Article
Biochemistry & Molecular Biology
Qiaoqiao Liu, Yao D. Cai, Ling Ma, Hangrui Liu, Tianye Linghu, Shaokun Guo, Shujun Wei, Fan Song, Li Tian, Wanzhi Cai, Hu Li
Summary: Research found that thrips mitochondrial genomes have highly rearranged gene orders, with Tubulifera having more complex pathways in gene order evolution compared to Terebrantia. Molecular calibration showed that the divergence of the two suborders occurred in the middle Triassic, and the radiation of thrips was associated with the rise and flourish of angiosperms. The study also found that gene inversion increases nonsynonymous substitution rates and provides an evolutionary hypothesis for driving diverse gene orders.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Liping Yan, Wentian Xu, Dong Zhang, Junqing Li
Summary: Flesh flies play vital roles in ecosystem, economic, forensic, and evolutionary studies due to their diverse habits as larvae. Phylogenetic studies have reached convergence, offering the opportunity to elucidate the evolution of these fast-evolving insects from the perspective of mitochondrial genome.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Plant Sciences
Yanlei Feng, Xiaoguo Xiang, Delara Akhter, Ronghui Pan, Zhixi Fu, Xiaohua Jin
Summary: This study decoded the mitochondrial genomes of Fagales, revealing their dynamic and mosaic characteristics, potentially influenced by independent and unequal transfers of third-party DNA.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Fengming Shi, Tao Yu, Yabei Xu, Sainan Zhang, Yiming Niu, Sixun Ge, Jing Tao, Shixiang Zong
Summary: In this study, the mitochondrial genomes of two Monochamus species were sequenced and annotated, revealing the characteristics and conservation of the genus' mitochondrial genomes. Phylogenetic analysis provided insights into the relationships among various species. This research is significant for understanding mitochondrial genome evolution and conducting population genetics studies.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biology
Emily Delorean, Liangliang Gao, Jose Fausto Cervantes Lopez, Brande B. H. Wulff, Maria Itria Ibba, Jesse Poland
Summary: The diversity of wheat products is largely influenced by the origin of hexaploid bread wheat, which improved dough properties in leavened breads by incorporating the D-genome of Aegilops tauschii. Despite the genetic bottleneck caused by polyploidization, Ae. tauschii remains a valuable resource for unique Glu-D1 alleles, potentially enhancing end-use quality improvement in wheat breeding programs. Through genomic analysis, researchers have identified novel Glu-D1 gene alleles in Ae. tauschii, suggesting a promising reservoir for generating higher quality wheat varieties.
COMMUNICATIONS BIOLOGY
(2021)
Article
Microbiology
John F. Wolters, Abigail L. Labella, Dana A. Opulente, Antonis Rokas, Chris Todd Hittinger
Summary: Mitochondrial genomes in eukaryotic organisms show significant variation in size, GC content, and structure across different groups. While certain species such as Metschnikowia and Saccharomyces exhibit larger mitochondrial genomes, other species may have lower GC content. The presence or absence of mitochondrially-encoded canonical Complex I genes can vary among different yeast species, with losses of these genes observed in various evolutionary lineages.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Patrice David, Cyril Degletagne, Nathanaelle Saclier, Aurel Jennan, Philippe Jarne, Sandrine Plenet, Lara Konecny, Clementine Francois, Laurent Gueguen, Noeline Garcia, Tristan Lefebure, Emilien Luquet
Summary: Cytoplasmic male sterility is a form of genetic conflict over sex determination that occurs due to differences in inheritance modes between genomic compartments. This phenomenon, which was previously known only in plants, has now been observed in animals for the first time. The study also suggests that genomic conflicts can lead to the independent evolution of similar sex determination systems in both plants and animals and greatly accelerate molecular evolution.
Review
Agriculture, Dairy & Animal Science
Vivien J. Chebii, Emmanuel A. Mpolya, Farai C. Muchadeyi, Jean-Baka Domelevo Entfellner
Summary: Ungulates are essential sources of food, labor, clothing, and transportation for humans, and they possess unique adaptive traits in various habitats. Genomics resources have helped identify genes associated with the adaptability of ungulates to their environments.
