Article
Biochemistry & Molecular Biology
Helena Westerdahl, Samantha Mellinger, Hanna Sigeman, Verena E. Kutschera, Estelle Proux-Wera, Max Lundberg, Matthias Weissensteiner, Allison Churcher, Ignas Bunikis, Bengt Hansson, Jochen B. W. Wolf, Maria Strandh
Summary: The MHC genomic region in birds, especially passerines, shows substantial structural differences and diversity in gene numbers. The MHC genes in passerines are found in two different chromosomal arrangements, with some genes being old and putatively orthologous among species, while others have evolved by simultaneous duplication of multiple genes.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Plant Sciences
Yingying Li, Wei Wang, Na Zhang, Yuxin Cheng, Saddam Hussain, Yating Wang, Hainan Tian, Hadia Hussain, Rao Lin, Yuan Yuan, Chen Wang, Tianya Wang, Shucai Wang
Summary: This study identifies ASDs as important regulators of plant responses to ABA and shows that ASDs enhance or decrease ABA sensitivity by regulating the expression of ABA response genes. ASD1/ASD3 and ASD2/ASD4 have opposite functions in this regulation.
Article
Biochemistry & Molecular Biology
Kyle E. McElroy, Stefan Mueller, Dunja Lamatsch, Laura Bankers, Peter D. Fields, Joseph R. Jalinsky, Joel Sharbrough, Jeffrey L. Boore, John M. Jr Jr Logsdon, Maurine Neiman
Summary: The study reveals that asexual reproduction in the New Zealand freshwater snail leads to significant changes in the important gene family rDNA, with asexual individuals harboring more rDNA-histone copies, potentially associated with functional consequences related to the loss of sexual reproduction.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Shyali Iroshani Rathnayaka Gamage, Anochar Kaewwongwal, Kularb Laosatit, Tarika Yimram, Yun Lin, Xin Chen, Mikio Nakazono, Prakit Somta
Summary: This study identified two genes responsible for resistance against the azuki bean weevil in TN67 and identified candidate genes for this resistance. Comparative genomics confirmed the presence of two tandemly duplicated genes, VacPGIP1 and VacPGIP2, which are likely key players in conferring resistance.
Article
Plant Sciences
Guo Xia-Yu, Zhang Meng, Zhu Ming-Dong, Long Ji-Rui, Wei Zhong-Wei, Li Jian-Wu, Zhou Bin, Ai Zhi-Yong, Deng Hua-Feng
Summary: This study investigates the salt tolerance mechanism of the super hybrid rice Chaoyouqianhao and identifies the importance of the ubiquitination pathway in its salt tolerance. Several novel candidate genes are also identified. This research provides a theoretical basis for breeding new salt-tolerant rice varieties.
Article
Biotechnology & Applied Microbiology
Pankaj Kumar Singh, Hukam C. Rawal, Alok Kumar Panda, Joy Roy, Tapan Kumar Mondal, Tilak Raj Sharma
Summary: This study aimed to understand the origin, domestication, and anthocyanin biosynthesis pathways in Black rice using next generation sequencing approaches. Various analyses were conducted for differential expression and construction of a pan-genome. The study identified and analyzed miRNAs and their target genes in regulating anthocyanin biosynthesis in NER rice for the first time, which will improve understanding of high or low anthocyanin content in different rice genotypes.
Article
Multidisciplinary Sciences
Yifeng Zhang, Jie Gao, Lin Ma, Lichan Tu, Tianyuan Hu, Xiaoyi Wu, Ping Su, Yujun Zhao, Yuan Liu, Dan Li, Jiawei Zhou, Yan Yin, Yuru Tong, Huan Zhao, Yun Lu, Jiadian Wang, Wei Gao, Luqi Huang
Summary: In this study, the authors identify two CYP82D enzymes as the 14-hydroxylases in triptolide biosynthesis and successfully produce the precursor of triptolide in engineered Saccharomyces cerevisiae. This discovery provides important genetic elements for understanding the downstream biosynthetic pathways and enabling the production of other 14-hydroxyl labdane-type secondary metabolites.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Licao Cui, Hao Cheng, Zhe Yang, Chuan Xia, Lichao Zhang, Xiuying Kong
Summary: Wheat is a staple food crop that provides 20% of total human calorie consumption. Duplicated genes in wheat evolved faster with shorter gene lengths, higher codon usage bias, lower expression levels, and higher tissue specificity. Duplicated genes have important biological functions, particularly in response to environmental stresses, and different duplication modes exhibit asymmetrical evolutionary patterns. This study lays the foundation for future functional studies on wheat.
