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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Exploration of migration directions in different populations of Eothenomys miletus in the Hengduan Mountains of Yunnan Province: a genome-based analysis by Yanfei Cai, Ting Jia, Wanlong Zhu, Wanlong Zhu, Wanlong Zhu

“…Our results indicated that the ALS population is positioned at the base of the phylogenetic tree, and admixture analysis revealed that the ALS population is more closely related to the JC and DQ populations. …”
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Nucleotide Sequencing and Identification of Some Wild Mushrooms by Sudip Kumar Das, Aninda Mandal, Animesh K. Datta, Sudha Gupta, Rita Paul, Aditi Saha, Sonali Sengupta, Priyanka Kumari Dubey

“…Although out of 8 mushrooms 4 could be identified up to species level, the nucleotide sequences of the rest may be relevant to further characterization. A phylogenetic tree is constructed using Neighbor-Joining method showing interrelationship between/among the mushrooms. …”
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Genetic Relationship Analysis of Genus Nomorhamphus from Lindu Lake, Central Sulawesi and Adaptive Responses to Exposure Different Light Wavelengths by Riva Hafidah, Dinar Tri Soelistyowati, Agus Oman Sudrajat, Alimuddin

“…The PCR amplification products were then sequenced and performed with phylogenetic tree analysis. The genetic diversity analysis suggests that the genus Nomorhamphus of all three rivers, Lindu Lake, Central Sulawesi is one species as Nomorhamphus sp.. …”
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Identification of <i>Tinomiscium petiolare</i> from Vietnam using the DNA barcode by B. B. Thinh, R. V. Doudkin, L. D. Chac, H. V. Chinh, Q. V. Hoi, N. T. Lien

“…These genetic sequences were analyzed and compared, and a phylogenetic tree was constructed using BioEdit, BLAST, and MEGA 6 programs.Results and conclusion. …”
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Biogeographic Insights Into the Late Miocene Diversification of the Giant Deep‐Ocean Amphipod Eurythenes by Carolina E. González, Johanna N. J. Weston, Reinaldo Rivera, Marcelo Oliva, Rubén Escribano, Osvaldo Ulloa

“…We constructed a time‐calibrated phylogeny using two mitochondrial DNA genes by analyzing publicly available data on 14 species of Eurythenes across a global depth range from 839 to 8081 m. The resulting phylogenetic tree reveals a diverse clade, with a common ancestor originating around 11.81 Ma. …”
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Molecular genetic and morphological characteristics of Micractinium thermotolerans and M. inermum (Trebouxiophyceae, Chlorophyta) from pyroclastic deposits of the Kamchatka Peninsu... by R. Z. Sushchenko, V. Yu. Nikulin, V. B. Bagmet, A. Yu. Nikulin

“…On the phylogenetic tree, strain VCA-93 was clustered in the Micractinium thermotolerans species clade. …”
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Oral Fusobacterium nucleatum resists the acidic pH of the stomach due to membrane erucic acid synthesized via enoyl-CoA hydratase-related protein FnFabM by Xiaocong Li, Shipeng Zhang, Huafang Sheng, Yan Zhen, Buling Wu, Zhuang Li, Dingqiang Chen, Hongwei Zhou

“…The survival was significantly increased in the presence of erucic acid C22:1(n9) in cell membranes. Phylogenetic tree analysis revealed that C22:1(n9) synthesis was significantly associated with FnFabM gene expression in F. nucleatum at pH 1.5. …”
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Genome wide identification of Dof transcription factors in Carmine radish reveals RsDof33 role in cadmium stress and anthocyanin biosynthesis by Caiming Gou, Jia Li, Bo Chen, Guoting Cheng, Zhangfei Zheng, Hua Peng, Ahmed H. El-Sappah

“…The radish genome has 59 RsDofs, which are divided into nine clusters (A: 8, B1: 10, B2: 10, C1: 3, C2.1: 5, C2.2: 4, C3: 11, D1: 4, and D2: 4). Phylogenetic tree analysis revealed significant Dof gene family resemblance between Arabidopsis thaliana and Brassica napus. …”
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Updates on hosts and distribution of pepper yellow leaf curl Indonesia virus and squash leaf curl China virus in Central Java Province, Indonesia by Adyatma Irawan Santosa, Adenisa Hanifah Irbati, Geby Nandita Cahyaning Pratiwi, Antama Surwadinata, Putri Laeshita, Krisnanda Surya Dharma, Reko Saputra Jaya, Annisa Lisa Andriyani, Chilya Qurrota A'yun, Chusnu Naura Syifa Fatika

“…PepYLCIV OR924279 and OR924280 formed a subgroup with LC542629 from Bali in the phylogenetic tree constructed using MEGA11, and shared 95.8 – 96.7% identities at nucleotide (nt) and 98.4 – 99.5% at amino acid (aa) levels according to Sequence Demarcation Tool v1.2 software. …”
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Genetic Diversity and Population Structure of <i>Macrobrachium nipponense</i> Populations in the Saline–Alkaline Regions of China by Romaric Iko, Zijian Gao, Sufei Jiang, Yiwei Xiong, Wenyi Zhang, Hui Qiao, Shubo Jin, Hongtuo Fu

