Genome-Wide In Silico Analysis of Microsatellite Loci in Rabbits by Hosam M. Safaa, Mostafa Helal, Seif Yasser, Zahra Raafat, Habiba Ayman, Hasnaa Mostafa, Milena Bozhilova-Sakova, Dalia A. A. Elsayed

“…Blood samples were collected from 15 Baladi rabbits and 18 New Zealand White (NZW rabbits). …”
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Heterogeneity among Mycobacterium ulcerans from French Guiana revealed by multilocus variable number tandem repeat analysis (MLVA). by Yann Reynaud, Julie Millet, David Couvin, Nalin Rastogi, Christopher Brown, Pierre Couppié, Eric Legrand

“…Our goal in the present study was to examine the genetic diversity of M. ulcerans strains in this region by using the Multilocus Variable Number Tandem Repeat Analysis (MLVA) approach. A total of 23 DNA samples were purified from ulcer biopsies or derived from pure cultures. …”
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De novo assembly of plasmodium interspersed repeat (pir) genes from Plasmodium vivax RNAseq data suggests geographic conservation of sub-family transcription by Timothy S. Little, Deirdre A. Cunningham, George K. Christophides, Adam James Reid, Jean Langhorne

“…For this purpose, a pipeline was written in Nextflow, and first tested on data from the rodent-infecting P. c. chabaudi parasite to ascertain its efficacy on a sample with a full, genome-based set of pir gene sequences. …”
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Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan. by Shyryn Almerekova, Moldir Yermagambetova, Smatulla Jumanov, Saule Abugalieva, Yerlan Turuspekov

“…A comparative assessment of pt genome sequences suggested the identification of 1145 simple sequence repeat markers. …”
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Identification of the first case of Penicillium marneffei infection in Shaanxi province by nanopore sequencing by Dongli Liu, Lin Ma, Lingfeng Mao, Yiqun Wang, Long Ding, Anli Wang

“…We performed nanopore genome sequencing on blood samples of the patient and obtained 84,000 reads in 3.5 hours. …”
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Role of Non-invasive Preimplantation Genetic Testing-Aneuploidy Using Spent Culture Media and its Concordance with Trophectoderm Biopsy: A Proof of Concept and Validation Study by Neeta Singh, Ankita Sethi, Lata Rani, Monika Saini, Ritu Gupta, Neena Malhotra, Reeta Mahey

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Comparative genomic insights into ecological adaptations and evolutionary dynamics of Trebouxiophyceae algae by Qian Xiong, Luqin Zheng, Qi Zhang, Tianli Li, Lingling Zheng, Lirong Song

“…This study presents a comprehensive genomic analysis of six newly sequenced strains of Trebouxiophyceae, expanding upon a foundation of 25 previously reported high-quality genomes to conduct comparative genomics and evolutionary assessments. …”
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Plastid genomic features and phylogenetic placement in Rosa (Rosaceae) through comparative analysis by Hui Jiang, Shuilian He, Jun He, Yunjuan Zuo, Wenling Guan, Yan Zhao, Xuejiao Li, Jing Meng

“…Through more comprehensive taxon sampling, this study analyzed 18 representative Rosa plastid genomes, including 13 new sequences, to elucidate their phylogeny within the genus as well as the variation patterns in the plastid genomes. …”
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Comprehensive genomic analysis of a BRCA2 deficient human pancreatic cancer. by Louise J Barber, Juan M Rosa Rosa, Iwanka Kozarewa, Kerry Fenwick, Ioannis Assiotis, Costas Mitsopoulos, David Sims, Jarle Hakas, Marketa Zvelebil, Christopher J Lord, Alan Ashworth

“…Furthermore, small insertions and deletions are detected more frequently in the context of short sequence repeats than in other genomes. We also identify a number of novel mutations that may represent genetic changes that have contributed to tumour progression. …”
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Transcriptomic profiling of unmethylated full mutation carriers implicates TET3 in FMR1 CGG repeat expansion methylation dynamics in fragile X syndrome by Grace Farmiloe, Veronika Bejczy, Elisabetta Tabolacci, Rob Willemsen, Frank Jacobs

“…RNA was extracted and comparative transcriptomic analysis was performed on all samples. Whole genome sequencing was carried out on DNA from the two UFM carriers and the results analysed to investigate DNA variants that could explain the observed differences in gene expression. …”
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Phylogeographic Analysis of Clade 2.3.4.4b H5N1 in Serbia Reveals Repeated Introductions and Spread Across the Balkans by Sofija Šolaja, Dimitrije Glišić, Ljubiša Veljović, Ivan Milošević, Emilija Nićković, Jakov Nišavić, Vesna Milićević

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Linkage disequilibrium and genome-wide association mapping in tetraploid wheat (Triticum turgidum L.). by Giovanni Laidò, Daniela Marone, Maria A Russo, Salvatore A Colecchia, Anna M Mastrangelo, Pasquale De Vita, Roberto Papa

