Article
Plant Sciences
Jeffrey P. Mower, Lilly Hanley, Kirsten Wolff, Natalia Pabon-Mora, Favio Gonzalez
Summary: Aragoa, a genus of North Andean plants, is closely related to Littorella and Plantago within the Plantagineae family. Analysis of mitochondrial genomes revealed the sister relationship between Aragoa and Littorella + Plantago. However, conflicting results were found in the placement of P. nubicola within the Plantago genus based on mitochondrial and nuclear data. Extensive substitution rate variation among lineages hindered the resolution of phylogenetic relationships using mitochondrial data.
Article
Genetics & Heredity
Xiaochen Zhu, Yingying Zhao, Hua Wei, Nan Hu, Qingbiao Hu, Yingdong Li
Summary: In this study, the complete mitochondrial genome of the poorly understood leech species Torix tukubana was sequenced using next-generation sequencing. The results showed that the mitogenome consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and 1 control region. The phylogenetic analysis indicated that T. tukubana belonged to the monophyletic group of Glossiphoniidae, consistent with previous research.
Article
Genetics & Heredity
Qilemoge, Ding Yang
Summary: The mitochondrial genome of Gymnopternus bomiensis was reported in this study, and it was found to be closely related to the subfamily Dolichopodinae.
MITOCHONDRIAL DNA PART B-RESOURCES
(2022)
Article
Genetics & Heredity
Junzong He, Zhihao Zhou, Yan Huang, Jinmei Feng, Wenxiang Li, Guitang Wang, Congjie Hua
Summary: The complete mitochondrial genome of Sinergasilus major was sequenced to explore the phylogeny and mitogenomic evolution of Copepoda. The study revealed that the nad2 gene may be a better marker for investigating phylogenetic relationships among closely related species in Copepoda than the commonly used cox1 gene. Additionally, the study recovered the sister-group relationship of Siphonostomatoida and Cyclopoida.
Article
Genetics & Heredity
Bing Zhang, Shang Gao, Ding Yang
Summary: The mitogenome of Epiphragma mediale was successfully sequenced, revealing the nucleotide bias towards A and T. Bayesian inference analysis supported the monophyly of Tipuloidea, with Pediciidae identified as the basal clade. Tipulidae and Cylindrotomidae were designated as sister clades within Tipuloidea.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Genetics & Heredity
Juan Wang, Yutong Ji, Lisheng Zhang, Mengqing Wang
Summary: The mitochondrial genome of the long-legged fly Neurigona zhejiangensis was sequenced and found to belong to the subfamily Neurigoninae of Dolichopodidae, with a bias towards A and T nucleotide compositions. The study supports the monophyly of Empidoidea, Empididae, and Dolichopodidae.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Entomology
Zhicheng Zhou, Yangyang Liu, Xiangsheng Chen
Summary: The mitochondrial genomes of Denierella emmerichi, Epicauta curvispina, and Meloe poggii contain 37 genes, including 13 protein-coding genes, with varying lengths and guanine-cytosine content. Phylogenetic analysis supports the relationship within the Meloidae family and Epicauta genus, providing insights into their evolutionary history.
