Technology
Hitesh Tikariha, Hemant J. Purohit
Summary: The study generated 27 high-quality genomes representing 70% of the community through co-assembly from metagenome data, revealing a functional hierarchy within the community. Genomic comparison showed various scenarios of genomic adaptation and the existence of metabolic plasticity, collectively increasing the community's metabolic capacity.
JOURNAL OF CLEANER PRODUCTION
(2021)
Article
Biochemistry & Molecular Biology
Joao Pedro de Magalhaes, Zoya Abidi, Gabriel Arantes dos Santos, Roberto A. Avelar, Diogo Barardo, Kasit Chatsirisupachai, Peter Clark, Evandro A. De-Souza, Emily J. Johnson, Ines Lopes, Guy Novoa, Ludovic Senez, Angelo Talay, Daniel Thornton, Paul Ka Po To
Summary: This article introduces the key features and recent enhancements of the Human Ageing Genomic Resources (HAGR), focusing on its six main databases. These databases cover information related to genes and ageing, longevity, life-history, cellular senescence, and genetic variants associated with human longevity. HAGR also provides various tools and gene expression signatures.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Na Liu, Danping Liu, Kexin Li, Songnian Hu, Zilong He
Summary: This study utilized Staphylococcus aureus as a model organism to investigate the driving factors influencing bacterial pan-genome composition. The research found that the sequence type plays a significant role in the dynamic distribution of bacterial genes. A new classification method and marker gene combination were proposed, providing insights for the classification of Staphylococcus aureus.
MICROBIOLOGY SPECTRUM
(2022)
Article
Plant Sciences
Di Wang, Tao Yang, Yangqian Li, Fang Deng, Shuai Dong, Wei Li, Yueyue He, Jinming Zhang, Liang Zou
Summary: This study investigated the effects of different climatic conditions on the quality of Tartary buckwheat and found that light intensity promotes the accumulation of flavonoids and the expression of key enzyme genes. Miqiao No. 1 had the highest flavonoid content and the expression levels of PAL and 4CL were positively correlated with the content of Tartary buckwheat flavonoids. Furthermore, the expression level of ANS was negatively correlated with the content of PAL, 4CL, and flavonoids.
Review
Biology
Elena Campoy, Marta Puig, Illya Yakymenko, Jon Lerga-Jaso, Mario Caceres
Summary: Supergenes play important roles in adaptation in various organisms, but their understanding in humans is limited. Genomic inversions are the main mechanism for generating and maintaining supergenes. This review focuses on two large inversions that serve as potential examples of human supergenes. The highly divergent haplotypes resulting from the 17q21.31 inversion of approximately 1.5 Mb are associated with multiple phenotypic effects, including brain-related traits, blood cells, lung function, and disease risk. By analyzing gene expression and nucleotide variation data, several candidate genes, such as CRHR1, KANLS1, and MAPT, have been identified to be responsible for these phenotypes. The 8p23.1 inversion is more complex, with no clear genetic differentiation, but it is associated with related phenotypes and gene expression differences. This study contributes to the understanding of exceptional variants and highlights the importance of inversions in human genomes.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Hooman K. Moghadam, Brede Fannemel, Ingunn Thorland, Carlos Lozano, Borghild Hillestad
Summary: Sex determination in salmonid fishes is regulated by genetic mechanisms, with males being heterogametic. The master sex-determining gene, sdY, shows variations in genomic location among and within species. Discordances in the association between sdY and gender have been reported, with some males lacking this locus and reports of females carrying sdY. This study confirmed the presence of an autosomal sdY copy in Atlantic salmon and found its localization on chromosome 3 and a putative copy on chromosome 6.
MARINE BIOTECHNOLOGY
(2023)
Article
Environmental Sciences
Dengyue Yuan, Xiaoqin Liu, Siya Wang, Haoyu Wang, Junting Li, Zhe Zhao, Lan Wei, Linfeng Cheng, Ran Teng, Zhijian Wang
Summary: In this study, three different types of chromatophores were identified in Sinibrama taeniatus, and their changes during different developmental stages were investigated. RNA-seq analysis revealed that retinol metabolism, thyroid hormone synthesis, purine metabolism, and pyrimidine metabolism pathways are closely associated with fish pigmentation. Several hub genes, including mitf, wnt 9a, wnt10b, wnt11, adcy5, edn1, adcy8, and rdh8, were identified and may play important roles in pigmentation.