Review
Biology
Fabrizio Ghiselli, Andre Gomes-dos-Santos, Coen M. Adema, Manuel Lopes-Lima, Joel Sharbrough, Jeffrey L. Boore
Summary: The mitochondrial genomes of mollusks exhibit significant variations in size, genome structure, gene duplications and losses. These features present a great potential for studying biological history, processes, and functions, providing valuable insights into evolution and the roles of mitochondria in organismal physiology.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Ching-Ching Wee, Nor Azlan Nor Muhammad, Vijay Kumar Subbiah, Masanori Arita, Yasukazu Nakamura, Hoe-Han Goh
Summary: This study reports the complete mitogenome of the Mesta variety of Garcinia mangostana L., which has great pharmaceutical potential. The mitogenome contains a total of 371,235 bp, with 1.7% possibly originating from plastid. The analysis of the mitogenome revealed various characteristics and evolutionary information about the Mesta variety.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Jun Chen, Yu Zang, Shuo Liang, Song Xue, Shuai Shang, Meiling Zhu, Ying Wang, Xuexi Tang
Summary: This study sequenced and compared the mitochondrial genomes of Zostera japonica and Phyllospadix iwatensis, providing new evidence of genome size reduction, gene loss, and adaptive evolution in seagrasses. It found a large number of repeat sequences and extensive loss of ribosomal protein genes in seagrass species. Additionally, it identified positive selection genes associated with seagrass adaptation to the marine environment.
Article
Genetics & Heredity
Xiaolei Yu, Hongxia Yang, Jie Liu, Yingju Qi, Liran Sun, Xiaoxuan Tian
Summary: Next-generation sequencing has greatly advanced insect mitogenomic research, but current methods relying on total DNA are not cost-effective. This study introduces a strategy using RCA technique to efficiently enrich insect mtDNA, achieving over 80% mtDNA content in tested insects. The strategy is also applicable to other invertebrates and some vertebrates, providing deep coverage for mitogenome assembly.
Article
Biochemistry & Molecular Biology
Solomon T. C. Chak, Juan Antonio Baeza, Phillip Barden
Summary: The study on socially diverse snapping shrimps in the marine realm reveals that eusociality impacted the evolution of mitochondrial genomes, influenced by extended generation times and reduced effective population sizes. This is the first direct evidence of eusociality affecting genome evolution in marine taxa.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Shiqian Feng, Andrea Pozzi, Vaclav Stejskal, George Opit, Qianqian Yang, Renfu Shao, Damian K. Dowling, Zhihong Li
Summary: "Contrary to expectations, this study found that mt-genome fragmentation is not correlated with the increase in mt-genome rearrangements in a genus of booklice, Liposcelis. The researchers proposed that fragmentation of the mt-genome may be a consequence of recombination errors between mt-genome copies, which is linked to a heightened mutation rate in clades exhibiting mt-fragmentation. Furthermore, the study showed that species with fragmented mt-genomes diverge more rapidly, despite experiencing strong purifying selection."
Article
Biochemistry & Molecular Biology
Kang-Kang Sun, Yi Ding, Lei Chen, Jing-Tao Sun
Summary: This study investigates the influence of climate on mitochondrial genome evolution by comparing the selection pressures acting on mitochondrial genomes of two rice planthoppers. The results show that the mitochondrial genomes of both species undergo primarily purifying selection, with varying degrees among different protein-coding genes. Additionally, stronger purifying selection is observed in the mitochondrial genomes of one species compared to the other.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Qinglan Sun, Chang Shu, Wenyu Shi, Yingfeng Luo, Guomei Fan, Jingyi Nie, Yuhai Bi, Qihui Wang, Jianxun Qi, Jian Lu, Yuanchun Zhou, Zhihong Shen, Zhen Meng, Xinjiao Zhang, Zhengfei Yu, Shenghan Gao, Linhuan Wu, Juncai Ma, Songnian Hu
Summary: This research established an evaluation and prewarning system to monitor the genomic variation risks of SARS-CoV-2. It analyzed the effects of known and virtual variations on viral properties from the perspectives of genomics and structural biology, and verified the effectiveness of these characteristics for risk prediction using an artificial intelligence algorithm.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Sen Wang, Shenghan Gao, Jingyi Nie, Xinyu Tan, Junhua Xie, Xiaochun Bi, Yan Sun, Sainan Luo, Qianhui Zhu, Jianing Geng, Wanfei Liu, Qiang Lin, Peng Cui, Songnian Hu, Shuangyang Wu
Summary: This study updated the 93-11 genome assembly to a gap-less sequence using various methods and techniques. The comparison with the reference genome confirmed the mapping of sequencing data from indica rice to the 93-11 genome. The study also identified gene expression patterns related to seed development, alternative splicing of starch synthesis-related genes, and genomic variations.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Li Wang, Tao Yu, Yaxin Zhu, Yingfeng Luo, Fan Dong, Xuemei Lin, Wenzhong Zhao, Zilong He, Songnian Hu, Zhiyang Dong
Summary: This study demonstrates that microbial networks on the scalp and hair surface of dandruff patients are less stable compared to their healthy counterparts, with lower node degree and more positive and stronger links. Lactobacillus bacteria have extensive interactions with other bacteria or fungi on the scalp and hair surface.