Article
Genetics & Heredity
Yasushi Totoki, Mihoko Saito-Adachi, Yuichi Shiraishi, Daisuke Komura, Hiromi Nakamura, Akihiro Suzuki, Kenji Tatsuno, Hirofumi Rokutan, Natsuko Hama, Shogo Yamamoto, Hanako Ono, Yasuhito Arai, Fumie Hosoda, Hiroto Katoh, Kenichi Chiba, Naoko Iida, Genta Nagae, Hiroki Ueda, Chen Shihang, Shigeki Sekine, Hiroyuki Abe, Sachiyo Nomura, Tetsuya Matsuura, Eiji Sakai, Takashi Ohshima, Yasushi Rino, Khay Guan Yeoh, Jimmy So, Kaushal Sanghvi, Richie Soong, Akihiko Fukagawa, Shinichi Yachida, Mamoru Kato, Yasuyuki Seto, Tetsuo Ushiku, Atsushi Nakajima, Hitoshi Katai, Patrick Tan, Shumpei Ishikawa, Hiroyuki Aburatani, Tatsuhiro Shibata
Summary: A study on a cross-ancestry genomic and transcriptomic cohort of gastric cancer reveals significantly mutated genes and mutational signatures, some of which are specific to certain ancestries. The research involves the analysis of 1,335 cases and identifies 77 significantly mutated genes, including ARHGAP5 and TRIM49C. Subtype-specific drivers, such as PIGR and SOX9, are also identified, particularly enriched in the diffuse subtype of the disease. The findings also highlight the association of non-protein-truncating CDH1 mutations with sporadic diffuse-type cases and the link between alcohol consumption or metabolism and RHOA mutations in patients with East Asian ancestry. The study provides comprehensive insights into the molecular landscape of gastric cancer across various subtypes and ancestries.
Article
Biotechnology & Applied Microbiology
Ranjita Thapa, Rodante E. Tabien, Charles D. Johnson, Endang M. Septiningsih
Summary: In this study, a comparative gene expression analysis was conducted on two rice genotypes under cold stress, anaerobic stress, and combined cold and anaerobic stress during germination. A large number of differentially expressed genes were identified, which can be used to screen promising candidate genes for rice crops that are more tolerant to flooding and cold stress.
Article
Microbiology
Xiao Li, Jing-Nan Ren, Gang Fan, Jin He, Lu-Lu Zhang, Si-Yi Pan
Summary: Yarrowia lipolytica is an unconventional yeast widely used in the food industry for its safety, and was found to be an efficient biocatalyst for transforming (+)-valencene into (+)-nootkatone. During this transformation, genes related to secondary metabolite biosynthesis and ATP-binding cassette transporters were up-regulated, while genes involved in energy metabolism were down-regulated. Several differentially expressed genes, such as cytochrome P450 and dehydrogenase, were identified to be responsible for the biotransformation process.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Chendan Wei, Zhenyi Wang, Jianyu Wang, Jia Teng, Shaoqi Shen, Qimeng Xiao, Shoutong Bao, Yishan Feng, Yan Zhang, Yuxian Li, Sangrong Sun, Yuanshuai Yue, Chunyang Wu, Yanli Wang, Tianning Zhou, Wenbo Xu, Jigao Yu, Li Wang, Jinpeng Wang
Summary: Duplicated genes in rice subspecies generated by ancient polyploidy around 100 million years ago are still being affected by gene conversion at a high frequency, impacting the divergence of rice subspecies. Ongoing gene conversion events maintain similarity between ancient duplicates, accelerate rice divergence, and affect biological functions associated with multiple genes. The converted genes tend to have more similar expression patterns than nonconverted duplicates, suggesting interaction opportunities among members of large gene families.
Article
Agronomy
Youxin Yu, Yuanyuan Zhang, Mingshi Qian, Qiuxin Zhang, Guoqing Yang, Gang Xu
Summary: This study used RNA sequencing to compare the transcriptional profiles in the head of SBPH to investigate the genes and gene functions regulated by RSV infection. A total of 336 differentially expressed genes were identified in viruliferous SBPH head samples, including genes associated with the nervous system, cytochrome P450s, sugar metabolism, the olfactory system, and cuticular process.