“…Association mapping is a powerful tool for the identification of quantitative trait loci through the exploitation of the differential decay of linkage disequilibrium (LD) between marker loci and genes of interest in natural and domesticated populations. Using a sample of 230 tetraploid wheat lines (Triticum turgidum ssp), which included naked and hulled accessions, we analysed the pattern of LD considering 26 simple sequence repeats and 970 mostly mapped diversity array technology loci. …”
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A directionally evolved genomic feature in BRSK2 harbors divergent alleles in neurocognitive disorders by M. Ohadi, H. Bayat, S. Khamse, A. Delbari, M. Arabfard

“…The evolution of the CGGCT island mainly coincided with the phylogenetic distance of the species studied, and the CGG STR was primate-specific, suggesting directional, rather than random evolution of this complex sequence. While (CGGCT)6 was strictly monomorphic in the human samples studied, a 7-repeat of this motif was detected in the controls only. …”
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Accurate cross-species 5mC detection for Oxford Nanopore sequencing in plants with DeepPlant by He-Xu Chen, Zhen-Dong Liu, Xin Bai, Bo Wu, Rong Song, Hui-Cong Yao, Ying Chen, Wei Chi, Qian Hua, Liang Cheng, Chuan-Le Xiao

“…Abstract Nanopore sequencing enables comprehensive detection of 5-methylcytosine (5mC), particularly in repeat regions. …”
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Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium. by Mónica J Pajuelo, María Eguiluz, Eric Dahlstrom, David Requena, Frank Guzmán, Manuel Ramirez, Patricia Sheen, Michael Frace, Scott Sammons, Vitaliano Cama, Sarah Anzick, Dan Bruno, Siddhartha Mahanty, Patricia Wilkins, Theodore Nash, Armando Gonzalez, Héctor H García, Robert H Gilman, Steve Porcella, Mirko Zimic, Cysticercosis Working Group in Peru

“…Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. …”
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Household clusters of SARS-CoV-2 Omicron subvariants contemporaneously sequenced from dogs and their owners by Francisco C. Ferreira, Lisa D. Auckland, Rachel E. Busselman, Edward Davila, Wendy Tang, Ailam Lim, Nathan Sarbo, Hayley D. Yaglom, Heather Centner, Heather L. Mead, Ying Tao, Juan Castro, Yan Li, Jing Zhang, Haibin Wang, Lakshmi Malapati, Peter Cook, Adam Retchless, Suxiang Tong, Italo B. Zecca, Ria R. Ghai, Casey Barton Behravesh, Rebecca S. B. Fischer, Gabriel L. Hamer, Sarah A. Hamer

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Leveraging Whole-Genome Resequencing to Uncover Genetic Diversity and Promote Conservation Strategies for Ruminants in Asia by Qinqian Wang, Ying Lu, Mengfei Li, Zhendong Gao, Dongfang Li, Yuyang Gao, Weidong Deng, Jiao Wu

“…Whole-genome resequencing (WGRS) is a critical branch of whole-genome sequencing (WGS), primarily targeting species with existing reference genomes. …”
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A targeted tiled amplicon sequencing approach for clade and subclade level differentiation of monkeypox virus from wastewater by Mathew Fisher, Jennifer Ali, Shayna Giesbrecht, Raveena Roopra, Veronica Carroll, Amber Papineau, Cody Buchanan, Nicholas Duan, Chrystal Landgraff

“…Notably, clade-informing data was also achieved from partial sequences recovered from lower abundance samples. This study presents a new sequencing method targeting MPXV with enhanced genomic resolution compared to existing PCR-based approaches, providing critical genomic-level information informing MPXV surveillance and public health interventions.…”
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Molecular identification and phylogenetic analysis of confusing Tetrastigma species based on DNA barcoding and chloroplast genome by Xianjing Li, Yue Zhang, Meifang Song, Niaojiao Xu, Lu Qu, Haitao Li, Yunqiang Wang, Baozhong Duan, Zhonglian Zhang

“…Finally, to analyze the phylogenetic position of Tetrastigma species, we constructed a Maximum Likelihood (ML) phylogenetic tree using CP genome sequences of 46 species from seven genera within the Vitaceae family.Results and discussionThe CP genomes of Tetrastigma exhibited a typical circular tetramerous structure, including a large single-copy region (LSC) (87,381–88,979 bp), a small single-copy region (SSC) (18,649–19,339 bp), and a pair of inverted repeats (IRa and IRb) (26,288–26,934 bp). …”
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Feasibility of long-read sequencing to identify molecular alterations in an Indonesian cohort of locally advanced to advanced nasopharyngeal cancer by Handoko, Marlinda Adham, Lisnawati Rachmadi, Demak Lumban Tobing, Asmarinah, Fadilah, Wei Dai, Anne Wing Mui Lee, Soehartati A Gondhowiardjo

“…Six fresh-frozen nasopharyngeal biopsy samples were collected from the NPC biobank. DNA was extracted and sequenced using Oxford Nanopore’s Promethion 2 Solo long-read sequencer. …”
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