JOURNAL OF INSECT SCIENCE
(2021)
Article
Genetics & Heredity
Juan Wang, Yuyan Li, Lisheng Zhang, Mengqing Wang
Summary: The mitogenome of the long-legged fly Asyndetus clavipes, representing the subfamily Diaphorinae, is the first complete mitogenome sequenced within this subfamily. It has a high bias towards A and T nucleotides, and shares consistent phylogenetic relationships with other species within the family Dolichopodidae.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Genetics & Heredity
Yue Liu, Jingyu Wang, Ding Yang
Summary: The mitochondrial genome of a new representative of the family Rhagionidae, Desmomyia sinensis, was sequenced in this study, revealing a bias towards A and T nucleotides and a conservational gene arrangement similar to other published species. Bayesian inference analysis supported the monophyly of Rhagionidae and the sister relationship between Coenomyiidae and Xylophagidae.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Genetics & Heredity
Juan Wang, Yutong Ji, Lisheng Zhang, Mengqing Wang
Summary: The mitochondrial genome of the long-legged fly Xanthochlorus tibetensis was sequenced, representing the first complete mitogenome from the Xanthochlorinae subfamily. This 15,580 bp genome includes 13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs, with a bias towards A and T nucleotides. Bayesian inference supported the monophyly of Empidoidea, Empididae, and Dolichopodidae, and revealed the phylogenetic relationships within Empidoidea.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Kun Xing, Chen Kang, Fei Zhao
Summary: In this study, the complete mitochondrial genome of Tetanops sintenisi was sequenced and compared with other Diptera species. The mitogenome of T. sintenisi was found to be 15,763 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding A + T-rich region. Phylogenetic analysis based on the mitogenome sequence confirmed the close relationship between T. sintenisi and the Tephritidae family.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Genetics & Heredity
Yuanyuan Wang, Guangming Liu, Jiayu Wang, Zhipeng Sun, Ning Wang
Summary: This study reports the mitochondrial genome of the long-legged fly Dolichopus galeatus for the first time. The genome consists of 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. Phylogenetic analysis reveals the relationship between Dolichopus and Lichtwardtia.
MITOCHONDRIAL DNA PART B-RESOURCES
(2023)
Article
Genetics & Heredity
Bea A. Crisostomo, Richard V. Dumilag, Michael Y. Roleda, Arturo O. Lluisma
Summary: Researchers assembled the mitochondrial genome of Kappaphycus malesianus and found that its structure and gene arrangement were similar to other red algae mitochondrial genomes, indicating a close evolutionary relationship.
MITOCHONDRIAL DNA PART B-RESOURCES
(2023)
Article
Genetics & Heredity
Ying Wang, Jinjun Cao, David Muranyi, Xiling Chen, Fenming Yan
Summary: The genus Amphinemura, belonging to the family Nemouridae, has been studied in terms of its mitochondrial genome sequencing, revealing unique gene coding characteristics. The phylogenetic analysis also provided insights into the relationship between Amphinemura and Nemoura.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Genetics & Heredity
Ti-Lin Yi, Meng-Ting Pei, Zhi-Wei Xu, Dai-Qing Yang
Summary: This study presents the complete mitochondrial genome sequence of a new leech species Hemiclepsis yangtzenensis collected in central China, with a focus on its gene structure, repetitive sequences, and phylogenetic relationships.
MITOCHONDRIAL DNA PART B-RESOURCES
(2022)
Article
Genetics & Heredity
Na Chen, Sen Zhao, Angad Jolly, Lianlei Wang, Hongxin Pan, Jian Yuan, Shaoke Chen, Andre Koch, Congcong Ma, Weijie Tian, Ziqi Jia, Jia Kang, Lina Zhao, Chenglu Qin, Xin Fan, Katharina Rall, Zeynep Coban-Akdemir, Zefu Chen, Shalini Jhangiani, Ze Liang, Yuchen Niu, Xiaoxin Li, Zihui Yan, Yong Wu, Shuangshuang Dong, Chengcheng Song, Guixing Qiu, Shuyang Zhang, Pengfei Liu, Jennifer E. Posey, Feng Zhang, Guangnan Luo, Zhihong Wu, Jianzhong Su, Jianguo Zhang, Eugenia Y. Chen, Konstantinos Rouskas, Stavros Glentis, Flora Bacopoulou, Efthymios Deligeoroglou, George Chrousos, Stanislas Lyonnet, Michel Polak, Carla Rosenberg, Irene Dingeldein, Ximena Bonilla, Christelle Borel, Richard A. Gibbs, Jennifer E. Dietrich, Antigone S. Dimas, Stylianos E. Antonarakis, Sara Y. Brucker, James R. Lupski, Nan Wu, Lan Zhu
