Two complete chloroplast genomes of Ceratophyllum, an aquatic genus with unresolved phylogenetic position by Shuangyan Ru, Zhigang Wu, Huijun Wang, Qi Li, Tao Li

“…Ceratophyllum is an aquatic genus noted for its enigmatic position in the angiosperm phylogenetic tree. In this study, we assembled and annotated the chloroplast genomes of two species. …”
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Sequencing and annotation of the complete mitochondrial genome of a threatened labeonine fish, by Mohammad Nazrul Islam, Shirin Sultana, Md. Jobaidul Alam

“…The complete mitochondrial genome was 16,597 bp in size, which formed a circular double-stranded DNA molecule containing a total of 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes) with two non-coding regions, an origin of light strand replication (OL) and a displacement loop (D-loop), similar structure with other fishes of Teleostei. The phylogenetic tree demonstrated its close relationship with labeonine fishes. …”
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New Hosts of Simplicimonas similis and Trichomitus batrachorum Identified by 18S Ribosomal RNA Gene Sequences by Kris Genelyn B. Dimasuay, Orlie John Y. Lavilla, Windell L. Rivera

“…Aligned isolate sequences together with retrieved 18S rRNA gene sequences of known trichomonads were utilized to generate phylogenetic trees using maximum likelihood and neighbor-joining analyses. …”
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Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation by Kris Van Poucke, Annelies Haegeman, Thomas Goedefroit, Fran Focquet, Leen Leus, Marília Horta Jung, Corina Nave, Miguel Angel Redondo, Claude Husson, Kaloyan Kostov, Aneta Lyubenova, Petya Christova, Anne Chandelier, Slavcho Slavov, Arthur de Cock, Peter Bonants, Sabine Werres, Jonàs Oliva Palau, Benoit Marçais, Thomas Jung, Jan Stenlid, Tom Ruttink, Kurt Heungens

“…Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.…”
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Molecular Markers for the Phylogenetic Reconstruction of <i>Trypanosoma cruzi</i>: A Quantitative Review by David Ramírez-Delgado, Carlos Alberto Flores-López

“…Although the mini-exon gene is by far the locus that has been most widely used, it is not the most appropriate marker for the typification of <i>T. cruzi</i> based on the construction of a resolved phylogenetic tree. Overall, the mitochondrial COII-NDI locus stands out as the best molecular marker for this purpose, followed by the Cytochrome b and the Lathosterol oxidase genes.…”
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New tribe-level classification of Hypostominae (Loricariidae) based on optimization of morphological states on DNA-based relationships, with descriptions of three new tribes and tw... by Jonathan W. Armbruster, Nathan K. Lujan

“…We re-optimized morphological character-state change by mapping states previously used to infer evolutionary history onto a composite phylogenetic tree inferred from DNA-sequence data. This revealed the strong influence on morphology-based phylogenies of a correlated suite of opercular character states related to the mechanism for cheek odontode eversion. …”
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Genome-wide analysis and characterization of TPD1 family proteins in pearl millet (Cenchrus americanus): Insights into reproductive regulation and phytohormone responses. by Zainab M Almutairi

“…Screening of cis-elements in the promoter of CaTPD1s revealed various cis-elements related to phytohormone regulation, wound response, abiotic stress defense, and light response. The phylogenetic tree revealed distinct clustering of CaTPD1_Ch6 and CaTPD1_Ch5 among the other CaTPD1s, which revealed close relationships with the orthologs from Arabidopsis and rice that are known to have a critical role in tapetum development and pollen and ovule production. …”
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Cloning, Characterization and Expression Pattern of the Ovarian Cytochrome P450 Cyp19a1aGene in Gonadal Developmental Period of Cobaltcap Silverside Hypoatherina tsurugae by Dilip Kumar Bej

“…It consists of an open reading frame (ORF) of 1551 bp that encodes a 517 aa protein, found to be identical to the sequence of other fish species. A phylogenetic tree was constructed by comparing the mRNA sequence of 41 different fishes across various taxa available in the NCBI database and using an outgroup as Acipenser sinensis. …”
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Application of internal transcribed spacer (ITS) sequences for identifying Anoectochilus setaceus Blume in Thanh Hoa, Vietnam by B. B. Thinh, L. D. Chac, L. T.M. Thu

“…This genetic sequence was analyzed, compared and used to establish a phylogenetic tree using BioEdit, BLAST and DNASTAR programs.Results and conclusion. …”
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Tumor-initiating and metastasis-initiating cells of clear-cell renal cell carcinoma by Dinh-Xuan Pham, Tien Hsu

“…MICs result from various genetic changes during subclonal evolution, while TICs reside in the stem of the ccRCC phylogenetic tree of clonal development. TICs likely originate from kidney tubule progenitor cells bearing VHL gene inactivation, including chromatin 3p loss. …”
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Complete mitochondrial genome assembly and comparative analysis of Colocasia esculenta by Huinan Li, Lili Liu, Zuyang Qiu, Fanglian He, Weiqing Dong

