Article
Biochemistry & Molecular Biology
Alan M. Cleary, Andrew D. Farmer
Summary: The Genome Context Viewer is a web application that identifies, aligns, and visualizes genomic regions based on micro and macrosyntenic structures. It allows real-time computation and display of relationships between regions across multiple assemblies, enabling users to explore annotated genomes and gain insight into evolutionary mechanisms associated with functional consequences.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Kenta Shirasawa, Sogo Nishio, Shingo Terakami, Roberto Botta, Daniela Torello Marinoni, Sachiko Isobe
Summary: This study utilized long-read sequencing and genetic mapping to generate genome sequences of Japanese chestnut at the chromosome level, revealing valuable information about its chromosomal structure and genetic makeup.
Article
Microbiology
Ching-Ting Huang, Shu-Ting Cho, Yu-Chen Lin, Choon-Meng Tan, Yi-Ching Chiu, Jun-Yi Yang, Chih-Horng Kuo
Summary: This study obtained the complete genome sequence of a phytoplasma associated with witches' broom disease of loofah and found that the genome has remarkably high repetitiveness. The study also classified the phytoplasma-specific mobile genetic elements into three types and showed their significance in phytoplasma genome variability.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Choon Meng Tan, Yu-Chen Lin, Jian-Rong Li, Yuan-Yu Chien, Chien-Jui Wang, Lin Chou, Cheng-Wei Wang, Yi-Ching Chiu, Chih-Horng Kuo, Jun-Yi Yang
Summary: This study successfully developed a method combining immunoprecipitation-based enrichment and MinION long-read DNA sequencing to tackle the challenges in phytoplasma genome studies, resulting in the first complete genome sequence available for 16SrII phytoplasmas. The research revealed key genes in 'Candidatus P. aurantifolia' NCHU2014 that may be associated with host nutrient acquisition and pathogenicity.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Genetics & Heredity
Ryosuke Tokuda, Nozomu Iwabuchi, Yugo Kitazawa, Takamichi Nijo, Masato Suzuki, Kensaku Maejima, Kenro Oshima, Shigetou Namba, Yasuyuki Yamaji
Summary: Phytoplasmas are bacteria that infect plants and cause abnormal floral organ development. They possess phyllogens, which are effector proteins responsible for this abnormal development. This study analyzed the synteny of phyllogen flanking genomic regions in 17 phytoplasma strains and found that phyllogens are often flanked by potential transposable elements. These elements drive the horizontal transfer of phyllogens among different phytoplasma species and strains. These findings shed light on the sharing of symptom-determinant genes among phytoplasmas.
FRONTIERS IN GENETICS
(2023)
Article
Plant Sciences
Chanjuan Lai, Jie Wang, Shenglong Kan, Shuo Zhang, Pan Li, Wayne Gerald Reeve, Zhiqiang Wu, Yonghua Zhang
Summary: The study reports and investigates the mitogenomes of three species of the genus Broussonetia. The results show significant variations in structure, gene content, synteny, intercellular gene transfer, phylogeny, and RNA editing among the three species.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Evolutionary Biology
Richard C. Winkworth, Grace Neal, Raeya A. Ogas, Briana C. W. Nelson, Patricia A. McLenachan, Stanley E. Bellgard, Peter J. Lockhart
Summary: This study compared and phylogenetically analyzed mitochondrial genome sequences from 15 out of the 19 recognized clades of Peronosporaceae, revealing conservation of mitochondrial genome size and gene content but limited conservation of synteny. It also provided strong support for higher-level relationships within the family using concatenated mitochondrial gene sequences.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Fisheries
Fan Liu, Silu Tian, Yang Feng, Zhenyang Qin, Yi Geng, Yangping Ou, Defang Chen, Xiaoli Huang, Hongrui Guo, Zhicai Zuo, Huidan Deng, Weimin Lai
Summary: In this study, a CMTV-like ranavirus infection was reported in the rare fish species P. pingi, originating from the upper Yangtze River system of China. Infected fish exhibited ulcers on their body surface and enlarged spleen and kidney. The hexagonal virus, named P. pingi ranavirus (PPRV), was confirmed to be the causative agent. Phylogenetic analysis revealed a close relationship between PPRV and other ranaviruses from China.
