Characterization of Two New Apodemus Mitogenomes (Rodentia: Muridae) and Mitochondrial Phylogeny of Muridae

Wu, Di; Zhou, Lizhi; Xue, Jiezhong; Xia, Qiliang; Meng, Lei

doi:10.3390/d14121089

Cited by 3 publications

(1 citation statement)

References 58 publications

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“…The features mentioned above not only reduce the cost of learning but also improve the efficiency of data preparation. The tool has been used in dozens of studies in 14 months after its release in October 2021 ( 12–30 ).…”

Section: Discussionmentioning

confidence: 99%

Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees

Xie

Chen

Cai

et al. 2023

Nucleic Acids Research

321

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tvBOT is a user-friendly and efficient web application for visualizing, modifying, and annotating phylogenetic trees. It is highly efficient in data preparation without requiring redundant style and syntax data. Tree annotations are powered by a data-driven engine that only requires practical data organized in uniform formats and saved as one table file. A layer manager is developed to manage annotation dataset layers, allowing the addition of a specific layer by selecting the columns of a corresponding annotation data file. Furthermore, tvBOT renders style adjustments in real-time and diversified ways. All style adjustments can be made on a highly interactive user interface and are available for mobile devices. The display engine allows the changes to be updated and rendered in real-time. In addition, tvBOT supports the combination display of 26 annotation dataset types to achieve multiple formats for tree annotations with reusable phylogenetic data. Besides several publication-ready graphics formats, JSON format can be exported to save the final drawing state and all related data, which can be shared with other users, uploaded to restore the final drawing state for re-editing or used as a style template for quickly retouching a new tree file. tvBOT is freely available at: https://www.chiplot.online/tvbot.html.

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Section: Discussionmentioning

confidence: 99%

Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees

Xie

Chen

Cai

et al. 2023

Nucleic Acids Research

321

View full text Add to dashboard Cite

show abstract

First complete mitogenome of Massarineae and its contribution to phylogenetic implications in Pleosporales

Wang,

Zhang,

et al. 2023

Sci Rep

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Endophytic fungi play an important role in the growth and development of traditional Chinese medicine plants. We isolated a strain of Acrocalymma vagum from the endophytic fungi of the traditional Chinese plants Paris. To accurately identify this endophytic fungal species of interest, we sequenced the mitochondrial genome of A. vagum, which is the first discovered mitochondrial genome in Massarineae. The A. vagum mitochondrial genome consists of a 35,079-bp closed circular DNA molecule containing 36 genes. Then, we compared the general sequence characteristics of A. vagum with those of Pleosporales, and the second structure of the 22 tRNAs was predicted. The phylogenetic relationship of A. vagum was constructed using two different data sets (protein-coding genes and amino acids). The phylogenetic tree shows that A. vagum is located at the root of Pleosporales. The analysis of introns shows that the number of introns increases with the increase in branch length. The results showed that monophyly was confirmed for all families in Pleosporales except for Pleosporaceae. A. vagum is an ancient species in the Pleosporales, and Pleosporaceae may require further revision. In Pleosporales, the number of introns is positively correlated with branch length, providing data for further study on the origin of introns.

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Complete mitochondrial genomes and phylogenetic analysis of native and non-native fishes in a national key wetland of China

Zhang,

Bai,

et al. 2024

Front. Environ. Sci.

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Fish are considered objective indicators of environmental health and ecosystem stability. Establishing regional reference databases of mitochondrial genome sequences from local fish communities can significantly enhance fish monitoring using environmental DNA (eDNA) analysis. For non-native species, the eDNA technique provides early detection and rapid monitoring. It is also crucial to include fundamental genetic information for both native and non-native species in genetic databases. This study presents the complete mitochondrial genomes of 17 fish species inhabiting the Baiyangdian Basin, a national key wetland in China. The mitochondrial DNA of these fish was analyzed to investigate their characteristics, and their phylogeny was determined using maximum likelihood (ML) methods. Various analyses were performed, including the examination of nucleotide composition, evaluation of AT-skew and GC-skew, analysis of codon frequency, and determination of relative synonymous codon usage (RSCU) values, and assessment of selection pressure on protein-coding genes (PCGs). The analysis showed that all PCGs in all fish underwent purifying selection. Using Xenocyprididae as a representative, this study investigated the genetic selection tendencies of native and non-native fish species in the Baiyangdian Basin. Significant differences were found in five of the 13 PCGs: COI, COII, COIII, Cytb, and ATP8. Except for ATP8, the findings indicated that the genes of non-native species underwent stronger purifying selection during evolution compared to native species. Additionally, comparing the population ω values of non-native species to those of native species showed that the Cytb and COIII genes exhibited greater differential purification selection than COI and COII. These differences may be the result of the evolution of non-native species to migrate and adapt to the Baiyangdian Basin, thereby affecting the evolution of related genes.

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Characterization of Two New Apodemus Mitogenomes (Rodentia: Muridae) and Mitochondrial Phylogeny of Muridae

Cited by 3 publications

References 58 publications

Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees

Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees

First complete mitogenome of Massarineae and its contribution to phylogenetic implications in Pleosporales

Complete mitochondrial genomes and phylogenetic analysis of native and non-native fishes in a national key wetland of China

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