Article
Microbiology
Yao Yu, Wenjuan Mo, Haiyan Ren, Xianmei Yang, Wanlin Lu, Tongyu Luo, Junyuan Zeng, Jungang Zhou, Ji Qi, Hong Lu
Summary: Kluyveromyces marxianus is a promising host for bioethanol and protein production, with high copies of genes involved in flocculation, iron transport, and biotin biosynthesis. Specific genes in K. marxianus are upregulated in rich medium, possibly related to glucose transport and mitochondrion functions. Transcriptomic analysis shows higher expression levels of TCA cycle, respiratory chain, and ATP biosynthesis genes in K. marxianus compared to S. cerevisiae under aerobic conditions.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Napaporn Sriden, Varodom Charoensawan
Summary: Comparative transcriptomic analysis provides a comprehensive understanding of transcriptional responses to temperature changes in different plant tissues, as well as the unique regulatory functions of temperature-mediating transcription factors. The goal of this study is to develop resilient cultivars to mitigate the threats of climate change on plant diversity and food security. By analyzing publicly available datasets, the researchers identified sets of temperature-responsive genes that were common or tissue-specific. Interestingly, some known temperature-responsive genes were found to be involved in cold response as well. Furthermore, the study elucidated the distinct DNA-binding patterns of key temperature transcription factors to their target genes with different transcriptional responses.
PLANT MOLECULAR BIOLOGY
(2022)
Review
Microbiology
Saraladevi Muthusamy, Daniel Lundin, Rui Miguel Mamede Branca, Federico Baltar, Jose M. Gonzalez, Janne Lehtio, Jarone Pinhassi
ENVIRONMENTAL MICROBIOLOGY
(2017)
Article
Microbiology
Hao Zhang, Susumu Yoshizawa, Ying Sun, Yongjie Huang, Xiao Chu, Jose M. Gonzalez, Jarone Pinhassi, Haiwei Luo
ENVIRONMENTAL MICROBIOLOGY
(2019)
Article
Ecology
Jose M. Gonzalez, Laura Hernandez, Iris Manzano, Carlos Pedros-Alio
Article
Biotechnology & Applied Microbiology
M. Royo-Llonch, P. Sanchez, J. M. Gonzalez, C. Pedros-Alio, S. G. Acinas
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2020)
Article
Microbiology
Laura Alonso-Saez, Xose Anxelu G. Moran, Jose M. Gonzalez
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Microbiology
Nestor Arandia-Gorostidi, Jose M. Gonzalez, Tamara M. Huete-Stauffer, Mohd Ansari, Xose Anxelu G. Moran, Laura Alonso-Saez
ENVIRONMENTAL MICROBIOLOGY
(2020)
Article
Multidisciplinary Sciences
Laura Hernandez, Alberto Vicens, Luis E. Eguiarte, Valeria Souza, Valerie De Anda, Jose M. Gonzalez
Article
Biotechnology & Applied Microbiology
Alberto J. Martin-Rodriguez, Jose A. Reyes-Darias, David Martin-Mora, Jose M. Gonzalez, Tino Krell, Ute Romling
Summary: Shewanella species have a wide respiratory adaptability, leading to differential biofilm responses to anaerobic electron acceptors among different isolates. The respiration-dependent biofilm formation may contribute to colonization in diverse environmental or host niches.