FRONTIERS IN MARINE SCIENCE
(2023)
Editorial Material
Biochemistry & Molecular Biology
Sigrid Bratlie, Kristin Halvorsen, Bjorn K. Myskja, Hilde Mellegard, Cathrine Bjorvatn, Petter Frost, Gunnar Heiene, Bjorn Hofmann, Arne Holst-Jensen, Torolf Holst-Larsen, Raino S. E. Malnes, Benedicte Paus, Bente Sandvig, Sonja Irene Sjoli, Birgit Skarstein, May B. Thorseth, Nils Vagstad, Dag Inge Vage, Ole J. Borge
Article
Multidisciplinary Sciences
Ingvild S. M. Gabrielsen, Hanna Helgeland, Helle Akselsenl, Hans Christian D. Aass, Arvind Y. M. Sundaraml, Isaac V. Snowhite, Alberto Pugliese, Siri T. Flam, Benedicte A. Lie
Article
Multidisciplinary Sciences
Alex K. Datsomor, Nikola Zic, Keshuai Li, Rolf E. Olsen, Yang Jin, Jon Olav Vik, Rolf B. Edvardsen, Fabian Grammes, Anna Wargelius, Per Winge
SCIENTIFIC REPORTS
(2019)
Article
Biotechnology & Applied Microbiology
Teshome Dagne Mulugeta, Torfinn Nome, Thu-Hien To, Manu Kumar Gundappa, Daniel J. Macqueen, Dag Inge Vage, Simen Rod Sandve, Torgeir R. Hvidsten
Article
Agriculture, Dairy & Animal Science
Hanne Fjerdingby Olsen, Saija Tenhunen, Nils Ivar Dolvik, Dag Inge Vage, Gunnar Klemetsdal
ACTA AGRICULTURAE SCANDINAVICA SECTION A-ANIMAL SCIENCE
(2020)
Article
Biochemistry & Molecular Biology
Fredrik S. Skedsmo, Giulia Malachin, Dag Inge Vage, Mie Marie Hammervold, Oyvind Salvesen, Cecilie Ersdal, Birgit Ranheim, Marit H. Stafsnes, Zdenka Bartosova, Per Bruheim, Karin H. Jaderlund, Kaspar Matiasek, Arild Espenes, Michael A. Tranulis
Article
Environmental Sciences
Erica Maremonti, Dag M. Eide, Deborah H. Oughton, Brit Salbu, Fabian Grammes, Yetneberk A. Kassaye, Remi Guedon, Catherine Lecomte-Pradines, Dag Anders Brede
SCIENCE OF THE TOTAL ENVIRONMENT
(2019)
Article
Biotechnology & Applied Microbiology
Hanna Helgeland, Ingvild Gabrielsen, Helle Akselsen, Arvind Y. M. Sundaram, Siri Tennebo Flam, Benedicte Alexandra Lie
Article
Biotechnology & Applied Microbiology
Yang Jin, Alex K. Datsomor, Rolf E. Olsen, Jon Olav Vik, Jacob S. Torgersen, Rolf B. Edvardsen, Anna Wargelius, Per Winge, Fabian Grammes
Article
Biotechnology & Applied Microbiology
Matthew Kent, Michel Moser, Inger Anne Boman, Kristine Lindtveit, Mariann Arnyasi, Kristil Kindem Sundsaasen, Dag Inge Vage
Summary: The study identified a new BCO2 allele in Norwegian spælsau sheep, with a 7.9kb enJSRV sequence inserted in the first intron of the BCO2 gene. This novel BCO2 allele provides an alternative functional mechanism for BCO2 inactivation, showcasing the benefits of searching for structural variants using long-read sequencing data.
Article
Biochemical Research Methods
Maksim Zakhartsev, Filip Rotnes, Marie Gulla, Ove Oyas, Jesse C. J. van Dam, Maria Suarez-Diez, Fabian Grammes, Robert Anton Hafthorsson, Wout van Helvoirt, Jasper J. Koehorst, Peter J. Schaap, Yang Jin, Liv Torunn Mydland, Arne B. Gjuvsland, Simen R. Sandve, Vitor A. P. Martins dos Santos, Jon Olav Vik
Summary: SALARECON is a model that links the genome of Atlantic salmon to metabolic fluxes and growth, allowing for the simulation of metabolism and growth. It can be used to explain Atlantic salmon physiology and address key challenges in aquaculture.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Veterinary Sciences
Nina Hardnes Tremoen, Maren Van Son, Ina Andersen-Ranberg, Eli Grindflek, Froydis Deinboll Myromslien, Ann Helen Gaustad, Dag Inge Vage
ACTA VETERINARIA SCANDINAVICA
(2019)
