Article
Genetics & Heredity
Annie Robic, Chloe Cerutti, Christa Kuehn, Thomas Faraut
Summary: Circular RNAs have been observed in a wide range of species and tissues and are now acknowledged as a key component of the transcriptome. This study utilized functional datasets within the FAANG consortium to delve into the prevalence of circular RNA transcription in farm animals, particularly examining the circular transcriptome in pig, sheep, and bovine tissues. The research identified variations in circular RNA content and types across liver, muscle, and testicular tissues, with a focus on sub-exonic circRNAs produced by multi-exonic and mono-exonic genes.
FRONTIERS IN GENETICS
(2021)
Article
Parasitology
Shaohua Zhang, Bingtian Jin, Weijia Liang, Aijiang Guo, Xuenong Luo, Lixia Pu, Xiaoqing Chen, Xuepeng Cai, Shuai Wang
Summary: In this study, a new member of the SUMO protein family, TpSUMO, was identified from Taenia pisiformis and found to play a crucial role in regulating worm growth and development.
EXPERIMENTAL PARASITOLOGY
(2022)
Article
Biology
Zhenzhen Xie, Dengdong Wang, Shoujia Jiang, Cheng Peng, Qing Wang, Chunren Huang, Shuisheng Li, Haoran Lin, Yong Zhang
Summary: In this study, a high-quality, chromosome-level genome assembly of Cephalopholis sonnerati was obtained, which provides valuable resources for genetic conservation, resistance breeding, and evolution studies of this species.
Article
Environmental Sciences
Xiang Li, Xiuhong Mao, Yujin Xu, Yan Li, Nan Zhao, Junxiu Yao, Yufeng Dong, Mulualem Tigabu, Xiyang Zhao, Shanwen Li
Summary: This study identified key genes involved in Cd stress responses of Populus canadensis 'Neva' through transcriptome sequencing, providing insights into the molecular mechanisms of the species' Cd tolerance and offering critical resources for phytoremediation applications.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Veterinary Sciences
Wen-Hui Li, Yang Yang, Nian-Zhang Zhang, Jian-Kui Wang, Yin-Ju Liu, Li Li, Hong-Bin Yan, Wan-Zhong Jia, Baoquan Fu
Summary: This study utilized RNA sequencing to investigate the transcriptome profiles of different stages of the life cycle of Taenia multiceps, providing insights into the mechanisms of development and parasitic life of the parasite. The results revealed a large number of differentially expressed genes involved in cellular and metabolic processes, binding and catalytic activity, genetic information processing, and environmental information processing, as well as genes related to development and parasite-host interaction.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Plant Sciences
Xiang Li, Kewei Cai, Qiushuang Zhao, Hanxi Li, Xuelai Wang, Mulualem Tigabu, Ronald Sederoff, Wenjun Ma, Xiyang Zhao
Summary: This study sequenced and analyzed the needle transcriptomes of three major five-needle pines in northeast China to understand their genetic differentiation, evolutionary history, and adaptation to the environment. The results provide valuable insights into the genetic improvement of five-needle pines and the adaptation and evolution of Pinus species.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
P. Vignesh, C. Mahadevaiah, R. Parimalan, R. Valarmathi, S. Dharshini, Singh Nisha, G. S. Suresha, S. Swathi, H. K. Mahadeva Swamy, V Sreenivasa, K. Mohanraj, G. Hemaprabha, Ram Bakshi, C. Appunu
Summary: A comparative study on salt-responsive genes and metabolic pathways between salt-tolerant E. arundinaceus genotype IND99-907 and salinity-sensitive sugarcane genotype Co 97010 revealed that IND99-907 exhibited higher proline content, higher relative water content, intact root anatomical structures, and lower Na+/K+, Ca2+/K+, and Mg2+/K+ ratio compared to Co 97010. The differences in gene expression patterns and metabolic pathways between the two genotypes indicate unique characteristics of each in response to salt stress.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Ramon E. Rivera-Vicens, Catalina A. Garcia-Escudero, Nicola Conci, Michael Eitel, Gert Woerheide
Summary: The use of RNA sequencing and de novo transcriptome assembly is crucial for ecological and evolutionary studies, especially for nonmodel organisms lacking genome information. A multi-assembler approach, followed by a reduction step, is often employed to improve the assembly quality. TransPi is a comprehensive pipeline for de novo transcriptome assembly that achieves higher completeness percentages and reduces duplication rates compared to single assembler approaches. It is easy to configure and can be seamlessly deployed using Conda, Docker, and Singularity.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Yichao Liu, Yongtan Li, Shuxiang Feng, Shufang Yan, Jinmao Wang, Yinran Huang, Minsheng Yang
Summary: This study aimed to investigate the chloroplast genomes of five Ulmus species and compare them with other Ulmus and Ulmaceae species. The results showed that the five species had typical tetrad structure with similar GC contents. Additionally, a number of potential markers and hotspots were identified for species identification and phylogeny reconstruction within Ulmus.