Article
Microbiology
Na Liu, Xin Zheng, Qianhui Zhu, Zilong He, Songnian Hu
Summary: Acinetobacter baumannii is a common hospital pathogen that has been increasing in strains carrying the NDM-1 gene. Through investigating 186 strains with the NDM-1 gene, this study aims to provide a theoretical basis for preventing the dissemination of NDM-1 in A. baumannii.
CURRENT MICROBIOLOGY
(2022)
Article
Environmental Sciences
Kexin Li, Qianhui Zhu, Fan Jiang, Huixia Li, Jingying Liu, Tao Yu, Yiyang Du, Li Yang, Zilong He, Songnian Hu
Summary: Our study revealed significant changes in microbial composition within months in ICUs, with significant differences in alpha and beta diversities among the 12 sampling months in each ICU. Additionally, several HAI-related bacteria persisted, including Acinetobacter, Pseudomonas, Staphylococcus, Escherichia, and Enterococcus. Source tracking analysis indicated that most bacteria in both ICUs originated from buildings or human skin.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Mianzhi Yao, Qianhui Zhu, Jin Zou, Abebe Mekuria Shenkutie, Songnian Hu, Jiuxin Qu, Zilong He, Polly H. M. Leung
Summary: In this study, the genome assembly and characterization of a uropathogenic E. coli ST405 strain, SZESBLEC201, were reported. The strain carries three plasmids, with two of them harboring antibiotic resistance genes. Only one plasmid can be transferred via conjugation. The unique virulence pattern of SZESBLEC201 compared to genetically similar strains and the global spread of antibiotic resistance genes were highlighted.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Medicine, General & Internal
Yuting Wang, SongNian Hu, XinYu Tan, Qingqing Sang, Peng Shi, Chun Wang, Daoqian Sang
Summary: This study aimed to identify possible pathogenic gene mutations in a family with tuberous sclerosis complexes (TSCs). Through clinical evaluations and genetic sequencing, a splicing site mutation was found in the 9th intron region of TSC1. This suggests that mutations in intron regions may contribute to the development of TSC.
INTERNATIONAL JOURNAL OF GENERAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Jianing Geng, Sainan Luo, Hui-Ru Shieh, Hsing-Yi Wang, Songnian Hu, Yi-Ywan M. Chen
Summary: This study identified CodY orthologues and corresponding regulons in Gram-negative Synergistetes, and confirmed a novel palindromic sequence with AT-rich arms in the promoters of putative codY-containing operons. The function of this consensus sequence was tested using a recombinant CodY protein in Synergistetes, showing similarities to Firmicutes CodY.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Yongqin Liu, Mukan Ji, Tao Yu, Julian Zaugg, Alexandre M. Anesio, Zhihao Zhang, Songnian Hu, Philip Hugenholtz, Keshao Liu, Pengfei Liu, Yuying Chen, Yingfeng Luo, Tandong Yao
Summary: The study presents a comprehensive glacier microbial genome and gene catalog from Tibetan glaciers, which includes genomes and metagenome-assembled genomes representing 968 candidate species from 30 phyla. The catalog also contains over 25 million non-redundant protein-encoding genes and has demonstrated its utility in exploring secondary metabolite biosynthetic potentials, identifying virulence factors, and comparing global glacier metagenomes.
