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Journal articles on the topic 'Whole genome sequencing PacBio'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

PARK, Jongsun, Yunho YUN, Hong XI, Woochan KWON, and Janghyuk SON. "Current status of whole-genome sequences of Korean angiosperms." Korean Journal of Plant Taxonomy 53, no. 3 (2023): 181–200. http://dx.doi.org/10.11110/kjpt.2023.53.3.181.

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Owing to the rapid development of sequencing technologies, more than 1,000 plant genomes have been sequenced and released. Among them, 69 Korean plant taxa (85 genome sequences) contain at least one whole-genome sequence despite the fact that some samples were not collected in Korea. The sequencing-by-synthesis method (next-generation sequencing) and the PacBio (third-generation sequencing) method were the most commonly used in studies appearing in 65 publications. Several scaffolding methods, such as the Hi-C and 10x types, have also been used for pseudo-chromosomal assembly. The most abundan

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Kim, Justin, Rebecca L. Lindsey, Lisley Garcia-Toledo, et al. "High-Quality Whole-Genome Sequences for 59 HistoricalShigellaStrains Generated with PacBio Sequencing." Genome Announcements 6, no. 15 (2018): e00282-18. http://dx.doi.org/10.1128/genomea.00282-18.

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ABSTRACTShigellaspp. are enteric pathogens that cause shigellosis. We report here the high-quality whole-genome sequences of 59 historicalShigellastrains that represent the four species and a variety of serotypes.

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Fatima, Nazeefa, Anna Petri, Ulf Gyllensten, Lars Feuk, and Adam Ameur. "Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes." Genes 11, no. 12 (2020): 1444. http://dx.doi.org/10.3390/genes11121444.

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Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high resolution. However, few studies have evaluated the performance of different single molecule sequencing platforms for SV detection in human samples. Here we performed Oxford Nanopore Technologies (ONT) whole-genome sequencing of two Swedish human samples (average 32× coverage) and compared the results to previously generated Pacific Biosciences (PacBio) data for the same individuals (average 66× covera

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Sockell, Alexandra, Khi Pin Chua, Christopher Kingsley, et al. "Abstract 6624: Comprehensive, multi-omic detection of somatic variants from the GIAB HG008 matched tumor-normal pair using highly accurate long- and short-read whole-genome sequencing." Cancer Research 85, no. 8_Supplement_1 (2025): 6624. https://doi.org/10.1158/1538-7445.am2025-6624.

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Abstract Disentangling the molecular drivers of cancer progression requires a precise understanding of the somatic alterations that take place at the DNA level during tumor development. These include not only small changes like SNVs and indels, but also structural variants, changes in repetitive elements, differential methylation, as well as the haplotype context in which these changes occur. Existing short-read sequencing methods using sequencing by synthesis (SBS) chemistry lack the read length to characterize large structural variants or to span longer repetitive regions as well as to phase

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Subirana, Juan A., and Xavier Messeguer. "How Long Are Long Tandem Repeats? A Challenge for Current Methods of Whole-Genome Sequence Assembly: The Case of Satellites in Caenorhabditis elegans." Genes 9, no. 10 (2018): 500. http://dx.doi.org/10.3390/genes9100500.

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Repetitive genome regions have been difficult to sequence, mainly because of the comparatively small size of the fragments used in assembly. Satellites or tandem repeats are very abundant in nematodes and offer an excellent playground to evaluate different assembly methods. Here, we compare the structure of satellites found in three different assemblies of the Caenorhabditis elegans genome: the original sequence obtained by Sanger sequencing, an assembly based on PacBio technology, and an assembly using Nanopore sequencing reads. In general, satellites were found in equivalent genomic regions,

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Zhang, Pengfei, Dike Jiang, Yin Wang, Xueping Yao, Yan Luo, and Zexiao Yang. "Comparison of De Novo Assembly Strategies for Bacterial Genomes." International Journal of Molecular Sciences 22, no. 14 (2021): 7668. http://dx.doi.org/10.3390/ijms22147668.

