A New AB Initio Repeats Finding Algorithm for Reference Genome by Shuaibin Lian, Ke Gong, Xiangli Zhang, Xinwu Chen

“…It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution. …”
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Improvement of Nanopore sequencing provides access to high quality genomic data for multi-component CRESS-DNA plant viruses by Daniel H. Otron, Denis Filloux, Andy Brousse, Murielle Hoareau, Babbitha Fenelon, Cécile Hoareau, Emmanuel Fernandez, Fidèle Tiendrébéogo, Jean-Michel Lett, Justin S. Pita, Philippe Roumagnac, Pierre Lefeuvre

“…Originally, using the tandem-repeat nature of RCA products, we were able to improve the quality of each viral read and assemble high-quality genomic components. …”
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Flanking monomer repeats define lower context complexity of sites containing single nucleotide polymorphisms in the human genome by N. S. Safronova, M. P. Ponomarenko, I. I. Abnizova, G. V. Orlova, I. V. Chadaeva, Y. L. Orlov

“…The changes in point mutation frequency were shown previously for microsatellite containing sequences. Using enhanced mathematical tools and larger data sets this work shows enrichment of polytracks and simple sequence repeats in local genome surroundings of SNP containing sites. …”
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Validation of a comprehensive long-read sequencing platform for broad clinical genetic diagnosis by Siddhartha Sen, Hillary P. Handler, Alec Victorsen, Zach Flaten, Aidan Ellison, Todd P. Knutson, Sarah A. Munro, Ryan J. Martinez, Charles John Billington, Jennifer J. Laffin, Sarah Bray, Pawel Mroz, Sophia Yohe, Andrew C. Nelson, Matthew Bower, Bharat Thyagarajan

“…Though short read high-throughput sequencing, commonly known as Next-Generation Sequencing (NGS), has revolutionized genomics and genetic testing, there is no single genetic test that can accurately detect single nucleotide variants (SNVs), small insertions/deletions (indels), complex structural variants (SVs), repetitive genomic alterations, and variants in genes with highly homologous pseudogenes. …”
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Mitochondrial genome complexity in Erodium stephanianum (Geraniaceae): nanopore sequencing reveals chloroplast gene transfer and DNA rearrangements by Xinchen Xu, Xinchen Xu, Xinchen Xu, Qingfei Meng, Qingfei Meng, Na Li, Na Li, Zichuan Zou, Zichuan Zou, Haonan Yang, Haonan Yang, Ang Li, Ang Li, Fusheng Ge, Fusheng Ge, Jian Meng, Jian Meng, Zixue Ding, Zixue Ding

“…Furthermore, codon usage analysis revealed preferential codon utilization, while microsatellite and repeat sequence analyses identified numerous SSRs and tandem repeats within the mitogenome. …”
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Analysis of targeted and whole genome sequencing of PacBio HiFi reads for a comprehensive genotyping of gene-proximal and phenotype-associated Variable Number Tandem Repeats. by Sara Javadzadeh, Aaron Adamson, Jonghun Park, Se-Young Jo, Yuan-Chun Ding, Mehrdad Bakhtiari, Vikas Bansal, Susan L Neuhausen, Vineet Bafna

“…We compared these results against HiFi whole genome sequencing (WGS) data from 28 samples in the Human Pangenome Reference Consortium (HPRC). …”
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Effective DNA fragmentation technique for simple sequence repeat detection with a microsatellite-enriched library and high-throughput sequencing by Keisuke Tanaka, Rumi Ohtake, Saki Yoshida, Takashi Shinohara

“…Two different techniques for genomic DNA fragmentation before microsatellite-enriched library construction—restriction enzyme (NlaIII and MseI) digestion and sonication—were compared to examine their effects on simple sequence repeat (SSR) detection using high-throughput sequencing. …”
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Genome re-sequencing and functional analysis places the Phytophthora sojae avirulence genes Avr1c and Avr1a in a tandem repeat at a single locus. by Ren Na, Dan Yu, B Patrick Chapman, Yun Zhang, Kuflom Kuflu, Ryan Austin, Dinah Qutob, Jun Zhao, Yuanchao Wang, Mark Gijzen

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GenomeDelta: detecting recent transposable element invasions without repeat library by Riccardo Pianezza, Anna Haider, Robert Kofler

“…Abstract We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. …”
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Sample Size Impact (SaSii): An R script for estimating optimal sample sizes in population genetics and population genomics studies. by Matheus Scaketti, Patricia Sanae Sujii, Alessandro Alves-Pereira, Kaiser Dias Schwarcz, Ana Flávia Francisconi, Matheus Sartori Moro, Kauanne Karolline Moreno Martins, Thiago Araujo de Jesus, Guilherme Brener Ferreira de Souza, Maria Imaculada Zucchi

