Article
Biochemistry & Molecular Biology
Qi Wang, Jie Wang, Qiong Wu, Xinyi Xu, Pei Wang, Zhengfei Wang
Summary: The study on the mitogenomes of Brachyura identified 15 gene rearrangement patterns and determined their rearrangement mechanisms. The results showed that Dromiacea did not support the monophyly of Podotremata, and Potamoidea had a close relationship with Thoracotremata.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Xun Jin, Xingle Guo, Jian Chen, Jiasheng Li, Shufei Zhang, Sixu Zheng, Yunpeng Wang, Ying Peng, Kun Zhang, Yifan Liu, Bingjian Liu
Summary: This study identified and analyzed the complete mitochondrial genome of Hemigrapsus sinensis for the first time. The genome was approximately 15,900 bp long and encoded 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. Phylogenetic analysis revealed a close relationship between H. sinensis and Hemigrapsus, and clustering with the Varunidae. This research is significant for molecular taxonomy, phylogenetic relationship, and breeding optimization within the Grapsoidea superfamily.
Article
Biology
Zhengfei Wang, Yuqing Zheng, Xinyue Zhao, Xinyi Xu, Zhiwen Xu, Chong Cui
Summary: The current classification system of the Brachyura suborder lacks representative species, leading to confusion and incomplete taxonomy. This study sequenced the mitochondrial genomes of four Gecarcinidae species and compared them with existing crab mitochondrial genomes. The results provided evidence for Tuerkayana and clarified the division of genera within Gecarcinidae. The selective pressure in the nad6 gene suggests its role in the evolutionary history of Gecarcinidae.
Article
Oceanography
Ying Zhang, Li Gong, Xinting Lu, Zengliang Miao, Lihua Jiang, Bingjian Liu, Liqin Liu, Pengfei Li, Xu Zhang, Zhenming Lu
Summary: By sequencing and comparing the mitochondrial genomes of the Varunidae genus, it was found that these genomes have similar molecular features and gene orders. Furthermore, the occurrence of large-scale gene rearrangement events can be explained by the tandem duplication/random loss model. Phylogenetic analysis revealed that all Varunidae species form a group and are sister to the Macrophthalmidae. However, the phylogenetic relationships within Varunidae are not completely consistent.
ACTA OCEANOLOGICA SINICA
(2022)
Article
Genetics & Heredity
Xinbing Duan, Xiangli Dong, Jiji Li, Jiayin Lu, Baoying Guo, Kaida Xu, Yingying Ye
Summary: The complete mitogenome of Pilumnopeus makianus was sequenced and annotated for the first time, revealing a length of 15,863 base pairs and a high AT content. Comparisons with ancestral species suggested gene rearrangement in P. makianus, and phylogenetic analysis supported the monophyly of the Pilumnidae family.
Article
Entomology
Shu-Yi Li, Yan-Min Zhao, Bing-Xin Guo, Chen-Hong Li, Bing-Jiao Sun, Xiao-Long Lin
Summary: This study reports the complete mitochondrial genome sequences of 12 Chironomus species and one Microchironomus species for the first time. The analysis of these mitogenomes, combined with previously reported ones, provides insights into the nucleotide composition, codon usage, selection pressure, and heterogeneity of Chironomus species. The phylogenetic relationships of Chironomus based on these mitogenomes were also reconstructed. The findings demonstrate the conservative nature of Chironomus mitogenomes in terms of nucleotide composition and gene order, enriching the existing knowledge of chironomid mitochondrial genomes and contributing to a better understanding of the evolutionary history of Chironomus.
Article
Environmental Sciences
Shao'e Sun, Wei Jiang, Ziming Yuan, Zhongli Sha
Summary: In this study, 12 new mitogenomes from four thoracotreme superfamilies were sequenced, and the evolution of gene rearrangement and internal phylogenetic relationships of Thoracotremata were described. Additionally, the phylogenetic position of Cryptochiroidea and Pinnotheroidea was evaluated. It was found that there are nine distinct patterns of mitochondrial gene order in Thoracotremata, and these gene orders may be correlated to specialized lifestyles.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Multidisciplinary Sciences
Jiayin Lu, Liping Xia, Xiaojuan Liu, Yanwen Ma, Jiji Li, Yingying Ye, Baoying Guo
Summary: This study determined the complete mitochondrial DNA sequence of the herbivorous crab Grapsus albolineatus and identified gene rearrangement phenomena. Phylogenetic analysis showed that Grapsidae crabs clustered as a group, with strong monophyly support for all families except Menippidae.
SCIENTIFIC REPORTS
(2022)
Article
Agriculture, Dairy & Animal Science
Laura Iacolina, Elena Buzan, Toni Safner, Nino Basic, Urska Geric, Toni Tesija, Peter Lazar, Maria Cruz Arnal, Jianhai Chen, Jianlin Han, Nikica Sprem
Summary: This study aims to resolve the controversy over the phylogeny and taxonomy of chamois species by including mitochondrial genomes of all available subspecies, resulting in the confirmation of three clades within the genus. However, further archaeological research is needed to fully understand the classification and evolution of chamois species.