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(1) Background: Short-read sequencing allows for the rapid and accurate analysis of the whole bacterial genome but does not usually enable complete genome assembly. Long-read sequencing greatly assists with the resolution of complex bacterial genomes, particularly when combined with short-read Illumina data. However, it is not clear how different assembly strategies affect genomic accuracy, completeness, and protein prediction. (2) Methods: we compare different assembly strategies for Haemophilus parasuis, which causes Glässer’s disease, characterized by fibrinous polyserositis and arthritis,

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Gao, Yahui, Li Ma, and George E. Liu. "Initial Analysis of Structural Variation Detections in Cattle Using Long-Read Sequencing Methods." Genes 13, no. 5 (2022): 828. http://dx.doi.org/10.3390/genes13050828.

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Structural variations (SVs), as a great source of genetic variation, are widely distributed in the genome. SVs involve longer genomic sequences and potentially have stronger effects than SNPs, but they are not well captured by short-read sequencing owing to their size and relevance to repeats. Improved characterization of SVs can provide more advanced insight into complex traits. With the availability of long-read sequencing, it has become feasible to uncover the full range of SVs. Here, we sequenced one cattle individual using 10× Genomics (10 × G) linked read, Pacific Biosciences (PacBio) co

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An, Dong, Yong Zhou, Changsheng Li, et al. "Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of Spirodela." Proceedings of the National Academy of Sciences 116, no. 38 (2019): 18893–99. http://dx.doi.org/10.1073/pnas.1910401116.

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Aquatic plants have to adapt to the environments distinct from where land plants grow. A critical aspect of adaptation is the dynamics of sequence repeats, not resolved in older sequencing platforms due to incomplete and fragmented genome assemblies from short reads. Therefore, we used PacBio long-read sequencing of the Spirodela polyrhiza genome, reaching a 44-fold increase of contiguity with an N50 (a median of contig lengths) of 831 kb and filling 95.4% of gaps left from the previous version. Reconstruction of repeat regions indicates that sequentially nested long terminal repeat (LTR) retr

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Lin, Guan, Juntao Gao, Junxian Zou, et al. "Whole-Genome Sequence and Characterization of Ralstonia solanacearum MLY102 Isolated from Infected Tobacco Stalks." Genes 15, no. 11 (2024): 1473. http://dx.doi.org/10.3390/genes15111473.

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Background/Objectives: Bacterial wilt disease is a soil-borne disease caused by Ralstonia solanacearum that causes huge losses to crop economies worldwide. Methods: In this work, strain MLY102 was isolated and further identified as R. solanacearum from a diseased tobacco stalk. The genomic properties of MLY102 were explored by performing biochemical characterization, genome sequencing, compositional analysis, functional annotation and comparative genomic analysis. Results: MLY102 had a pinkish-red color in the center of the colony surrounded by a milky-white liquid with fluidity on TTC medium.

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Jiang, Wansheng, Yunyun Lv, Le Cheng, et al. "Whole-Genome Sequencing of the Giant Devil Catfish, Bagarius yarrelli." Genome Biology and Evolution 11, no. 8 (2019): 2071–77. http://dx.doi.org/10.1093/gbe/evz143.

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AbstractAs one economically important fish in the southeastern Himalayas, the giant devil catfish (Bagarius yarrelli) has been known for its extraordinarily large body size. It can grow up to 2 m, whereas the non-Bagarius sisorids only reach 10–30 cm. Another outstanding characteristic of Bagarius species is the salmonids-like reddish flesh color. Both body size and flesh color are interesting questions in science and also valuable features in aquaculture that worth of deep investigations. Bagarius species therefore are ideal materials for studying body size evolution and color depositions in

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Yang, Jianfei, Wenshuai Zang, Jie Chen, et al. "Genomic Analysis of Penicillium griseofulvum CF3 Reveals Potential for Plant Growth Promotion and Disease Resistance." Journal of Fungi 11, no. 2 (2025): 153. https://doi.org/10.3390/jof11020153.

