Diet-derived urolithin A is produced by a dehydroxylase encoded by human gut Enterocloster species by Reilly Pidgeon, Sacha Mitchell, Michael Shamash, Layan Suleiman, Lharbi Dridi, Corinne F. Maurice, Bastien Castagner

“…Here, we use a combination of untargeted bacterial transcriptomics, proteomics, and comparative genomics to uncover an inducible uroC dehydroxylase (ucd) operon in Enterocloster species. …”
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Computational problems of analysis of short next generation sequencing reads by R. te Boekhorst, F. M. Naumenko, N. G. Orlova, E. R. Galieva, A. M. Spitsina, I. V. Chadaeva, Y. L. Orlov, I. I. Abnizova

“…Short read next generation sequencing (NGS) has significant impacts on modern genomics, genetics, cell biology and medicine, especially on meta-genomics, comparative genomics, polymorphism detection, mutation screening, transcriptome profiling, methylation profiling, chromatin remodelling and many more applications. …”
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Complete Genome Sequencing of Polar Arthrobacter sp. PAMC25284, Copper Tolerance Potential Unraveled with Genomic Analysis by Jayram Karmacharya, Prasansah Shrestha, So-Ra Han, Hyun Park, Tae-Jin Oh

“…The strain PAMC25284 genome consists of a circular chromosome with a GC content of 65.6% and is projected to contain 3,588 genes, of which 3,150 are protein coding, 366 are pseudogenes, 19 are rRNA coding, and 50 are tRNA coding genes. Using comparative genomics, we showed that PMAC25284 has copper-transporting ATPases, copper chaperone, copper-responsive transcriptional regulator, and multi-copper oxidase domains, which are found in both Gram-positive (like Mycobacterium tuberculosis and Enterococcus hirae) and Gram-negative bacteria (like E. coli and Pseudomonas aeruginosa). …”
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Chromosome-level genome assembly of Fistularia commersonii (Syngnathiformes, Fistulariidae) by Zufa Ding, Cheng Wang, Yuting Qian, Wenjun Chen, Dan Yu, Yang Liu, Liandong Yang, Ying Wang

“…This high-quality assembly provides crucial resources for future studies on the invasion mechanisms of F. commersonii, as well as for comparative genomics research on seahorses and pipefish.…”
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A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa by Kazumichi Fujiwara, Atsushi Toyoda, Bhim B. Biswa, Takushi Kishida, Momi Tsuruta, Yasukazu Nakamura, Noriko Kimura, Shoko Kawamoto, Yutaka Sato, Toshio Katsuki, Sakura 100 Genome Consortium, Tsuyoshi Koide

“…Detailed structural analysis of these putative centromeric regions revealed that the centromeric regions of C. speciosa comprised repetitive sequences with monomer lengths of 166 or 167 bp. Comparative genomic analysis with Prunus sensu lato genome revealed structural variations and conserved syntenic regions. …”
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Penicillium psychrofluorescens sp. nov., a naturally autofluorescent Antarctic fungus by Alinta Furnell, Nicole Benaud, Xabier Vázquez-Campos, Edward C.Y. Liew, Allison Mertin, Jordan A. Vink, Kate Montgomery, Marc R. Wilkins, Brett A. Summerell, Belinda C. Ferrari

“…Penicillium psychrofluorescens is named for its intense autofluorescence derived from a combination of compounds that may include NADPH, porphyrins, and secondary metabolites, such as polyketides. Comparative genomics with both Antarctic and mesophilic Penicillium spp. shows that Penicillium psychrofluorescens has a wide repertoire of glycoside hydrolases, but almost no polysaccharide lyases, has comparably large effector proteins, lacks the machinery to use nitrate as an N-source, but has the genes for the assimilation of phosphorus from phosphonates via oxidative pathway. …”
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<i>Macrostomum lignano</i> as a model to study the genetics and genomics of parasitic flatworms by K. V. Ustyantsev, V. Yu. Vavilova, A. G. Blinov, E. V. Berezikov

“…Due to the availability of an increasing number of genome and transcriptome assemblies of different parasitic flatworm species, new knowledge generated by studying M. lignano can be easily translated to parasitic f latworms with the help of modern bioinformatic methods of comparative genomics and transcriptomics. In support of this, we provide the results of our bioinformatics search and analysis of genes homologous between M. lignano and parasitic flatworms, which predicts a list of promising gene targets for subsequent research.…”
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Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species by Kristopher J. L. Irizarry, Doug Bryant, Jordan Kalish, Curtis Eng, Peggy L. Schmidt, Gini Barrett, Margaret C. Barr

“…In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management.…”
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Complete Genome Sequence Analysis of Bacillus subtilis MC4-2 Strain That against Tobacco Black Shank Disease by Chunlan Shi, Shuquan Zeng, Xi Gao, Mehboob Hussain, Mingchuan He, Xurong Niu, Congcong Wei, Rui Yang, Mingxian Lan, Yonghui Xie, Zhijiang Wang, Guoxing Wu, Ping Tang

“…Based on 16S rRNA and gyrB genes, ANI analysis, and other comparative genomics methods, it was determined that the MC4-2 strain was Bacillus subtilis. …”
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VibrioBase: A Model for Next-Generation Genome and Annotation Database Development by Siew Woh Choo, Hamed Heydari, Tze King Tan, Cheuk Chuen Siow, Ching Yew Beh, Wei Yee Wee, Naresh V. R. Mutha, Guat Jah Wong, Mia Yang Ang, Amir Hessam Yazdi