“…We also confirmed that the minimum sample sizes for SNP (single-nucleotide polymorphism) analysis are usually smaller than for SSR (simple sequence repeat) analysis and discussed other patterns observed from empirical plant and animal datasets.…”
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Genotyping TOMM40′523 poly-T polymorphisms using whole-genome sequencing by Ricardo A. Vialle, Lei Yu, Yan Li, Roberto T. Raittz, Jose M. Farfel, Philip L. De Jager, Julie A. Schneider, Lisa L. Barnes, Shinya Tasaki, David A. Bennett

“…Challenges in processing whole-genome sequencing (WGS) data traditionally require additional PCR and targeted sequencing assays to genotype these polymorphisms. …”
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Exploring Genetic Diversity: Optimizing Simple Sequence Repeat (SSR) Markers in Crotalaria for Enhanced Precision in Biodiversity Research by Phenny Sharon Odhoch, Nancy L. M. Budambula, Felix Kiprotich, Joshua Kiilu Muli

“…The current study aimed to optimize and validate simple sequence repeat (SSR) markers polymerase chain reaction—conditions for the assessment of genetic diversity in Crotalaria. …”
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Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Melanoseris cyanea group by Qianqian Zhong, Zehuan Wang, Jiaju Xu, Li Yan, Qingwen Sun

“…We analyzed the chloroplast genomes of 16 Melanoseris samples, including 12 new genomes from the M. cyanea group. …”
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High-throughput PacBio library preparation and sequencing techniques for genomic DNA and TNA by Meghan L. Bentz, Cristina Clines, Jasmine Padilla, Christopher Horn, Justin Lee, Mili Sheth

“…Test sequencing was performed on 380 genomic DNA samples, of which 28 (7.4%) failed sequencing and needed to be repeated. …”
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When old metagenomic data meet newly sequenced genomes, a case study. by Xin Li, Saleh A Naser, Annette Khaled, Haiyan Hu, Xiaoman Li

“…To see how newly sequenced genomes affect the analysis results, we re-analyzed a shotgun metagenomic dataset composed of twelve colitis free metagenomic samples and ten colitis-related metagenomic samples. …”
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Comprehensive identification of pathogenic tandem repeat expansions in sporadic amyotrophic lateral sclerosis: advantages of long-read vs. short-read sequencing by Eleonora Sabetta, Karin Rallmann, Jonas Bergquist, Pille Taba, Pille Taba, Abigail L. Pfaff, Abigail L. Pfaff, Bal Hari Poudel, Davide Ferrari, Massimo Locatelli, Sulev Kõks, Sulev Kõks

“…Blood samples from 47 sporadic ALS cases were subjected to SRS by Illumina Whole Genome Sequencing. …”
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Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus by Sarwar Azam, Abhisek Sahu, Naveen Kumar Pandey, Mahesh Neupane, Curtis P Van Tassell, Benjamin D Rosen, Ravi Kumar Gandham, Subha Narayan Rath, Subeer S Majumdar

“…Results Five representative genomes of prominent dairy breeds, including Gir, Kankrej, Tharparkar, Sahiwal, and Red Sindhi, were sequenced using 10X Genomics ‘linked-read’ technology. …”
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Genetic Variation of Golden Silk-Producing Insect Cricula trifenestrata Helf. (Lepidoptera: Saturniidae) Using ISSR (Inter Simple Sequence Repeats) Molecular Marker by Agnes Herlina Dwi Hadiyanti

“…<p>The aims of this research were to conduct a study on genetic variation C. trifenestrata collected from several sampling locations using ISSR (Inter-Simple Sequence Repeat) molecular markers. …”
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Evaluation of long-read sequencing for Ostreid herpesvirus type 1 genome characterization from Magallana gigas infected tissues by Aurélie Dotto-Maurel, Camille Pelletier, Lionel Degremont, Serge Heurtebise, Isabelle Arzul, Benjamin Morga, Germain Chevignon

“…We then evaluated the ability of ONT sequencing to produce an accurate OsHV-1 genome from both whole-genome and “adaptive sampling” (AS) sequencing approaches. …”
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The evolutionary dynamics of organellar pan-genomes in Arabidopsis thaliana by Yi Zou, Weidong Zhu, Yingke Hou, Daniel B. Sloan, Zhiqiang Wu

“…We find that mitochondrial and plastid genomes share common types of structural and small-scale variants driven by similar DNA sequence features. …”
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