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Penicillium griseofulvum CF3 is a fungus isolated from healthy strawberry soil, with the potential to promote the growth of plants and enhance their resistance to diseases. However, the genome sequence of P. griseofulvum CF3 remains unclear. Therefore, we performed the whole-genome CCS sequencing of P. griseofulvum CF3 using the PacBio Sequel II platform. The assembled genome comprised 104 contigs, with a total length of 37,564,657 bp, encoding 13,252 protein-coding genes. Comprehensive functional annotation was performed using various BLAST databases, including the non-redundant (Nr) protein

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Trisakul, Kanwara, Yothin Hinwan, Jukgarin Eisiri, et al. "Comparisons of genome assembly tools for characterization of Mycobacterium tuberculosis genomes using hybrid sequencing technologies." PeerJ 12 (August 29, 2024): e17964. http://dx.doi.org/10.7717/peerj.17964.

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Background Next-generation sequencing of Mycobacterium tuberculosis, the infectious agent causing tuberculosis, is improving the understanding of genomic diversity of circulating lineages and strain-types, and informing knowledge of drug resistance mutations. An increasingly popular approach to characterizing M. tuberculosis genomes (size: 4.4 Mbp) and variants (e.g., single nucleotide polymorphisms (SNPs)) involves the de novo assembly of sequence data. Methods We compared the performance of genome assembly tools (Unicycler, RagOut, and RagTag) on sequence data from nine drug resistant M. tub

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Lysenkova Wiklander, Mariya, Gustav Arvidsson, Ignas Bunikis, et al. "A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing." Life Science Alliance 7, no. 8 (2024): e202302481. http://dx.doi.org/10.26508/lsa.202302481.

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The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21)ETV6::RUNX1translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, the cell line offers a practical model for the study of pediatric B-ALL. In recent years, short- and long-read DNA and RNA sequencing have emerged as a complement to karyotyping techniques in the resolution of structural variants in an oncological context. Here, we explore the integration of long-read PacBio and Oxford Nanopore whole-genome sequencing, IsoSeq

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Al-kaabi, Hasanain Qasim Mezaal, and Rahman Laibi Chelab. "Whole genome sequence of Lactiplantibacillus plantarum strain HA9 isolated from conventional Iraqi cheese: First report." Advancements in Life Sciences 11, no. 2 (2024): 438. http://dx.doi.org/10.62940/als.v11i2.2649.

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Background: Lactiplantibacillus plantarum is a renowned probiotic known for its ability to enhance health when ingested in sufficient quantities. While L. plantarum typically exhibits unique characteristics, variations in strains and environments can occur. Therefore, it is crucial to conduct genetic identification of the strain before incorporating it into products or administering it for health benefits.Methods: After being isolated from classic artisanal milk cheeses, the bacterial DNA extraction kit from GENEAID, Korea, was used, and strain HA9's genomic DNA was isolated. Then, the highly

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Toropov, Vyacheslav, Elena Demyanova, Olga Shalaeva, Stanislav Sitkin, and Timur Vakhitov. "Whole-Genome Sequencing of Lactobacillus helveticus D75 and D76 Confirms Safety and Probiotic Potential." Microorganisms 8, no. 3 (2020): 329. http://dx.doi.org/10.3390/microorganisms8030329.

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Whole-genome DNA sequencing of Lactobacillus D75 and D76 strains (Vitaflor, Russia) was determined using the PacBio RS II platform, which was followed by de novo assembly with SMRT Portal 2.3.0. The average nucleotide identity (ANI) test showed that both strains belong to the Lactobacillus helveticus, but not to the L. acidophilus, as previously assumed. In addition, 31 exopolysaccharide (EPS) production genes (nine of which form a single genetic cluster), 13 adhesion genes, 38 milk protein and 11 milk sugar utilization genes, 13 genes for and against specific antagonistic activity, eight anti

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Yi, Xu Jing. "Mycoplasma pathogenicity for humans and animals: an effort of complete genome sequencing and gene family analysis of Mycoplasma synoviae." Pakistan Journal of Agricultural Sciences 58, no. 04 (2021): 1379–85. http://dx.doi.org/10.21162/pakjas/21.673.