“…VibrioBase currently houses a total of 252 Vibrio genomes developed in a user-friendly manner and useful to enable the analysis of these genomic data, particularly in the field of comparative genomics. Besides general data browsing features, VibrioBase offers analysis tools such as BLAST interfaces and JBrowse genome browser. …”
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Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits by A. M. A. M. Zonaed Siddiki, Gous Miah, Md. Sirazul Islam, Mahadia Kumkum, Meheadi Hasan Rumi, Abdul Baten, Mohammad Alamgir Hossain

“…The availability of reference whole-genome assembly of goats, annotated genes, and transcriptomics makes comparative genomics a useful tool for systemic genetic upgradation. …”
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Genome Analysis of Rhodococcus Sp. DSSKP-R-001: A Highly Effective β-Estradiol-Degrading Bacterium by Hongyan Zhao, Kejian Tian, Qing Qiu, Yu Wang, Hongyan Zhang, Shuang Ma, Shenbao Jin, Hongliang Huo

“…The existence and expression of estradiol-degrading enzymes were verified by PCR and RTPCR. Finally, comparative genomics was used to compare multiple strains of Rhodococcus. …”
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Polytene chromosomes reflect functional organization of the Drosophila genome by D. S. Sidorenko, T. Yu. Zykova, V. A. Khoroshko, G. V. Pokholkova, S. A. Demakov, J. Larsson, E. S. Belyaeva, I. F. Zhimulev

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Staphylococcus aureus carriage is associated with microbiome composition in the nares and oropharynx, not the hand, of monozygotic twins by Mark R. Dalman, W. Brian Simison, Danny Nielsen, Sabana Bhatta, Noor Ramahi, Clair Yee, Dipendra Thapaliya, Jhalka Kadariya, Shanice Cheatham, Hailee Olson, Tara C. Smith

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Chromosome-level genome assembly and annotation of largemouth bronze gudgeon (Coreius guichenoti) by Xuemei Li, Xingbing Wu, Yongjiu Zhu, Xiaoli Li, Zihao Meng, Nian Wei, Miao Xiang, Deguo Yang, Tingbing Zhu

“…In the future, the utilization of comparative genomics research is important in elucidating the molecular mechanisms of Ichthyophthirius disease and ensuring the conservation of biological resources.…”
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Detailed cytogenetic analysis of three duck species (the northern pintail, mallard, and common goldeneye) and karyotype evolution in the family Anatidae (Anseriformes, Aves) by V. R. Beklemisheva, K. V. Tishakova, S. A. Romanenko, D. A. Andreushkova, V. A. Yudkin, E. А. Interesova, F. Yang, M. A. Ferguson-Smith, A. S. Graphodatsky, A. A. Proskuryakova

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From Natural Hosts to Agricultural Threats: The Evolutionary Journey of Phytopathogenic Fungi by Asanka Madhushan, Dulan Bhanuka Weerasingha, Evgeny Ilyukhin, Paul W. J. Taylor, Amila Sandaruwan Ratnayake, Jian-Kui Liu, Sajeewa S. N. Maharachchikumbura

“…The study of pathogen evolution has been transformed by advancements in molecular biology, genomics, and bioinformatics, utilizing methods like next-generation sequencing, comparative genomics, transcriptomics and population genomics. …”
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Comprehensive identification, characterization and expression analyses of the class III POD gene family in water lily (Nymphaea colorata) by Wasi Ullah Khan, Wasi Ullah Khan, Latif Ullah Khan, Noor Muhammad Khan, Ji Zhang, Wang Wenquan, Wang Wenquan, Fei Chen, Fei Chen

“…These findings provide valuable insights for future exploration of NcPOD functions in water lily growth and stress tolerance, laying a foundation for further comparative genomics and functional studies of this important class of antioxidant genes.…”
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Decoding the anomalies: a genome-based analysis of Bacillus cereus group strains closely related to Bacillus anthracis by Thuto Gomolemo Magome, Marius Surleac, Marius Surleac, Ayesha Hassim, Cornelius Carlos Bezuidenhout, Henriette van Heerden, Kgaugelo Edward Lekota

“…Taxonomic challenges persist due to inconsistent classification methods, particularly for B. cereus isolates that resemble B. anthracis in genetic clustering.MethodsThis study investigated B. cereus group isolates from blood smears of animal carcasses in Kruger National Park, uncovering an unusual isolate with B. cereus features based on classical microbiological tests yet B. anthracis-like genomic similarities with an Average Nucleotide Identity (ANI) of ≥95%. Using comparative genomics, pan-genomics and whole genome Single Nucleotide Polymorphism (wgSNP) analysis, a total of 103 B. cereus group genomes were analyzed, including nine newly sequenced isolates from South Africa and a collection of isolates that showed some classification discrepancies, thus classified as “anomalous.”Results and discussionOf the 36 strains identified as B. anthracis in GenBank, 26 clustered phylogenetically with the four confirmed B. anthracis isolates from South Africa and shared 99% ANI. …”
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Prevalence and genomic insights of carbapenem resistant and ESBL producing Multidrug resistant Escherichia coli in urinary tract infections by Vidhyalakshmi Sivarajan, Amirtha Varshini Ganesh, Pavithra Subramani, Priyanka Ganesapandi, R. N. Sivanandan, Sneha Prakash, Nithyasri Manikandan, Arunasalam Dharmarajan, Frank Arfuso, Sudha Warrier, Marquess Raj, Kumar Perumal

“…The use of pangenome analysis enhances our understanding of resistance traits of isolates ST167, ST405, and ST448, offering valuable insights into comparative genomics of uropathogenic MDR E. coli.…”
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