Decoding mutational signatures in breast cancer: Insights from a multi-cohort study by Margaux Betz, Andréa Witz, Julie Dardare, Cassandra Michel, Vincent Massard, Romain Boidot, Pauline Gilson, Jean-Louis Merlin, Alexandre Harlé

“…This work aims to compare genomic data and signatures extracted from tissue samples collected in the CICLADES study to existing cohorts. …”
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Degenerated vision, altered lipid metabolism, and expanded chemoreceptor repertoires enable Lindaspio polybranchiata to thrive in deep-sea cold seeps by Yujie Yan, Inge Seim, Yang Guo, Xupeng Chi, Zhaoshan Zhong, Dantong Wang, Mengna Li, Haining Wang, Huan Zhang, Minxiao Wang, Chaolun Li

“…We sequenced and assembled the genome of L. polybranchiata and performed comparative genomic analyses to investigate the genetic basis of adaptation to the deep sea. …”
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DNA Amplifications and Aneuploidy, High Proliferative Activity and Impaired Cell Cycle Control Characterize Breast Carcinomas with Poor Prognosis by Harald Blegen, John S. Will, B. Michael Ghadimi, Hesed‐Padilla Nash, Anders Zetterberg, Gert Auer, Thomas Ried

“…In order to explore whether specific cytogenetic abnormalities can be used to stratify tumors with a distinctly different clinical course, we performed comparative genomic hybridization (CGH) of tumors from patients who were diagnosed with metastatic disease after an interval of less than 2 years or who remained free from distant metastases for more than 10 years. …”
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The genomes of the most diverse AA genome rice species provide a resource for rice improvement and studies of rice evolution and domestication by Muhammad Abdullah, Agnelo Furtado, Ardashir Kharabian Masouleh, Pauline Okemo, Robert Henry

“…We utilized long read sequencing (PacBio HiFi) and chromatin mapping (Hi-C) to produce de novo chromosomal level genomes of Oryza meridionalis, the most divergent AA gnome species, and the unique Australian Oryza rufipogon like taxon that is a sister to the clade of domesticated and wild AA genome rice species of Asia and Africa. Comparative genomic analyses were conducted to identify structural variations and syntenic relationships between these wild taxa and the domesticated rice variety Nipponbare. …”
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DNA Quality Assessment for Array CGH by Isothermal Whole Genome Amplification by Tineke E. Buffart, Marianne Tijssen, Thijs Krugers, Beatriz Carvalho, Serge J. Smeets, Ruud H. Brakenhoff, Heike Grabsch, Gerrit A. Meijer, Henry B. Sadowski, Bauke Ylstra

“…Background: Array Comparative Genomic Hybridization (array CGH) is increasingly applied on DNA obtained from formalin-fixed paraffin-embedded (FFPE) tissue, but in a proportion of cases this type of DNA is unsuitable. …”
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Characterization and genomic insights into bacteriophages Kpph1 and Kpph9 against hypervirulent carbapenem-resistant Klebsiella pneumoniae by Ye Huang, Yuan Huang, Zhiping Wu, Ziyue Fan, Fanglin Zheng, Yang Liu, Xinping Xu

“…Through phylogenetic analysis, it has been revealed that Kpph1 belongs to the new species of Webervirus genus, and Kpph9 to the Drulisvirus genus. Comparative genomic analysis suggests that the tail fiber protein region exhibits the greatest diversity in the genomes of phages within the same genus, which implies distinct co-evolution histories between phages and their corresponding hosts. …”
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A Chromosome-Scale Genome of <i>Trametes versicolor</i> and Transcriptome-Based Screening for Light-Induced Genes That Promote Triterpene Biosynthesis by Yang Yang, Xuebo Hu

“…Phylogenetic analysis showed that <i>T. versicolor</i> is most closely related to <i>T. pubescens</i>, followed by <i>T. cinnabarina</i> and <i>T. coccinea</i>. Comparative genomic analysis identified 266 syntenic blocks between <i>T. versicolor</i> and <i>Wolfiporia cocos</i>, indicating a conserved evolutionary pattern between the two species. …”
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Priestia flexa as a Novel Urinary Tract Pathogen in Daloa, Côte d’Ivoire: Insights From Genomic Sequencing by Dého Aristide Gbégbé, Okran Beyosse Christophe Kacou, N’goran Parfait N’zi, Djédoux Maxime Angaman

“…Based on average nucleotide identity (ANI) analysis, DNA-DNA digital hybridisation (dDDH), and other comparative genomic methods, strains 21LM07, 21LM367, and 21LM1136 were determined to be Priestia flexa. …”
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Novel Genomic Aberrations in Testicular Germ Cell Tumors by Array-CGH, and Associated Gene Expression Changes by Rolf I. Skotheim, Reija Autio, Guro E. Lind, Sigrid M. Kraggerud, Peter W. Andrews, Outi Monni, Olli Kallioniemi, Ragnhild A. Lothe