Article
Biochemistry & Molecular Biology
Xiaoxiao Hu, Zeyuan Jiang, Yao Ming, Jianbo Jian, Sanjie Jiang, Dandan Zhang, Jiayong Zhang, Shanjian Zheng, Xiaodong Fang, Yulan Yang, Rongquan Zheng
Summary: This study reports the chromosomal level genome of Q. spinosa, which shows clear chromosomal differences compared to other frog species. Population analysis reveals that Chinese Q. spinosa can be divided into two genetic clusters, with the western population showing higher genetic diversity.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Public, Environmental & Occupational Health
A. Muyldermans, F. Crombe, P. Bosmans, F. Cools, D. Pierard, I Wybo
Summary: Analysis of a Serratia marcescens outbreak in an NICU from 2018-2019 revealed that replacing siphons and weekly decontamination with acetic acid were key infection control measures. Whole-genome sequencing (WGS) enabled faster recognition and accurate mapping of the outbreak, facilitating the implementation of control measures. Additionally, WGS provided valuable insights into the spread of antibiotic resistance and virulence genes.
JOURNAL OF HOSPITAL INFECTION
(2021)
Article
Biochemistry & Molecular Biology
Yunjie Pan, Gangqi Fang, Zhibo Wang, Yanghui Cao, Yongjian Liu, Guiyun Li, Xiaojing Liu, Qiang Xiao, Shuai Zhan
Summary: This study fully sequenced and de novo assembled the reference genome of the tea geometrid Ectropis grisescens, providing insight into its genome structure and characteristics, and focusing on gene families related to host plant adaptation and camouflage.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Plant Sciences
Heling Jiang, Xiaoni Zhang, Luhong Leng, Desheng Gong, Xiaohui Zhang, Junyang Liu, Dan Peng, Zhiqiang Wu, Yingxue Yang
Summary: In this study, the haplotype-resolved genome of D. caryophyllus 'Aili' was assembled for the first time at the chromosome level. The lengths of the two assembled haplotypes were determined, and structural variations between the haplotypes were identified. Phylogenetic analysis revealed the species differentiation time between carnation and gypsophila to be approximately 54.43 million years ago. This assembled and annotated genome will facilitate molecular biology studies and contribute to genome-level evolutionary research.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Qian Xiong, Yuxin Hu, Wenqi Lv, Qinghua Wang, Guoxiang Liu, Zhengyu Hu
Summary: The study identified five chloroplast genomes of Oedogonium species, revealing their structural conservation but variation in genome sizes, AT contents, introns, and repeats. Phylogenetic analyses suggested that both Oedocladium and Oedogonium are polyphyletic groups. The identification of a positively selected gene in certain species indicates adaptive evolution in terrestrial Oedogoniales taxa.
Review
Biology
Wei Wei, Yan Zhao
Summary: Phytoplasmas, vector-borne and graft-transmissible bacteria, cause various plant diseases leading to economic losses. Their identification relies on molecular techniques. Recent advances in phytoplasma taxonomy, including nomenclature, classification based on gene sequences, and fine differentiation of strains, are summarized. Challenges and future perspectives in phytoplasma taxonomy are outlined.
Article
Biotechnology & Applied Microbiology
Hongbiao Li, Ting Liu, Xiuqin Zhang, Zhiguo Xiong, Qing Hong, Shuang Jia, Yi Lin, Liping Wang, Yueliang Zhao
Summary: This study used genomic tools to characterize the probiotic and bactericidal potential of Lactiplantibacillus plantarum HY41. It was found that HY41 carried multiple functional genes and a putative bacteriocin biosynthetic cluster. A silent gene cluster responsible for producing a potent bacteriocin was also identified in HY41. The mode of action of the bacteriocin was studied and it was found to cause cell death by disrupting the cell membrane of Listeria monocytogenes. These findings confirm the probiotic and bactericidal properties of HY41 and demonstrate its potential for industrial probiotic applications.
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2023)