De Novo Assembly of the Polyhydroxybutyrate (PHB) Producer <i>Azohydromonas lata</i> Strain H1 Genome and Genomic Analysis of PHB Production Machinery by Daniele Traversa, Carlo Pazzani, Pietro D’Addabbo, Lucia Trisolini, Matteo Chiara, Marta Oliva, Angelo Marzella, Camilla Mandorino, Carla Calia, Guglielmina Chimienti, Caterina Manzari, Graziano Pesole, Maria Scrascia

“…In addition to the <i>phaCAB</i> operon, single genes ascribable to PhaC and PhaA functions and auxiliary genes were also detected. A comparative genomic analysis of the available genomes of the genus <i>Azohydromonas</i> revealed the presence of <i>phaCAB</i> and auxiliary genes in all <i>Azohydromonas</i> species investigated, suggesting that the PHB production is a common feature of the genus. …”
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Ammonifying and phosphorus-solubilizing function of Aliikangiella maris sp. nov. isolated from Phaeocystis globosa bloom and algal–bacterial interactions by Fei Li, Fei Li, Ming-Ben Xu, Liang-Hao Pan, Jie Li, Cai-Bi Lan, Zhe Li, Shan Lu, Jun-Xiang Lai, Jun-Xiang Lai, Peng-Fu Li

“…According to phenotypic, chemotaxonomic, phylogenomic, and comparative genomic analyses data, strains GXAS 306T and GXAS 311 were considered to represent a novel species of the genus Aliikangiella. …”
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Prenatal Identification and Molecular Characterization of Two Simultaneous De Novo Interstitial Duplications of Chromosomal Regions 7p22.1p21.1 and 15q24.1 by Sabrina C. Burn, Kali Swift, Maria Palmquist

“…Cytogenetic analysis of cultured amniocytes by conventional chromosome analysis, comparative genomic hybridization, and fluorescence in situ hybridization revealed two interstitial duplications of the chromosomal regions 7p22.1p21.1 and 15q24.1, leading to partial trisomy of 7p and 15q and karyotype 46,XY,dup(7)(p22.1-p21.1),dup (15)(q24.1). …”
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Multi-omics investigation of high-transglutaminase production mechanisms in Streptomyces mobaraensis and co-culture-enhanced fermentation strategies by Huanan Chang, Ziyu Zheng, Hao Li, Yanqiu Xu, Gengyao Zhen, Yao Zhang, Xidong Ren, Xidong Ren, Xinli Liu, Xinli Liu, Deqiang Zhu, Deqiang Zhu

“…Using this strain as a forward mutation gene pool, comparative genomic research identified 95 mutated genes, which were mostly due to base substitutions that led to changes in codon usage preference. …”
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Clinical Report of a 17q12 Microdeletion with Additionally Unreported Clinical Features by Jennifer L. Roberts, Stephanie K. Gandomi, Melissa Parra, Ira Lu, Chia-Ling Gau, Majed Dasouki, Merlin G. Butler

“…Subsequently, a 400 K array-based comparative genomic hybridization (aCGH) + SNP analysis was performed which identified a de novo suspected pathogenic deletion on chromosome 17q12 encompassing 28 genes. …”
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A Biphasic Pleural Tumor with Features of an Epithelioid and Small Cell Mesothelioma: Morphologic and Molecular Findings by Sarah Hackman, Richard D. Hammer, Lester Layfield

“…Fluorescence in situ hybridization testing for the t(11;22)(p13;q12) translocation disclosed loss of the EWSR1 gene in 94% of tumor cell nuclei, but there was no evidence of the classic translocation. Array based-comparative genomic hybridization (a-CGH) confirmed the tumor had numerous chromosome copy number losses, including 11p15.5-p11.12 and 22q12.1-q13.33, with loss of the EWSR1 and WT1 gene regions. …”
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Enhancement of Streptomyces aureoverticillatus HN6 through mutagenesis for improved biocontrol of banana wilt disease: an WGS approach by Xiangnan Yan, Shakil Ahmad, Nazia Manzar, Yunfei Zhang, Coline C. Jaworski, Abhijeet Shankar Kashyap, Lanying Wang, Yanping Luo

“…Moreover, the fermentation broth of the mutant strain E95 substantially improved the bacterial inhibitory activity. Comparative genomic analysis revealed the presence of seven single-nucleotide polymorphisms (SNPs), one multiple nucleotide polymorphism (MNP), and three insertion-deletions when comparing the mutant strain E95 with the original strain HN6. …”
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Promoter Methylation Precedes Chromosomal Alterations in Colorectal Cancer Development by Sarah Derks, Cindy Postma, Peter T. M. Moerkerk, Sandra M. van den Bosch, Beatriz Carvalho, Mario A. J. A. Hermsen, Walter Giaretti, James G. Herman, Matty P. Weijenberg, Adriaan P. de Bruïne, Gerrit A. Meijer, Manon van Engeland

“…Chromosomal alterations were evaluated by comparative genomic hybridization. Results: Our data demonstrate that nonprogressed adenomas, progressed adenomas and carcinomas show similar frequencies of promoter methylation for the majority of the genes. …”
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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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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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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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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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