SCIENTIFIC REPORTS
(2022)
Article
Veterinary Sciences
Mengting Cai, Yating Li, Guitian He, Xiaola Guo, Shaohua Zhang, Lujun Yan, Jing Zhang, Juntao Ding
Summary: The study used LC-MS/MS to profile the proteomes of Taenia hydatigena cyst scolex and the cyst without scolex, identifying 764 different proteins. Comparative analysis showed that proteins associated with growth and development were more abundant in CS, while proteins constituting a scaffolding and protective extracellular matrix were more abundant in CWS. Validation by Western blotting confirmed higher abundance of selected proteins in CWS compared to CS.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Plant Sciences
Lixiu Hou, Furui Zhang, Xincheng Yuan, Song Li, Weijun Tian, Weirong Tian, Jiaru Li
Summary: Paris species accumulate a large amount of steroidal saponins, which have numerous pharmacological activities and are important components in many patented drugs. This study investigated the composition of steroidal saponins and the molecular basis behind the differences between species. The results showed that the accumulation of steroidal saponins was tissue- and species-specific, and the differentially expressed genes related to their biosynthesis were abundantly expressed in rhizomes.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Genetics & Heredity
Mohammed Bakkali, Ruben Martin-Blazquez, Mercedes Ruiz-Estevez, Manuel A. Garrido-Ramos
Summary: The sporophyte transcriptome of Killarney fern was sequenced, revealing the species' genome characteristics and providing important data for evolutionary studies. The analysis offered insights into genes involved in key functions and genetic control of plant development, stress response, and transcription factors. Overall, this study represents a significant step towards understanding gene expression in ferns and land plants.
Article
Biotechnology & Applied Microbiology
Ning Chen, Hao Zhang, En Zang, Zhi-Xia Liu, Ya-Fei Lan, Wei-Li Hao, Shan He, Xing Fan, Gen-Lou Sun, Yi-Ling Wang
Summary: Opisthopappus taihangensis and O. longilobus are two species in the Taihang Mountains, adapted to sub-humid warm temperate and temperate continental monsoon climates, respectively. O. longilobus exhibits higher expression levels in terpenes biosynthesis, which may contribute to the divergence in fragrances between O. longilobus and O. taihangensis. 1203 genes related to adaptative divergence were identified, primarily associated with mitochondrial electron transport, starch degradation, secondary metabolism, nucleotide synthesis, and S-metabolism pathway processes.
Article
Genetics & Heredity
Chenkang Yang, Qi Zhao, Ying Wang, Jiajia Zhao, Ling Qiao, Bangbang Wu, Suxian Yan, Jun Zheng, Xingwei Zheng
Summary: The usage of synonymous codons varies among different organisms, with a bias towards G/C-ending codons observed in hexaploid wheat compared to its progenitor species. Mutation has a limited effect on codon usage, with selection playing a larger role in shaping the preferences. High GC content, gene length, chromosomal distribution density, and tRNA abundance all influence codon usage in these species. Gene Ontology enrichment analysis reveals that genes with GC bias are enriched in physiological processes, such as photosynthesis and response to acid chemical in hexaploid wheat. Additionally, certain gene families in hexaploid wheat show changes in codon usage during evolution.
FRONTIERS IN GENETICS
(2021)
Article
Environmental Sciences
Ming Liu, Shanshan Ge, Shivish Bhandari, Chunlei Fan, Yu Jiao, Chunlei Gai, Youhong Wang, Hongjun Liu
Summary: The genomes of three economically important swimming crabs, Portunus trituberculatus, Charybdis japonica, and Callinectes sapidus, were sequenced and analyzed. The study revealed high heterozygosity and repeat content in the genomes. Comparative analysis showed that P. trituberculatus and C. japonica had higher genome similarity despite belonging to different subfamilies. This finding contradicts the phylogenetic relationship inferred from previous studies. The researchers speculated that the similarity might be due to their shared habitat and different evolutionary rates of coding DNA and non-coding DNA under environmental selection.
FRONTIERS IN MARINE SCIENCE
(2022)