NPJ BIOFILMS AND MICROBIOMES
(2021)
Article
Biology
Silvia G. Acinas, Pablo Sanchez, Guillem Salazar, Francisco M. Cornejo-Castillo, Marta Sebastian, Ramiro Logares, Marta Royo-Llonch, Lucas Paoli, Shinichi Sunagawa, Pascal Hingamp, Hiroyuki Ogata, Gipsi Lima-Mendez, Simon Roux, Jose M. Gonzalez, Jesus M. Arrieta, Intikhab S. Alam, Allan Kamau, Chris Bowler, Jeroen Raes, Stephane Pesant, Peer Bork, Susana Agusti, Takashi Gojobori, Dolors Vaque, Matthew B. Sullivan, Carlos Pedros-Alio, Ramon Massana, Carlos M. Duarte, Josep M. Gasol
Summary: The deep sea, being the largest ocean compartment, plays a crucial role in planetary-scale biogeochemical cycling. This study highlights the functional differences in microbial communities in the deep ocean, with free-living and particle-attached lifestyles driving distinct metabolic pathways. The findings also reveal unique bacterial species and metabolic capabilities that expand our understanding of the largest Earth aquatic ecosystem.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Clara Martinez-Perez, Chris Greening, Sean K. Bay, Rachael J. Lappan, Zihao Zhao, Daniele De Corte, Christina Hulbe, Christian Ohneiser, Craig Stevens, Blair Thomson, Ramunas Stepanauskas, Jose M. Gonzalez, Ramiro Logares, Gerhard J. Herndl, Sergio E. Morales, Federico Baltar
Summary: Using a multi-omics approach, this study provides insights into the microbial communities beneath the Ross Ice Shelf in coastal Antarctica. The findings reveal a taxonomically distinct microbial community adapted to a highly oligotrophic marine environment, with aerobic lithoautotrophic archaea and bacteria driving the production of new organic carbon, and aerobic organoheterotrophic bacteria capable of degrading complex organic carbon substrates.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Benjamin Pontiller, Sandra Martinez-Garcia, Vanessa Joglar, Dennis Amnebrink, Clara Perez-Martinez, Jose M. Gonzalez, Daniel Lundin, Emilio Fernandez, Eva Teira, Jarone Pinhassi
Summary: Coastal upwelling zones are important areas of oceanic productivity. Bacteria play a vital role in the remineralization of dissolved organic matter (DOM) produced by phytoplankton, but the molecular processes involved in the regulation of phytoplankton-derived DOM turnover by bacterial taxa are not well understood. This study used metatranscriptome analysis to compare the gene expression of bacterioplankton in the Northwest Iberian upwelling system. The results showed that different bacterial taxa had specific transcriptional responses during different phases of phytoplankton bloom development, decay, and senescence. The study also highlighted the importance of gene systems involved in the degradation and uptake of carbohydrates and nitrogen-rich compounds in shaping the fate of organic matter in these upwelling-driven ecosystems.
Article
Environmental Sciences
Marta Masdeu-Navarro, Jean-Francois Mangot, Lei Xue, Miguel Cabrera-Brufau, Stephanie G. Gardner, David J. Kieber, Jose M. Gonzalez, Rafel Simo
Summary: Volatile organic compounds (VOCs) are found in marine ecosystems, including coral reefs, but their light-driven dynamics are poorly understood. A study in French Polynesia found that VOC and DMSPC concentrations varied with microbial abundances in coral reefs.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Microbiology
Laura Alonso-Saez, Antonio S. Palacio, Ana M. Cabello, Semidan Robaina-Estevez, Jose M. Gonzalez, Laurence Garczarek, Angel Lopez-Urrutia
Summary: This study analyzed the transcriptional response of Prochlorococcus under different temperatures and found that the transcriptional suppression of photosynthetic machinery at low temperature may be one of the reasons for the restricted distribution of Prochlorococcus in temperate zones.
Article
Microbiology
Federico Baltar, Clara Martinez-Perez, Chie Amano, Marion Vial, Semidan Robaina-Estevez, Thomas Reinthaler, Gerhard J. Herndl, Zihao Zhao, Ramiro Logares, Sergio E. Morales, Jose M. Gonzalez
Summary: Through studying the samples collected beneath the Ross Ice Shelf in Antarctica using single-cell genomics, community metagenomics, metatranscriptomics, and single-cell activity measurements, we identified a ubiquitous mixotrophic bacterial group (UBA868) that plays a dominant role in the expression of sulfur oxidation and dissolved inorganic carbon fixation genes, thus highlighting its global distribution and importance in the mesopelagic ocean.
NATURE MICROBIOLOGY
(2023)
Article
Microbiology
Benjamin Pontiller, Clara Perez-Martinez, Carina Bunse, Christofer M. G. Osbeck, Jose M. Gonzalez, Daniel Lundin, Jarone Pinhassi
Summary: This study utilized metatranscriptomics analysis to reveal the distribution of key gene systems involved in organic matter utilization in a stratified marine system. It found pronounced shifts in the transcription of genes encoding CAZymes, peptidases, and membrane transporters among key prokaryotic orders over depth, implying that sequential utilization and transformation of organic matter through the water column is a key feature that ultimately influences the efficiency of the biological carbon pump.
