Molecular network analysis for detecting HIV transmission clusters: insights and implications by Yangyang Liu, Lichun Hua, Wenqian Wu, You Ge, Wei Li, Pingmin Wei

“…With an accuracy of 86.25%, the optimal parameter for the phylogenetic tree and gene distance approach was 90 + 0.045 substitution/loci. …”
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Mining versatile feruloyl esterases: phylogenetic classification, structural features, and deep learning model by Liang Guo, Yuxin Dong, Deyong Zhang, Xinrong Pan, Xinjie Jin, Xinyu Yan, Yin Lu

“…Subsequent phylogenetic analysis of these clusters unveiled a correlation between phylogenetic classification and substrate promiscuity, and enzymes with broad substrate scope tended to locate within specific branches of the phylogenetic tree. Further, molecular dynamics simulations and dynamical cross-correlation matrix analysis were employed to explore structural dynamics differences between promiscuous and substrate-specific FEs. …”
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Molecular Identification, Histopathology and Antibiotic Susceptibility Profiling of Aeromonas veronii Isolated from Oreochromis niloticus in Bangladesh by Sayed Mashequl Bari, Mohammad Muttakinul Islam, Aktia Amina, Marufa Khatun, A. M. Shahabuddin

“…MT071624) in the NCBI BLAST search, and in the phylogenetic tree, they grouped in a single clade. This close genetic relationship is also supported by the low genetic distance between the isolates. …”
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Chloroplast Genome Sequencing and Comparative Analysis of Six Medicinal Plants of Polygonatum by Jinchen Yao, Zhaohuan Zheng, Tao Xu, Duomei Wang, Jingzhe Pu, Yazhong Zhang, Liangping Zha

“…Notably, P. sibiricum emerged as a standalone clade, and our phylogenetic tree reinforces the classification of P. sibiricum as forming a monophyly. …”
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Molecular Detection and Determination of Phylogenetic Position of Watermelon Chlorotic Stunt Virus Khouzestan Isolate Based on Coat Protein Gene by Samira Pakbaz, Zahra Jelavi, Ehsan Hasanvand, Hossein Mirzaei Najafgholi

“…The sequencing results confirmed WmCSV infection in the samples. In the phylogenetic tree drawn based on the coat protein gene (AV1), Khouzestan isolates were placed in a group next to other Iranian isolates and they had most similarities to Noorabad isolate from Fars province. …”
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Characterization of Streptomyces Isolates Associated with Estuarine Fish Chanos chanos and Profiling of Their Antibacterial Metabolites-Crude-Extract by Muhammad A. Kurnianto, Harsi D. Kusumaningrum, Hanifah N. Lioe

“…Three isolates were suspected as novel isolate candidates based on homology presentations and phylogenetic tree analysis. Disk-diffusion assay of the metabolite-crude-extract from the isolates showed broad-spectrum inhibitory activities against Staphylococcus aureus ATCC 25923, Bacillus cereus ATCC 10876, Escherichia coli ATCC 25922, and Pseudomonas aeruginosa InaCC B52 with minimum inhibitory concentration and minimum bactericidal concentration ranging from 2.5–10 mg/mL and 5–10 mg/mL, respectively. …”
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A new species of Semisulcospira O. Boettger, 1886 (Gastropoda, Cerithoidea, Semisulcospiridae) from Fujian, China with mitochondrial genome and its phylogenetic implications by Yi-Bin Xu, Yuan-Zheng Meng, Sheng Zeng, Hang-Jun Wang, Shen Zhong, De-Yuan Yang, Xi-Ping Zhou, Christopher J. Glasby

“…Phylogenetic analyses based on just COI and 16S exhibited low resolution rendering the phylogenetic position of the new species within the genus uncertain. In contrast, phylogenetic tree analyses of complete mitochondrial genomes, which include 13 protein-coding genes (PCGs), were better resolved. …”
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Evaluation of genetic diversity of rose (Rosa sp.) collection in Tra Vinh by Nguyễn Thị Ảnh, Hà Thị Loan, Phan Diễm Quỳnh, Lê Thị Thu Hằng, Lưu Thị Bích Liên

“…The results show that based on 22 main morphological characteristics of plant, leaves, and flower phenotype, flower color, and fragrances. The phylogenetic tree was divided into six main groups when the genetic similarity coefficient was 0.78.…”
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Molecular Identification of Fusarium proliferatum from toenails: A case report by Sazan Jamal Gharib, Nawroz Abdul-razzak Tahir

“…DNA sequence analysis and Phylogenetic tree of the amplified ITS-rDNA was used for species identification of this strain of F. proliferatum. …”
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Freshwater fungi in the karst plateau wetlands from Guizhou Province, China: taxonomic novelties in Melanommataceae (Pleosporales) by Ling-Ling Liu, Yong-Xiang Liu, Ya-Ya Chen, Jiu-Lan Gou, Feng Chi, Yi Liu, Xiao-Feng Gu, Quan-Quan Wei, Meng Zhang, Zuo-Yi Liu, Si Zhou