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Like humans, chickens can become sick from bacterial infections. Mycoplasma is a very small, slow-growing bacterium. There are multiple types of Mycoplasma that affect different animals, humans, and even plants and insects. In the current study, the whole genome of Mycoplasma synoviae was sequenced through the joint sequencing method of the third-generation PacBio and second-generation Illumina of the high-throughput sequencing platform, and the complete genome map of the Mycoplasma synoviae was successfully obtained. SMRT sequencing and assembly of whole genome: Canu v1.5/ WTDBG v2.2 software

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Holland, Sophie I., Richard J. Edwards, Haluk Ertan, et al. "Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture." PeerJ 7 (October 2, 2019): e7775. http://dx.doi.org/10.7717/peerj.7775.

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Bacteria capable of dechlorinating the toxic environmental contaminant dichloromethane (DCM, CH2Cl2) are of great interest for potential bioremediation applications. A novel, strictly anaerobic, DCM-fermenting bacterium, “DCMF”, was enriched from organochlorine-contaminated groundwater near Botany Bay, Australia. The enrichment culture was maintained in minimal, mineral salt medium amended with dichloromethane as the sole energy source. PacBio whole genome SMRTTM sequencing of DCMF allowed de novo, gap-free assembly despite the presence of cohabiting organisms in the culture. Illumina sequenci

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Han, Bangxing, Yi Jing, Jun Dai, et al. "A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data." Genome Biology and Evolution 12, no. 12 (2020): 2486–90. http://dx.doi.org/10.1093/gbe/evaa215.

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Abstract Dendrobium huoshanense is used to treat various diseases in traditional Chinese medicine. Recent studies have identified active components. However, the lack of genomic data limits research on the biosynthesis and application of these therapeutic ingredients. To address this issue, we generated the first chromosome-level genome assembly and annotation of D. huoshanense. We integrated PacBio sequencing data, Illumina paired-end sequencing data, and Hi-C sequencing data to assemble a 1.285 Gb genome, with contig and scaffold N50 lengths of 598 kb and 71.79 Mb, respectively. We annotated

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Liu, Yiqun, and Yunxiang Mao. "Chromosome-Level Genome Assembly and Genomic Analysis of the Hybrid Grouper ShanHu (Epinephelus fuscoguttatus ♀ × Epinephelus polyphekadion ♂)." International Journal of Molecular Sciences 26, no. 11 (2025): 5036. https://doi.org/10.3390/ijms26115036.

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Groupers are important aquaculture species, and hybridization is an effective breeding method for genetic improvement and to enhance production efficiency in groupers. The ShanHu grouper (Epinephelus fuscoguttatus ♀ × Epinephelus polyphekadion ♂) is a hybrid grouper with potential for aquaculture development and research value. Using Illumina and PacBio sequencing platforms, as well as PacBio SMRT technology and Hi-C auxiliary mounting technology, the whole genome sequencing and assembly of the ShanHu grouper were completed, resulting in a chromosome-level genome information for this hybrid gr

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Prodanov, Timofey, and Vikas Bansal. "Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications." Nucleic Acids Research 48, no. 19 (2020): e114-e114. http://dx.doi.org/10.1093/nar/gkaa829.