Summary: This study identified 12 likely gene-disrupting variants in 7 genes that are essential for Mullerian/Wolffian ducts development in individuals with MRKHS, and these variants were not found in control samples. Interestingly, there was a sex-limited penetrance with paternal inheritance in multiple families. Furthermore, a syndromic condition characterized by congenital hypothyroidism and MRKHS was identified in one individual from a PAX8-associated cohort.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Jianke Yang, Hengwu Ding, Xianzhao Kan
Summary: This study provides a comprehensive analysis on the codon usage and molecular evolution of HSP60 across birds, revealing a weak codon usage bias with high ENC values and A/T-ending codons being preferred. The evolutionary patterns of HSP60 in birds are shaped by mutation, natural selection, and genetic drift, with different lineages possibly under similar selective pressures and positive selection sites undergoing radical changes. This research contributes to a better understanding of the function diversity and molecular evolution of HSP60 in birds.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Correction
Genetics & Heredity
Jian Yuan, Qi Jiang, Tongyang Gong, Dandan Fan, Ji Zhang, Fukun Chen, Xiaolin Zhu, Xinyu Wang, Yunbo Qiao, Hongyan Chen, Zhihua Liu, Jianzhong Su
NPJ GENOMIC MEDICINE
(2021)
Article
Ophthalmology
Liangde Xu, Youyuan Zhuang, Guosi Zhang, Yunlong Ma, Jian Yuan, Changseng Tu, MiaoMiao Li, Wencan Wang, Yaru Zhang, Xiaoyan Lu, Jing Li, Xinting Liu, Zhengbo Xue, Meng Zhou, Jie Sun, Jinhua Bao, Ming Li, Fan Lu, Hong Wang, Jianzhong Su, Jia Qu
Summary: The CAMS project successfully conducted a myopia survey on a million children and adolescents in Wenzhou, China, revealing high rates of myopia and high myopia among elementary, middle, and high school students. The project utilized an efficient screening model and demonstrated significant reductions in staff, cost, and time compared with previous surveys. The findings provide valuable insights for public health intervention and myopia prevention.
Article
Plant Sciences
Qingyu Huang, Wenmin Qiu, Miao Yu, Shaocui Li, Zhuchou Lu, Yue Zhu, Xianzhao Kan, Renying Zhuo
Summary: In this study, the HMA gene family in Sedum plumbizincicola was analyzed, and 8 SpHMA genes were identified and characterized. The structural analysis showed that SpHMAs were conserved, and the promoter analysis revealed their potential role in abiotic stress response. The expression profiles demonstrated tissue specificity and regulation by heavy metal stress. These findings provide insights into the evolutionary processes and potential functions of the HMA gene family in S. plumbizincicola.
Article
Plant Sciences
Shiyun Han, De Bi, Ran Yi, Hengwu Ding, Longhua Wu, Xianzhao Kan
Summary: This study reported 13 new plastomes from genus Aeonium and the closely related genus Monanthes, and observed new markers for phylogeny and DNA barcoding. The results suggest that highly polymorphic regions, novel putative pttRNA structures, and patterns of codon usage bias and aversion derived from plastomes could have important implications for phylogenetic research and DNA barcoding of plants.
Article
Medicine, General & Internal
Zhengbo Xue, Jian Yuan, Fukun Chen, Yinghao Yao, Shilai Xing, Xiangyi Yu, Kai Li, Chenxiao Wang, Jinhua Bao, Jia Qu, Jianzhong Su, Hao Chen
Summary: This study aimed to investigate the shared genetic etiology among age-related macular degeneration (AMD), diabetic retinopathy (DR), glaucoma, retinal detachment (RD), and myopia. The analysis of genome-wide association identified meaningful genetic correlations between these ocular diseases. Cross-trait meta-analysis revealed 23 shared loci associated with at least two ocular diseases and 14 loci unique to individual disorders.