“…Finally, based on 28 representative plant species, a phylogenetic tree was constructed, revealing a close relationship between C. esculenta and Araceae. …”
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Molecular Characterization of Wild and Cultivated Strawberry (Fragaria × ananassa) through DNA Barcode Markers by Awais Qarni, Khushi Muhammad, Abdul Wahab, Amir Ali, Chandni Khizar, Izhar Ullah, Abeer Kazmi, Tahira Sultana, Asma Hameed, Muhammad Younas, Mehdi Rahimi

“…The resultant sequences were analyzed using BLAST, MEGA 7.0, and Bio Edit software. The phylogenetic tree was constructed by using Fragaria current species sequences and reference sequences through the neighbor-joining method or maximum likelihood method. …”
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A Review of the Psyllid Genus <i>Epipsylla</i> (Hemiptera, Psyllidae) from the Chinese Mainland with Phylogenetic Considerations and the Description of a New Species by Zhixin He, Daniel Burckhardt, Xinyu Luo, Rongzhen Xu, Wanzhi Cai, Fan Song

“…Furthermore, we sequenced the mitochondrial genome of the new species and constructed a phylogenetic tree using thirteen protein-coding genes and two rRNA genes. …”
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In silico analysis of human herpes virus-8 genome: a comparison of the K1, VR1, and VR2 regions for genotyping and global geographical distribution by Nastaran Khodadad, Ava Hashempour, Shokufeh Akbarinia

“…Afterwards, the VR1 and VR2 regions were derived from the K1 genes, and genotyping of the K1, VR1, and VR2 sequences was performed by applying phylogenetic tree and BioAfrica methods. The K1 genotyping result was most similar to that of VR1, followed by VR2. …”
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Microscopic and molecular detection of Cytauxzoon spp. in cats in Mosul city, Iraq by Sura S. Aghwan, Enas S. Hussein, Salam A Esmaeel

“…One novel isolate was discovered: the Cytauxzoon felis Sesa gene LC775709.1 for 18S rRNA. The phylogenetic tree was constructed, and it was discovered that the local sequence LC775709.1 is very closely related genetically to the sequences from Europe and the USA while showing some genetic differences with the sequences from Brazil and South Africa.…”
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Combining and congruence evaluation of phylogenetic signals from different genes based on geometric approach by V. M. Efimov, V. Yu. Kovaleva, Yu. N. Litvinov

“…In addition, the joint matrix of interspecies distances is used for building a phylogenetic tree which is consistent with the zoological systematics accepted for today. …”
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Mitogenome Phylogenetics of Spiruromorpha Porpoise Parasite: Insights Into Phylogeny of <i>Crassicauda magna</i> by Lei Han, Yuling Yang, Maolin Lu, Hongyan Yu, Yaxian Lu, Mengchao Zhou, Tianlu Liu, Ruisi Zhang, Bingyao Chen, Zhijun Hou

“…The reconstruction of the ancestral state showed that the gene orders of all species in Spirurina were conserved. The phylogenetic tree indicates that <i>C. magna</i> is closer to <i>Heliconema longissimum</i> (Physalopteroidea) than <i>Tetrameres grusi</i> (Habronematoidea). (4) Conclusions: This study provides new evidence that <i>C. magna</i> is phylogenetically closer to Physalopteroidea at the molecular taxonomic level.…”
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Molecular Diversity of Sapovirus Infection in Outpatients Living in Nanjing, China (2011–2013) by Hong-ying Zhang, Meng-kai Qiao, Xuan Wang, Min He, Li-min Shi, Guo-xiang Xie, Hei-ying Jin

“…All sequences were edited and analyzed. A phylogenetic tree was drawn with the MEGA 5.0 software. …”
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Cryo-EM structure and evolutionary history of the conjugation surface exclusion protein TraT by Chloe Seddon, Sophia David, Joshua L. C. Wong, Naito Ishimoto, Shan He, Jonathan Bradshaw, Wen Wen Low, Gad Frankel, Konstantinos Beis

“…Unexpectedly, we identify chromosomal TraT homologues from multiple Gram-negative phyla which form numerous divergent lineages in a phylogenetic tree of TraT sequences. Plasmid-associated TraT sequences are found in multiple distinct lineages, including two separate clades incorporating TraT from Enterobacteriaceae IncF/F-like and Legionellaceae F-like plasmids. …”
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Metagenomic investigation of viruses in green sea turtles (Chelonia mydas) by Hongwei Li, Yuan Chen, Zhongrong Xia, Daohua Zhuang, Feng Cong, Yue-Xiao Lian

“…Furthermore, KEGG enrichment analysis showed that the viral genes were mainly involved in phage-associated and metabolic pathways. Phylogenetic tree reconstruction of Caudovirales terminase large-subunit (TerL) protein showed that most of the sequences were phylogenetically distant. …”
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