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Abstract The ability to characterize repetitive regions of the human genome is limited by the read lengths of short-read sequencing technologies. Although long-read sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies can potentially overcome this limitation, long segmental duplications with high sequence identity pose challenges for long-read mapping. We describe a probabilistic method, DuploMap, designed to improve the accuracy of long-read mapping in segmental duplications. It analyzes reads mapped to segmental duplications using existing long-read a

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Liang, Xinmin, Jing Han, Yuqin Cui, et al. "Whole-Genome Sequencing of Flammulina filiformis and Multi-Omics Analysis in Response to Low Temperature." Journal of Fungi 11, no. 3 (2025): 229. https://doi.org/10.3390/jof11030229.

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The growth of Flammulina filiformis is strongly dependent on low-temperature cues for the initiation of primordia formation. To obtain a comprehensive understanding of the molecular mechanisms that govern the mycelial response to cold stress, de novo genome sequencing of the F. filiformis monokaryon and multi-omics data (transcriptome and metabolome) analyses of the mycelia, primordia, and fruiting bodies were conducted in the present study. Genome sequencing based on PacBio HiFi and Hi-C resulted in a 36.3 Mb genome sequence that mapped to 12 chromosomes, comprising 11,886 protein-coding gene

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Liu, Yanbo, Junying Fu, Linlin Wang, et al. "Isolation, identification, and whole-genome sequencing of high-yield protease bacteria from Daqu of ZhangGong Laojiu." PLOS ONE 17, no. 4 (2022): e0264677. http://dx.doi.org/10.1371/journal.pone.0264677.

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A total of 296 strains of protease-producing bacteria were isolated and purified from medium-temperature Daqu produced by ZhangGong LaoJiu Wine Co. Ltd. After calculating the ratio of transparent ring diameter to colony diameter and measuring the protease activities, a strain of high-yield protease bacteria, called DW-7, was screened out with a protease activity of 99.54 U/mL. Through morphological observation, 16S rDNA sequence analysis, and physiological and biochemical tests, the isolated bacteria DW-7 was determined to be Bacillus velezensis. In addition, whole-genome sequencing (WGS), usi

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Liu, Yanbo, Junying Fu, Linlin Wang, et al. "Isolation, identification, and whole-genome sequencing of high-yield protease bacteria from Daqu of ZhangGong Laojiu." PLOS ONE 17, no. 4 (2022): e0264677. http://dx.doi.org/10.1371/journal.pone.0264677.

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A total of 296 strains of protease-producing bacteria were isolated and purified from medium-temperature Daqu produced by ZhangGong LaoJiu Wine Co. Ltd. After calculating the ratio of transparent ring diameter to colony diameter and measuring the protease activities, a strain of high-yield protease bacteria, called DW-7, was screened out with a protease activity of 99.54 U/mL. Through morphological observation, 16S rDNA sequence analysis, and physiological and biochemical tests, the isolated bacteria DW-7 was determined to be Bacillus velezensis. In addition, whole-genome sequencing (WGS), usi

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Radosavljević, Ivan, Krešimir Križanović, Sara Laura Šarančić, and Jernej Jakše. "Towards the Investigation of the Adaptive Divergence in a Species of Exceptional Ecological Plasticity: Chromosome-Scale Genome Assembly of Chouardia litardierei (Hyacinthaceae)." International Journal of Molecular Sciences 24, no. 13 (2023): 10755. http://dx.doi.org/10.3390/ijms241310755.

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One of the central goals of evolutionary biology is to understand the genomic basis of adaptive divergence. Different aspects of evolutionary processes should be studied through genome-wide approaches, therefore maximizing the investigated genomic space. However, in-depth genome-scale analyses often are restricted to a model or economically important species and their closely related wild congeners with available reference genomes. Here, we present the high-quality chromosome-level genome assembly of Chouardia litardierei, a plant species with exceptional ecological plasticity. By combining Pa

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Paloi, Soumitra, Wuttichai Mhuantong, Janet Jennifer Luangsa-ard, and Noppol Kobmoo. "Using High-Throughput Amplicon Sequencing to Evaluate Intragenomic Variation and Accuracy in Species Identification of Cordyceps Species." Journal of Fungi 7, no. 9 (2021): 767. http://dx.doi.org/10.3390/jof7090767.