Article
Entomology
Ning Liu, Lijun Fang, Yalin Zhang
Summary: This study sequenced and analyzed the mitochondrial genomes of four species in the subfamily Limenitidinae, revealing similarities in gene orientation and arrangement. Phylogenetic analysis showed that tribe levels are well-supported monophyletic groups. This work will provide a clear framework for future research on this subfamily.
Article
Entomology
Tinghao Yu, Yalin Zhang
Summary: Mileewinae, a small subfamily of Cicadellidae, has been found to form a monophyletic group within the family with a closer phylogenetic relationship to Typhlocybinae. The analysis of mitochondrial genomes provides valuable insights into the taxonomic status and phylogenetic relationships of Mileewinae.
Article
Entomology
Jin Shang, Wentian Xu, Xiaofang Huang, Dong Zhang, Liping Yan, Thomas Pape
Summary: Flesh flies (Diptera: Sarcophagidae) are a rapidly evolving group with over 3000 known species, known for their diverse breeding habits. By sequencing the complete mitochondrial genomes of five species of flesh flies and comparing them, the study found that the mitochondrial genomes matched the hypothetical condition of the insect ancestor. The evolutionary rates of the subfamilies within Sarcophagidae differed significantly, and the phylogenetic analysis supported the monophyly of Sarcophagidae and each subfamily. This study suggests that phylogenetic analysis using mitochondrial genomes may not be suitable for rapidly evolving subfamilies and that the genes ND2 and ND6 have potential as DNA markers for species identification and delimitation in flesh flies.
Article
Entomology
Huifeng Zhao, Ye Chen, Zitong Wang, Haifeng Chen, Yaoguang Qin
Summary: Chalcididae is a moderate-sized family within the superfamily Chalcidoidea in Hymenoptera, with 1548 species worldwide. Phylogenetic analysis based on mitogenomes supports the basal position and monophyly of Chalcididae within Chalcidoidea. The newly sequenced mitochondrial genomes of two Chalcididae species show similarities in structure and feature, providing insights into the evolutionary relationships among families in the Chalcidoidea superfamily.
Article
Entomology
Qi Sun, Yumeng Yang, Xiangyu Hao, Jintian Xiao, Jiaqi Liu, Xiangqun Yuan
Summary: This study sequenced and analyzed the complete mitochondrial genomes of five Coeliadinae species, showing their typical characteristics and high conservation, contributing to the understanding of their phylogenetic relationships. Expanding sampling and utilizing gene data from GenBank, the study supports the monophyletic nature of Coeliadinae through phylogenetic analyses using maximum likelihood and Bayesian inference methods.
Article
Entomology
Yan Jiang, Hao-Xi Li, Xiao-Fei Yu, Mao-Fa Yang
Summary: Atkinsoniella is a large genus with around 99 species, and analysis of their mitochondrial genomes can provide valuable data for understanding their characteristics and phylogenetic relationships.
Article
Fisheries
Dan Tang, Xueling Shi, Huayun Guo, Yuze Bai, Chenchen Shen, Yiping Zhang, Zhengfei Wang
FISH & SHELLFISH IMMUNOLOGY
(2020)
Article
Chemistry, Multidisciplinary
Daizhen Zhang, Peisong Zhao, Jun Liu, Tingting Qi, Quning Liu, Senhao Jiang, Huabin Zhang, Zhengfei Wang, Boping Tang, Ge Ding
Article
Marine & Freshwater Biology
Zhengfei Wang, Dan Tang, Huayun Guo, Xueling Shi
Article
Biochemistry & Molecular Biology
Xinyi Xu, Qi Wang, Qiong Wu, Jiayan Xu, Jie Wang, Zhengfei Wang
Summary: Brachyuran crabs are the most species-rich clades among extant Decapoda, with Varunidae and Macrophthalmidae forming a monophyletic clade as sister groups. The study of Macrophthalmus abbreviatus' mitochondrial genome revealed A+T bias and clarified the polyphyly of Ocypodoidea and Grapsoidea within Brachyura. The research provides valuable insights for the molecular classification and gene rearrangements of Macrophthalmidae and Brachyura as a whole.
BIOCHEMICAL GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Chenchen Shen, Dan Tang, Yiping Zhang, Lv Wu, Yaqi Luo, Boping Tang, Zhengfei Wang
Summary: The study identified olfactory receptors and related gene expressions in crabs, revealing their unique olfactory molecular mechanism. The research showed a specific evolutionary trend in crustaceans and two possible olfactory transduction pathways in Eriocheir japonica sinensis.