“…We analyzed 17 TGCTs, three precursor lesions, and the embryonal carcinoma cell lines, NTERA2 and 2102Ep, by comparative genomic hybridization microarrays (array-CGH), and integrated the data with transcriptome profiles of the same samples. …”
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Prenatal ultrasound phenotype of fetuses with recurrent 1q21.1 deletion and duplication syndrome by Fengyang Wang, Huijuan Peng, Guiyu Lou, Yanxin Ren, Shixiu Liao

“…In total, 43 fetuses were diagnosed with recurrent 1q21.1 deletion or duplication syndrome via array comparative genomic hybridization (array CGH) or copy number variation sequencing (CNV-seq). …”
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Molecular Characterization of a Multidrug-Resistant Klebsiella pneumoniae Strain R46 Isolated from a Rabbit by Fei Wu, Yuanyuan Ying, Min Yin, Yi Jiang, Chongyang Wu, Changrui Qian, Qianqian Chen, Kai Shen, Cong Cheng, Licheng Zhu, Kewei Li, Teng Xu, Qiyu Bao, Junwan Lu

“…Sequencing and comparative genomic methods were used to analyze the structures of the resistance gene-related sequences. …”
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Characterization of an IncR Plasmid with Two Copies of ISCR-Linked qnrB6 from ST968 Klebsiella pneumoniae by Changrui Qian, Xinyi Zhu, Junwan Lu, Kai Shen, Qianqian Chen, Wangxiao Zhou, Hongmao Liu, Wei Lu, Danying Zhou, Zhewei Sun, Xi Lin, Kewei Li, Qiyu Bao, Teng Xu, Shunfei Lu

“…To characterize the molecular structure of IncR plasmid-related sequences, comparative genomic analysis was conducted using 261 IncR plasmid backbone-related sequences. …”
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Correlation among blastocoel fluid DNA level, apoptotic genes expression and preimplantation aneuploidy by Fattaneh Khajehoseini, Zahra Noormohammadi, Poopak Eftekhari-Yazdi, Hamid Gourabi, Reza Pazhoomand, Shirzad Hosseinishenatal, Masood Bazrgar

“…Human blastocysts were classified into three groups; survivable embryo (SE), fatal single and double aneuploidy (FSDA) and multiple aneuploidy (MA) using array comparative genomic hybridization (array-CGH) by trophectoderm biopsy. …”
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First whole genome report of Mangrovibacter phragmitis PSU-3885–11 isolated from a patient in Thailand by Nattarika Chaichana, Thunchanok Yaikhan, Mingkwan Yingkajorn, Nonthawat Thepsimanon, Sirikan Suwannasin, Kamonnut Singkhamanan, Sarunyou Chusri, Rattanaruji Pomwised, Monwadee Wonglapsuwan, Komwit Surachat

“…The genome contains 4,651 coding sequences, along with 72 tRNA genes and 1 tmRNA. Moreover, comparative genomic analysis showed 99.32 % average nucleotide identity (ANI) similar to M. phragmitis MP23, and several antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were identified in the PSU-3885–11 genome which may contribute to its ability to survive in diverse environments, including human hosts. …”
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The β-Lactamase Gene Profile and a Plasmid-Carrying Multiple Heavy Metal Resistance Genes of Enterobacter cloacae by Chongyang Wu, Chaoqin Lin, Xinyi Zhu, Hongmao Liu, Wangxiao Zhou, Junwan Lu, Licheng Zhu, Qiyu Bao, Cong Cheng, Yunliang Hu

“…The extended-spectrum β-lactamases (ESBLs) (blaSHV-12 and blaCTX-M-9a) and AmpC (blaMIR) were encoded on the chromosome, and the pY546 plasmid contained several clusters of genes conferring resistance to metals, such as copper (pco), arsenic (ars), tellurite (ter), and tetrathionate (ttr), and genes encoding many divalent cation transporter proteins. The comparative genomic analyses of the whole plasmid sequence and of the heavy metal resistance gene-encoding regions revealed that the plasmid sequences of Klebsiella pneumoniae (such as pKPN-332, pKPN-3967, and pKPN-262) shared the highest similarity with those of pY546. …”
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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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Putative evolution of Myxococcus fulvus 124B02 plasmid pMF1 from a chromosomal segment in another Myxococcus species by Shruti Jain, Gaurav Sharma

“…To comprehend the relationship among these three species, we conducted phylogenetic analyses using 16S and concatenated housekeeping genes and genome-to-genome distance calculator (GGDC) analysis, which confirmed that M. stipitatus CYD1 is a distinct and novel species within the genus Myxococcus. Overall, this comparative genomic study sheds light on the putative emergence of the pMF1 plasmid from a common ancestor of closely related yet distinct species, M. stipitatus CYD1, possibly through the partition from its chromosome as a segment.IMPORTANCEMyxobacteria are not well known to have plasmids. …”
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