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While recent sequencing technologies (third generation sequencing) can successfully sequence all copies of nuclear ribosomal DNA (rDNA) markers present within a genome and offer insights into the intragenomic variation of these markers, high intragenomic variation can be a source of confusion for high-throughput species identification using such technologies. High-throughput (HT) amplicon sequencing via PacBio SEQUEL I was used to evaluate the intragenomic variation of the ITS region and D1–D2 LSU domains in nine Cordyceps species, and the accuracy of such technology to identify these species

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Karimi, Karim, Duy Ngoc Do, and Younes Miar. "PSVIII-9 Genome assembly of American mink (Neovison vison) using high-fidelity long reads." Journal of Animal Science 99, Supplement_3 (2021): 241–42. http://dx.doi.org/10.1093/jas/skab235.440.

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Abstract Development of genome-enabled selection and providing new insights in the genetic architecture of economically important traits are essential parts of mink breeding programs. Availability of a contagious genome assembly would guarantee the fundamental genomic studies in American mink (Neovison vison). Advances in long-read sequencing technologies have provided the opportunity to obtain high quality and free-gaps assemblies for different species. The objective of this study was to generate an accurate genome assembly using Single Molecule High-Fidelity (HiFi) Sequencing for American mi

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Luo, Yan, Jae Hee Jang, Maria Balkey, and Maria Hoffmann. "217 closed Salmonella reference genomes using PacBio sequencing." BMC Genomic Data 26, no. 1 (2025). https://doi.org/10.1186/s12863-025-01304-7.

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Abstract Objectives Whole Genome Sequencing (WGS) is widely used in food safety for the detection, investigation, and control of foodborne bacterial pathogens. However, the WGS data in most public databases, such as the National Center for Biotechnology Information (NCBI), primarily consist of Illumina short reads which lack some important information for repetitive regions, structural variations, and mobile genetic elements, and the genomic location of certain important genes like antimicrobial resistance genes (AMR) and virulence genes. To address this limitation, we have contributed 217 clo

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Kim, Hui-Su, Sungwon Jeon, Changjae Kim, et al. "Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information." GigaScience 8, no. 12 (2019). http://dx.doi.org/10.1093/gigascience/giz125.

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Abstract Background Long DNA reads produced by single-molecule and pore-based sequencers are more suitable for assembly and structural variation discovery than short-read DNA fragments. For de novo assembly, Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) are the favorite options. However, PacBio's SMRT sequencing is expensive for a full human genome assembly and costs more than $40,000 US for 30× coverage as of 2019. ONT PromethION sequencing, on the other hand, is 1/12 the price of PacBio for the same coverage. This study aimed to compare the cost-effectiveness of ONT Pro

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Jain, Tanya, and Claire Clelland. "nf-core/pacvar: a pipeline for analyzing longread PacBio whole genome and repeat expansion sequencing data." Bioinformatics, March 17, 2025. https://doi.org/10.1093/bioinformatics/btaf116.

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Abstract Motivation Pacific Biosciences (PacBio) single molecule, long-read sequencing enables whole genome annotation and the characterization of 20 complex repetitive repeat regions especially relevant to neurodegenerative diseases through their PureTarget panel. Long-read whole genome sequencing (WGS) also allows for the detection of structural variants that would be difficult to detect with traditional short-read sequencing. However, the raw unaligned Binary Alignment Map (BAM) data needs to be processed before analysis. There is a need for an intuitive comprehensive bioinformatic pipeline

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Nishii, Kanae, Michael Möller, Robert G. Foster, et al. "A high quality, high molecular weight DNA extraction method for PacBio HiFi genome sequencing of recalcitrant plants." Plant Methods 19, no. 1 (2023). http://dx.doi.org/10.1186/s13007-023-01009-x.