Article
Biotechnology & Applied Microbiology
Lv Wu, Dan Tang, Chenchen Shen, Yuze Bai, Kaiqin Jiang, Qian Yu, Zhengfei Wang
Summary: Cardisoma armatum, a typical member of the Gecarcinidae, exhibits significant adaptations for extended activities on land through its special gills. However, the molecular mechanisms responsible for air exposure in C. armatum are still not well understood. This study provides new insights into the molecular genetic basis of terrestrial adaptation in crabs by categorizing differentially expressed genes related to terrestrial adaptation into four broad categories.
Article
Biochemistry & Molecular Biology
Qi Wang, Jie Wang, Qiong Wu, Xinyi Xu, Pei Wang, Zhengfei Wang
Summary: The study on the mitogenomes of Brachyura identified 15 gene rearrangement patterns and determined their rearrangement mechanisms. The results showed that Dromiacea did not support the monophyly of Podotremata, and Potamoidea had a close relationship with Thoracotremata.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Marine & Freshwater Biology
Zhengfei Wang, Dan Tang, Chenchen Shen, Lv Wu
Summary: This study investigated the transcriptomic profiles of mudflat crab Parasesarma pictum and P. affine to identify key genes related to food digestion and absorption. The analysis revealed hundreds of unigenes classified as digestive enzymes, including four types of alpha amylase genes and two types of EGs in these species. This transcriptomic information will contribute to further research on crustacean biology and the molecular basis of herbivorous diet in crabs.
Article
Ecology
Dan Tang, Ruobing Liu, Xueling Shi, Chenchen Shen, Yuze Bai, Boping Tang, Zhengfei Wang
Summary: Copper (Cu2+), a major challenge in crab culture, can impact immunity, metabolism, antioxidant activity, and detoxification processes. Under Cu2+ stress, the immune response and cellular level of crabs are affected.
Article
Biochemistry & Molecular Biology
Chenchen Shen, Dan Tang, Yuze Bai, Yaqi Luo, Lv Wu, Yiping Zhang, Zhengfei Wang
Summary: Procambarus clarkii is an important model crustacean organism. This study investigated molecular mechanisms in response to ammonia stress, finding up-regulation of immune-related genes and signaling pathways to enhance immune defense, while activities of ion transport enzymes were changed for adaptation to ammonia environment. These key genes play an important role in resistance to ammonia stress for survival in high concentrations.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Fisheries
Yaqi Luo, Chenchen Shen, Dan Tang, Yuze Bai, Lv Wu, Yiping Zhang, Ya Wu, Zhengfei Wang
Summary: This study investigated the effects of ammonia exposure on immune response, oxidative stress, and apoptosis in Procambarus clarkii through transcriptomic analysis. The upregulation of immune-related genes and pathways suggests that P. clarkii can strengthen immune defense to counteract ammonia toxicity.
AQUACULTURE INTERNATIONAL
(2022)
Article
Biochemistry & Molecular Biology
Dan Tang, Ya Wu, Lv Wu, Yuze Bai, Ying Zhou, Zhengfei Wang
Summary: This study utilized comparative transcriptome analysis to identify key genes and pathways in the hepatopancreas of Chinese mitten crab under ammonia stress. The results showed significant downregulation of genes involved in protein degradation and energy metabolism, indicating decreased overall biological activity. Additionally, five genes related to high concentrations of ammonia were discovered and validated.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Marine & Freshwater Biology
Dan Tang, Ya Wu, Suping Huang, Lv Wu, Yaqi Luo, Zhengfei Wang
Summary: This study investigated the molecular mechanism of low salinity adaptation in Chinese shrimp using transcriptome analysis. Illumina sequencing technology was employed to obtain a large number of gene sequences, and differentially expressed genes were identified through comparative transcriptome analysis. The study found that Chinese shrimp accumulate reactive oxygen species (ROS) under low salinity stress, and multiple signaling pathways and the antioxidant system play important roles. Heat shock proteins also contribute to low salinity adaptation. Real-time quantitative PCR was used to validate genes associated with low salinity response.
Article
Biology
Zhengfei Wang, Yuqing Zheng, Xinyue Zhao, Xinyi Xu, Zhiwen Xu, Chong Cui
Summary: The current classification system of the Brachyura suborder lacks representative species, leading to confusion and incomplete taxonomy. This study sequenced the mitochondrial genomes of four Gecarcinidae species and compared them with existing crab mitochondrial genomes. The results provided evidence for Tuerkayana and clarified the division of genera within Gecarcinidae. The selective pressure in the nad6 gene suggests its role in the evolutionary history of Gecarcinidae.
Article
Fisheries
Dan Tang, Huayun Guo, Xueling Shi, Zhengfei Wang
TURKISH JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2020)
Article
Biotechnology & Applied Microbiology
Zutan Li, Bingbing Jin, Jingya Fang
Summary: In this study, we propose MetaAc4C, an advanced deep learning model for accurate identification of N4-acetylcytidine (ac4C) sites using pre-trained BERT and various optimization techniques. By adapting generative adversarial networks to address data imbalance and augmenting training RNA samples, our model outperforms existing methods in terms of ACC, MCC, and AUROC.