NATURE BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Tao Yang, Rong Liu, Yingfeng Luo, Songnian Hu, Dong Wang, Chenyu Wang, Manish K. Pandey, Song Ge, Quanle Xu, Nana Li, Guan Li, Yuning Huang, Rachit K. Saxena, Yishan Ji, Mengwei Li, Xin Yan, Yuhua He, Yujiao Liu, Xuejun Wang, Chao Xiang, Rajeev K. Varshney, Hanfeng Ding, Shenghan Gao, Xuxiao Zong
Summary: In this study, a de novo assembly and annotation of a pea cultivar ZW6 was reported, which showed significant improvements in contig length and sequence quality compared to existing ones. The genome diversity analysis revealed that Pisum abyssinicum is a distinct species from P. fulvum and P. sativum within Pisum. Quantitative trait locus analyses identified Mendel's genes related to stem length and seed shape, as well as candidate genes for pod form. The construction of a pan-genome of 116 pea accessions revealed distinct functional enrichment in preferred genes of P. abyssinicum and P. fulvum. These findings provide insights into pea genome evolution and domestication, and offer valuable genomic resources for pea improvement.
Article
Immunology
Si Yu, Xiaomeng Ge, Hui Xu, Bei Tan, Bowen Tian, Yujie Shi, Yimin Dai, Yue Li, Songnian Hu, Jiaming Qian
Summary: This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI. The results showed that IBD patients with CDI had decreased bacterial alpha diversity and significant differences in bacterial and fungal beta diversity compared to healthy individuals and IBD patients without CDI. Specific bacterial and fungal taxa were overrepresented in IBD patients with CDI. These findings provide insights into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Microbiology
Yahui Guo, Xiaojie Yu, Jixiao Wang, De Hua, Yuanhai You, Qingbo Wu, Qinglong Ji, Jianzhong Zhang, Liefei Li, Yuan Hu, Zhonghui Wu, Xiaoyue Wei, Lianqun Jin, Fanliang Meng, Yuhua Yang, Xiaofeng Hu, Lijin Long, Songnian Hu, Heyuan Qi, Juncai Ma, Wenwen Bei, Xiaomei Yan, Haibin Wang, Zilong He
Summary: ST7 Staphylococcus aureus, which is highly prevalent in humans, pigs, and food in China, has rarely been reported to cause staphylococcal food poisoning (SFP). However, a recent outbreak of SFP caused by ST7 S. aureus strains occurred in two kindergartens in Hainan Province, China. Whole-genome sequencing analysis revealed the genetic characteristics and phylogenetic relationships of these SFP strains and provided insights into the potential risk of this emergent ST7 clone for SFP.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Zhi-Lin Ling, Bin Cao, Song-Nian Hu, Jia-Ning Geng, Fei Liu, Dong-Mei Liu, Rui-Lin Zhao
Summary: Agaricus sinodeliciosus, a rare wild edible mushroom from northwest China, shows unique genome changes and activates specific genes for saline-alkali tolerance. Transcriptomic analyses reveal the importance of carbon and nitrogen utilization, cell stability, and fruit body formation under mildly alkaline conditions. This research enhances our understanding of the genomic evolution and mechanisms of A. sinodeliciosus in tolerance to saline-alkali environments.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Qianhui Zhu, Shenghan Gao, Binghan Xiao, Zilong He, Songnian Hu
Summary: In this study, a novel plasmid prediction tool called Plasmer was proposed, which combines the advantages of shared k-mers and genomic features. Plasmer can predict plasmids in multiple species and has achieved high accuracy on contigs above 500 bp. It outperforms existing methods in terms of performance and has balanced sensitivity and specificity.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Chang Shu, Qinglan Sun, Guomei Fan, Kesheng Peng, Zhengfei Yu, Yingfeng Luo, Shenghan Gao, Juncai Ma, Tao Deng, Songnian Hu, Linhuan Wu
Summary: The VarEPS-Influ database is a risk assessment system for influenza virus variations that comprehensively evaluates various aspects of mutations, including physical and chemical properties, structural features, receptor affinity, antibody binding capacity, etc., and considers factors such as time and spatial distribution and host species distribution. It accurately evaluates and predicts the risk of influenza virus variations.
NUCLEIC ACIDS RESEARCH
(2023)