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Abstract Background PacBio HiFi sequencing provides highly accurate long-read sequencing datasets which are of great advantage for whole genome sequencing projects. One limitation of the method is the requirement for high quality, high molecular weight input DNA. This can be particularly challenging for plants that frequently contain common and species-specific secondary metabolites, which often interfere with downstream processes. Cape Primroses (genus Streptocarpus), are some of these recalcitrant plants and are selected here as material to develop a high quality, high molecular weight DNA e

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Vellas, Camille, Amira Doudou, Sofiane Mohamed, et al. "Comparison of short‐read and long‐read next‐generation sequencing technologies for determining HIV‐1 drug resistance." Journal of Medical Virology 96, no. 10 (2024). http://dx.doi.org/10.1002/jmv.29951.

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AbstractAccurate HIV‐1 genome sequencing is necessary to identify drug resistance mutations (DRMs) in people with HIV‐1 (PWH). Next‐generation‐sequencing (NGS) allows the detection of minor variants and is now available in many laboratories. Our study aimed to compare two NGS approaches, a “short read” sequencing protocol using DeepChek® Whole Genome HIV‐1 Assay on Illumina, and a “long read” sequencing protocol of HIV‐1 pol and env single‐molecule real‐time sequencing (SMRT) on Pacific Biosciences (PacBio). We analyzed 16 plasma samples and 13 cellular samples from PWH. HIV‐1 whole genome was

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Schamann, Alexandra, Rolf Geisen, and Markus Schmidt-Heydt. "Whole-Genome Sequences of Two Kenyan Aspergillus minisclerotigenes Strains." Microbiology Resource Announcements, July 5, 2023. http://dx.doi.org/10.1128/mra.00219-23.

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Here, we report the sequencing of the whole genome, including the mitochondrial DNA, of the two highly aflatoxigenic Aspergillus minisclerotigenes strains MRI390 and MRI400 using the MiSeq and PacBio platforms and the generated assemblies. The strains were isolated from Kenyan maize kernels.

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Wang, Zhijie, Chen Liu, Wanxin Liu, et al. "Long-read sequencing reveals the structural complexity of genomic integration of HPV DNA in cervical cancer cell lines." BMC Genomics 25, no. 1 (2024). http://dx.doi.org/10.1186/s12864-024-10101-y.

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Abstract Background Cervical cancer (CC) causes more than 311,000 deaths annually worldwide. The integration of human papillomavirus (HPV) is a crucial genetic event that contributes to cervical carcinogenesis. Despite HPV DNA integration is known to disrupt the genomic architecture of both the host and viral genomes in CC, the complexity of this process remains largely unexplored. Results In this study, we conducted whole-genome sequencing (WGS) at 55-65X coverage utilizing the PacBio long-read sequencing platform in SiHa and HeLa cells, followed by comprehensive analyses of the sequence data

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Faino, Luigi, Michael F. Seidl, Erwin Datema, et al. "Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome." mBio 6, no. 4 (2015). http://dx.doi.org/10.1128/mbio.00936-15.

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ABSTRACT Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include P

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Nebenführ, Marcel, David Prochotta, Alexander Ben Hamadou, et al. "High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog’s genome." Gigabyte 2024 (September 13, 2024). http://dx.doi.org/10.46471/gigabyte.134.

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The time required for genome sequencing and de novo assembly depends on the interaction between laboratory work, sequencing capacity, and the bioinformatics workflow, often constrained by external sequencing services. Bringing together academic biodiversity institutes and a medical diagnostics company with extensive sequencing capabilities, we aimed at generating a high-quality mammalian de novo genome in minimal time. We present the first chromosome-level genome assembly of the Whippet, using PacBio long-read high-fidelity sequencing and reference-guided scaffolding. The final assembly has a

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Chiu, Shih-Hau, Chien-Chi Chen, Li-Ting Wang, and Lina Huang. "Whole-Genome Sequencing of Lactobacillus salivarius Strains BCRC 14759 and BCRC 12574." Genome Announcements 5, no. 47 (2017). http://dx.doi.org/10.1128/genomea.01336-17.