“…The descriptions, illustrations, and notes of the novel taxa are provided along with an updated phylogenetic tree of Melanommataceae. Two synopses of the species in Byssosphaeria and Camposporium are also provided.…”
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Complete chloroplast genomes of 13 species of the Impatiens genus for genomic features and phylogenetic relationships studies by Qinqin Yong, Meijun Li, Zhi Li, Chao Luo, Jinling Zhang, Xinxiang Bai

“…Five mutation hotspots were detected: rps16-trnQ-UUG, ndhF, ccsA-ndhD, ycf1, and trnN-GUU, among which ycf1 had the highest Pi value and the greatest potential as a DNA barcode marker. Our phylogenetic tree shows that all 13 species belong to Section Impatiens. …”
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Molecular Detection and Phylogenetic Analysis of the alkB Gene in Klebsiella oxytoca Strains Isolated from the Gut of Tenebrio molitor by Tsitsi Lynn Mupamhadzi, Oleen Machona, Farisai Chidzwondo, Rumbidzai Mangoyi

“…The amplified alkB gene was then sequenced using the Sanger sequencing technique, blasted on NCBI to look for similar sequences, and a phylogenetic tree was constructed. Based on the 16S ribosomal RNA gene sequences, the isolated bacterial strains were confirmed to be Klebsiella oxytoca NBRC 102593, Klebsiella oxytoca JCM 1665, and Klebsiella oxytoca ATCC 13182. …”
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Pan-genome analysis and expression verification of the maize ARF gene family by Quan-cai Man, Yan-qun Wang, Shun-juan Gao, Zhi-chang Gao, Zheng-ping Peng, Jiang-hui Cui

“…The construction of a phylogenetic tree using Arabidopsis thaliana revealed that the G3 subfamily comprises the highest number of core genes, with a total of 10, and exhibits relative stability throughout the evolution of maize. …”
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Prediction of some peroxidase functions in <i>Arabidopsis thaliana</i> L. by bioinformatic search by A. S. Tugbaeva, A. A. Ermoshin, I. S. Kiseleva

“…They formed six clusters on the phylogenetic tree, three of which contained only A. thaliana peroxidases. …”
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Chromosome Numbers and Reproductive Life Cycles in Green Plants: A Phylotranscriptomic Perspective by Rijan R. Dhakal, Alex Harkess, Paul G. Wolf

“…Within green plants, the derived condition of heterosporous reproduction has emerged from the ancestral condition of homospory in disparate locations on the phylogenetic tree at least 11 times, of which three lineages are extant. …”
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Genome-wide identification of high-affinity nitrate transporter 2 (NRT2) gene family under phytohormones and abiotic stresses in alfalfa (Medicago sativa) by Yanyan Luo, Lili Nan

“…They were named MsNRT2.1-2.3 based on their chromosomal location. The phylogenetic tree revealed that NRT2 proteins were categorized into two main subgroups, which were further confirmed by their gene structure and conserved motifs. …”
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Chromosome-scale genome assembly of three-spotted seahorse (Hippocampus trimaculatus) with a unique karyotype by Ning Li, Xinhui Zhang, Xin Liu, Xueqiang Lin, Cancan Hu, Jieming Chen, Shengchao Wang, Dong Zhang, Shuguang Wei, Qiong Shi

“…Based on construction of a phylogenetic tree, we estimated that Hippocampus and Syngnathoides diverged approximately 50.1 million years ago (Mya). …”
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Comparative genomic analysis revealed that dietary habits affected the adaptation of Bifidobacterium bifidum to the intestinal tract in different geographic populations by Min Li, Jie Yu, Weicheng Li, Qiong Wu, Jiaqi Sun, Zhihong Sun

“…Results at the genome level indicated that the GC content of American isolates was significantly higher than that of Chinese and Russian isolates. The phylogenetic tree, based on 919 core genes showed that B. bifidum might be related to the geographical characteristics of isolation region. …”
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Chloroplast genome characteristics and phylogenetic analysis of Macropanax rosthornii (Harms) C.Y. Wu ex G. Hoo (Araliaceae) by Shuxin Du, Huiying Huang, Shuhui Yang, Tianyi Gu, Mengli Zhou, Ruihong Wang

“…There are 109 genes in the chloroplast genome of M. rosthornii, including 78 protein-coding genes, 21 tRNA genes, and 10 rRNA genes. The phylogenetic tree showed that M. rosthornii is closely related to Hydrocotyle vulgaris and Hydrocotyle sibthorpioides. …”
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A Nodulation-Proficient Nonrhizobial Inhabitant of Pueraria phaseoloides by W. M. M. Wedage, A. H. M. N. R. Aberathne, I. N. Harischandra, D. Gunawardana

“…When we constructed a phylogenetic tree with neighboring sequences, we encountered nifH sequences of Pseudacidovorax, forming a monophyletic cluster, which too contained a single Azospirillum species. …”
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