Article
Biochemistry & Molecular Biology
Shiyun Han, Rongbin Wang, Xin Hong, Cuilian Wu, Sijia Zhang, Xianzhao Kan
Summary: This study explores the phylogeny of Bletilla using plastomic markers and reveals the non-monophyletic status of the genus. It also identifies potential molecular markers for species identification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agriculture, Dairy & Animal Science
Hengwu Ding, De Bi, Shiyun Han, Ran Yi, Sijia Zhang, Yuanxin Ye, Jinming Gao, Jianke Yang, Xianzhao Kan
Summary: This study provides six new complete mitogenomes of the superfamily Certhioidea and analyzes their genomic characteristics, codon usages, evolutionary rates, and phylogenetic implications. The study suggests separating Salpornis from the family Certhiidae to maintain its monophyly. These findings contribute to further evolutionary studies within Certhioidea.
Article
Plant Sciences
Shiyun Han, Hengwu Ding, De Bi, Sijia Zhang, Ran Yi, Jinming Gao, Jianke Yang, Yuanxin Ye, Longhua Wu, Xianzhao Kan
Summary: Through the analysis of 208 plastomes from Saxifragales, this study identified genetic variations and important characteristics for intrafamilial phylogenetics, demonstrating rich lineage-specific characteristics within this order. The results provide a deeper understanding of the evolutionary patterns of Saxifragales.
Article
Biology
Hengwu Ding, De Bi, Sijia Zhang, Shiyun Han, Yuanxin Ye, Ran Yi, Jianke Yang, Birong Liu, Longhua Wu, Renying Zhuo, Xianzhao Kan
Summary: In this study, we sequenced the first mitogenome of Crassulaceae (presented by Sedum plumbizincicola) and comprehensively analyzed its structural evolution and RNA editing features. This research is important for further understanding the evolutionary history of plant mitogenomes.
Article
Biology
Hengwu Ding, Shiyun Han, Yuanxin Ye, De Bi, Sijia Zhang, Ran Yi, Jinming Gao, Jianke Yang, Longhua Wu, Xianzhao Kan
Summary: In this study, we sequenced ten plastomes of the genus Crassula and conducted comparative analysis. We found unique codon usage and aversion patterns in Crassula plastomes, and analyzed genomic features, evolutionary rates, and phylogenetic implications. Our findings are important for understanding the plastome evolution of the family Crassulaceae and provide potential molecular markers for DNA barcoding.
Article
Genetics & Heredity
De Bi, Shiyun Han, Jun Zhou, Maojin Zhao, Sijia Zhang, Xianzhao Kan
Summary: This study provides a comprehensive assessment of codon manipulation in Saxifragales plastid genes, showing a high preference for AT bases and AT-ending codons. Intrafamilial differences in codon bias were detected in three families. Selection was found to play a dominant role in codon usage bias in Saxifragales plastid genes, supported by ENC plots and neutrality analyses. The inferred phylogenetic affinities of Saxifragales were consistent with each other and enhance our understanding of the evolutionary processes in this order.
Article
Genetics & Heredity
Jian Yuan, Fukun Chen, Dandan Fan, Qi Jiang, Zhengbo Xue, Ji Zhang, Xiangyi Yu, Kai Li, Jia Qu, Jianzhong Su
Summary: Eye diseases are common and diverse, with omics technology providing large datasets, but efficient analysis is lacking. The EyeDiseases database integrates multi-omics data of human eye diseases, revealing genes associated with SARS-CoV-2 infection and AMD.
NAR GENOMICS AND BIOINFORMATICS
(2021)
Article
Ecology
Jifeng Zhang, Guopen Miao, Shunjie Hu, Qi Sun, Hengwu Ding, Zhicheng Ji, Pen Guo, Shoubao Yan, Chengrun Wang, Xianzhao Kan, Liuwang Nie
Summary: This study systematically investigated mitogenome arrangements of 232 amphibians, including newly sequenced Dicroglossidae mitogenomes. The results revealed that around 80% of species belonged to four major arrangement patterns, with the control region and trnL2 being the most frequently rearranged components. The typical neobatrachian arrangement may have appeared in the Late Jurassic according to possible estimation.
BMC ECOLOGY AND EVOLUTION
(2021)
