Genomic changes during the evolution of the Coxiella genus along the parasitism-mutualism continuum by Santos-Garcia, Diego, Morel, Olivier, Henri, Hélène, El Filali, Adil, Buysse, Marie, Noël, Valérie, McCoy, Karen D., Gottlieb, Yuval, Klasson, Lisa, Zenner, Lionel, Duron, Olivier, Vavre, Fabrice

“…Using these newly sequenced Coxiella-LEs and 43 Coxiellaceae genomes, we conducted comparative genomic and phylogenomic analyses to increase our knowledge of C. burnetii pathogenicity and the emergence of Coxiella-LEs. …”
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CGH, cDNA and Tissue Microarray Analyses Implicate FGFR2 Amplification in a Small Subset of Breast Tumors by Mervi Heiskanen, Juha Kononen, Maarit Bärlund, Joachim Torhorst, Guido Sauter, Anne Kallioniemi, Olli Kallioniemi

“…Multiple regions of the genome are often amplified during breast cancer development and progression, as evidenced in a number of published studies by comparative genomic hybridization (CGH). However, only relatively few target genes for such amplifications have been identified. …”
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Comprehensive Chloroplast Genome Analysis of Four <i>Callitriche</i> (Plantaginaceae) Species for Phylogenetic and Conservation Insights by Zirui Zhang, Wenbo Shi, Siqi Hu, Lanruo Mou, Chao Shi, Bingyue Zhu, Jing Yang

“…The genome sizes ranged from 150,042 to 150,879 bp, with a GC content of 37.5–37.8% and between 131 and 132 genes. Comparative genomic analysis revealed several highly variable intergenic regions (e.g., <i>rps</i>16–<i>psb</i>K, <i>trn</i>S-GCU–<i>trn</i>G-UCC, <i>ccs</i>A–<i>ndh</i>D, <i>ndh</i>F–<i>rpl</i>32, and <i>trn</i>N-UGG) and the <i>ycf</i>1 gene, highlighting their potential as phylogenetic markers. …”
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Analysis of the Genomes and Adaptive Traits of <i>Skermanella cutis</i> sp. nov., a Human Skin Isolate, and the Type Strains <i>Skermanella rosea</i> and <i>Skermanella mucosa</i> by Yujin Choi, Munkhtsatsral Ganzorig, Kyoung Lee

“…Genome sequencing and phylogenomic analyses revealed that the strain TT6^T is most closely related to <i>S. rosea</i> M1^T, with average nucleotide identity and digital DNA–DNA hybridization values of 94.14% (±0.5%) and 64.7%, respectively. Comparative genomic analysis showed that the strains TT6^T, <i>S. rosea</i> M1^T and <i>S. mucosa</i> 8-14-6^T share the Calvin cycle, and possess photosynthetic genes associated with the purple bacteria-type photosystem II. …”
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Omics-Based Comparison of Fungal Virulence Genes, Biosynthetic Gene Clusters, and Small Molecules in <i>Penicillium expansum</i> and <i>Penicillium chrysogenum</i> by Holly P. Bartholomew, Christopher Gottschalk, Bret Cooper, Michael R. Bukowski, Ronghui Yang, Verneta L. Gaskins, Dianiris Luciano-Rosario, Jorge M. Fonseca, Wayne M. Jurick

“…To shed light on this observation, we conducted a comparative genomic, transcriptomic, and metabolomic study of two <i>P. chrysogenum</i> (404 and 413) and two <i>P. expansum</i> (Pe21 and R19) isolates. …”
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GWAS identifies a polyembryony locus in mango: development of KASP and PACE markers for marker-assisted breeding by Gul Shad Ali, Shamseldeen Eltaher, Shamseldeen Eltaher, Jin Li, Barbie Freeman, Sukhwinder Singh

“…This locus contains the MiRWP/MiRKD4 gene, which codes for an RWP–RK domain-containing protein previously implicated in citrus apomixis. Comparative genomic analyses revealed synteny between the citrus and the mango polyembryony loci, suggesting a common evolutionary mechanism for this trait. …”
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Virulence factor discovery identifies associations between the Fic gene family and Fap2+ fusobacteria in colorectal cancer microbiomes by Geicho Nakatsu, Duhyun Ko, Monia Michaud, Eric A. Franzosa, Xochitl C. Morgan, Curtis Huttenhower, Wendy S. Garrett

“…We demonstrate that Fic family genes expand with the presence of Fap2 in the fusobacterial pangenome. Through comparative genomic analysis, we find that Fap2+ Fusobacteriota are highly enriched with Fic gene families compared to other cancer-associated and human gut microbiome bacterial taxa. …”
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Proteogenomic annotation of T6SS components identified in Bacteroides fragilis secretome by Natalya B. Zakharzhevskaya, Olga Yu Shagaleeva, Daria A. Kashatnikova, Daria A. Kashatnikova, Anton O. Goncharov, Anton O. Goncharov, Daria V. Evsyutina, Dmitry A. Kardonsky, Elizaveta A. Vorobeva, Artemiy S. Silantiev, Viktoria D. Kazakova, Irina V. Kolesnikova, Ivan O. Butenko, Anna A. Vanyushkina, Svetlana V. Smirnova, Andrei V. Chaplin, Andrei V. Chaplin, Boris A. Efimov, Boris A. Efimov

“…Proteogenomic annotation and comparative genomic study of the T6SS loci of the toxigenic Bf BOB25 were carried out by comparison with the reference genomes of the following Bf strains: JIM10, NCTC 9343 and 638R.ResultsAccording to the data obtained, T6SS components were represented in all types of the analysed samples. …”
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Toward autism spectrum disorders and Williams-Beuren syndrome co-occurrence condition in Tunisian patients: Genetic insights by Rim Khelifi, Afef Jelloul, Houda Ajmi, Wafa Slimani, Sarra Dimassi, Khouloud Rjiba, Manel Dardour, Moez Gribaa, Ali Saad, Soumaya Mougou-Zerelli

“…A comprehensive evaluation using karyotyping, fluorescence in situ hybridization (FISH), and array comparative genomic hybridization (array-CGH) was performed.ResultsAll patients were clinically diagnosed and confirmed to have WBS through karyotyping and FISH analysis. …”
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Whole-genome analysis of a ST45-SCCmec IVa (2B)-t116 methicillin-resistant Staphylococcus aureus strain isolated from the sputum of a 5-year-old child with pneumonia by Lin Huang, Rui Guo, Jingxian Lin, Xiaowei Li, Zhicong Li, Limei Zhang, Wenting Li, Rui Xue, Cheng Zhang, Xiaosan Feng, Xiaobin Li, Xiaobin Li

“…The carriage of antibiotic resistance genes, virulence genes, and mobile genetic elements were identified using bioinformatics tools. The comparative genomic analyses of MRSA strain SA2107 with other MRSA strains worldwide were performed.FindingsThe genome size of ST45-SCCmec IVa (2B)-t116 MRSA strain SA2107 was ~2.9 Mb. …”
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Genomic Alterations in Primary Gastric Adenocarcinomas Correlate with Clinicopathological Characteristics and Survival by Marjan M. Weiss, Ernst J. Kuipers, Cindy Postma, Antoine M. Snijders, Daniel Pinkel, Stefan G. M. Meuwissen, Donna Albertson, Gerrit A. Meijer

“…In order to investigate the patterns of chromosomal aberrations in gastric carcinomas, we performed genome‐wide microarray based comparative genomic hybridisation (microarray CGH). With this recently developed technique chromosomal aberrations can be studied with high resolution and sensitivity. …”
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