“…The cluster analyses and the phylogenetic tree identified two main groups. There is an association among sites by geographic location, and the JS site shows higher diversity. …”
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Molecular Detection and Genetic Characterization of Avian Leukosis Virus From Field Outbreaks in Bangladesh by Md. Golzar Hossain, Riman Pathan, SM Nazmul Hasan, Anandha Mozumder, Moslema Jahan Mou, Marjana Akter, Chandan Sikder, Riyan Al Islam Reshad, Roni Mia, Sukumar Saha, Tofazzal Islam, Sharmin Akter

“…Sequence analysis of the env genes demonstrated high homology among the identified strains (97%–98%) and with reference strains (92%–96%) at the nucleotide level. The phylogenetic tree revealed close relatedness of the three identified strains to reference strains from India, USA, and China. …”
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Streptococcus halichoeri: Comparative Genomics of an Emerging Pathogen by Kirsi Aaltonen, Ravi Kant, Marjut Eklund, Mirja Raunio-Saarnisto, Lars Paulin, Olli Vapalahti, Thomas Grönthal, Merja Rantala, Tarja Sironen

“…The core and pangenomes were formed by comparing the genomes against each other in an all-against-all comparison. A phylogenetic tree was constructed using the genes of the core genome. …”
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Isolation and characterization of a novel highly efficient bacterium Lysinibacillus boronitolerans QD4 for quantum dot biosynthesis by Xingyu Gu, Xingyu Gu, Xiaoju Li, Ruijia Zhang, Ruijia Zhang, Ruoli Zheng, Ruoli Zheng, Mingrui Li, Mingrui Li, Rong Huang, Xin Pang

“…Through the physio-biochemical characterization and 16S rRNA-based phylogenetic tree analysis, the strain is identified as Lysinibacillus boronitolerans QD4. …”
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Efflux Pump Activity and Mutations Driving Multidrug Resistance in Acinetobacter baumannii at a Tertiary Hospital in Pretoria, South Africa by Noel-David Nogbou, Granny M. Nkawane, Khanyisa Ntshane, Charles K. Wairuri, Dikwata T. Phofa, Kagiso K. Mokgokong, Mbudzeni Ramashia, Maphoshane Nchabeleng, Lawrence C. Obi, Andrew M. Musyoki

“…The Sanger sequencing method was used to sequence the parC and gyrA amplicons. A phylogenetic tree was drawn using MEGA 4.0 to evaluate evolutionary relatedness of the strains. …”
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The first two mitochondrial genomes for the genus Ramaria reveal mitochondrial genome evolution of Ramaria and phylogeny of Basidiomycota by Qiang Li, Lijiao Li, Ting Zhang, Peng Xiang, Qian Wu, Wenying Tu, Zhijie Bao, Liang Zou, Cheng Chen

“…Phylogenetic analyses using both Bayesian inference (BI) and Maximum Likelihood (ML) methods based on a combined mitochondrial gene dataset obtained an identical and well-supported phylogenetic tree for Basidiomycota, wherein R. cfr. rubripermanens and Turbinellus floccosus are sister species. …”
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TaWI12 may be involved in pistillody and leaf cracking in wheat by Yuhuan Guo, Yan Zhang, Yuhao Li, Yichao Wu, Mingli Liao, Zhengsong Peng, Zaijun Yang, Yonghong Zhou

“…The open reading frames (ORFs) of TaWI12-4A, TaWI12-4B and TaWI12-4D were 408 bp, 417 bp and 417 bp, respectively, and encoded 135, 138 and 138 amino acids, respectively. The phylogenetic tree revealed a high degree of homology between the protein sequences of TaWI12 and the wound-induced proteins of Hordeum vulgare (KAI4994568) and Aegilops tauschii (XP_020196548). …”
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Isolation and Genomic Characterization of a Novel Porcine Reproductive and Respiratory Syndrome Virus 1 from Severely Diseased Piglets in China in 2024 by Shuai Yang, Meng Cui, Chen Li, Ming Qiu, Xiaoyang Zhu, Yanhan Lin, Yifan Meng, Yuejia Qiu, Wenhao Qi, Hong Lin, Wanglong Zheng, Jianzhong Zhu, Kewei Fan, Nanhua Chen

“…Furthermore, a genome-based phylogenetic tree supported that the AHEU2024-2671-like isolates form a novel subgroup within subtype 1. …”
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Understanding the clinical and molecular epidemiological characteristics of carbapenem-resistant Acinetobacter baumannii infections within intensive care units of three teaching ho... by Pengyu Zhang, Jingchen Hao, Yafen Zhang, Junfeng Su, Guozhuang Sun, Jun Xie, Jian Hu, Guocai Li

“…Multilocus sequence typing and phylogenetic trees were used to assess the genetic similarity of isolates. …”
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Integrative analysis of metabolite and transcriptome reveals the biosynthetic pathway and candidate genes for iridoid glycoside biosynthesis in Neopicrorhiza scrophulariiflora (Pen... by Ke Rao, Ke Rao, Siyu Liu, Siyu Liu, Xiaohui Tang, Guofu Jia, Shaohua Yang, Chaoxiang Ren, Chaoxiang Ren, Jin Pei, Jin Pei

“…Using bioinformatics methods such as clustering analysis, phylogenetic tree construction, and weighted gene co-expression network analysis (WGCNA), 43 candidate genes were identified that may be involved in the biosynthesis of picroside-I and picroside-II, of which 26 genes were significantly correlated with the synthesis of picrosides and their intermediates. …”
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