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ABSTRACTLactobacillus salivariusBCRC 14759 has been identified as a high-exopolysaccharide-producing strain with potential as a probiotic or fermented dairy product. Here, we report the genome sequences ofL. salivariusBCRC 14759 and the comparable strain BCRC 12574, isolated from human saliva. The PacBio RSII sequencing platform was used to obtain high-quality assemblies for characterization of this probiotic candidate.

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Uchimura, Yasuhiro, Madeleine Wyss, Sandrine Brugiroux, et al. "Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2: TABLE 1." Genome Announcements 4, no. 5 (2016). http://dx.doi.org/10.1128/genomea.00951-16.

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We report here the complete genome sequences of 12 bacterial species of stable defined moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize germ-free mice with defined microbes. Whole-genome sequencing of these species was performed using the PacBio sequencing platform yielding circularized genome sequences of all 12 species.

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Coates-Brown, Rosanna, and Malcolm J. Horsburgh. "Whole-Genome Sequence of Staphylococcus hominis Strain J31 Isolated from Healthy Human Skin." Genome Announcements 5, no. 15 (2017). http://dx.doi.org/10.1128/genomea.01548-16.

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ABSTRACT We report here the first whole-genome sequence of a skin-associated strain of Staphylococcus hominis determined using the PacBio long-read sequencing platform. S. hominis is a major commensal of the skin microflora. This genome sequence adds to our understanding of this species and will aid studies of gene traffic between staphylococci.

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Lázaro-Díez, María, Santiago Redondo-Salvo, Aroa Arboleya-Agudo, et al. "Whole-Genome Sequence of Hafnia alvei HUMV-5920, a Human Isolate." Genome Announcements 4, no. 3 (2016). http://dx.doi.org/10.1128/genomea.00556-16.

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A clinical isolate of Hafnia alvei (strain HUMV-5920) was obtained from a urine sample from an adult patient. We report here its complete genome assembly using PacBio single-molecule real-time (SMRT) sequencing, which resulted in a chromosome with 4.5 Mb and a circular contig of 87 kb. About 4,146 protein-coding genes are predicted from this assembly.

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Sun, Peng, Haifeng Luo, Xin Zhang, Jingyi Xu, Yanan Guo, and Shenghu He. "Whole-Genome Sequence of Mycoplasma bovis Strain Ningxia-1." Genome Announcements 6, no. 4 (2018). http://dx.doi.org/10.1128/genomea.01367-17.

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ABSTRACT A genome sequence of the Mycoplasma bovis Ningxia-1 strain was tested by Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing technology. The strain was isolated from a lesioned calf lung in 2013 in Pengyang, Ningxia, China. The single circular chromosome of 1,033,629 bp shows differences between complete Mycoplasma bovis genome in insertion-like sequences (ISs), integrative conjugative elements (ICEs), lipoproteins (LPs), variable surface lipoproteins (VSPs), pathogenicity islands (PAIs), etc.

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Patel, Pooja N., Rebecca L. Lindsey, Lisley Garcia-Toledo, et al. "High-Quality Whole-Genome Sequences for 77 Shiga Toxin-Producing Escherichia coli Strains Generated with PacBio Sequencing." Genome Announcements 6, no. 19 (2018). http://dx.doi.org/10.1128/genomea.00391-18.

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ABSTRACT Shiga toxin-producing Escherichia coli (STEC) is an enteric foodborne pathogen that can cause mild to severe illness. Here, we report the availability of high-quality whole-genome sequences for 77 STEC strains generated using the PacBio sequencing platform.

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Chapartegui-González, Itziar, María Lázaro-Díez, Santiago Redondo-Salvo, et al. "Whole-Genome Sequence of Acinetobacter pittii HUMV-6483 Isolated from Human Urine." Genome Announcements 5, no. 29 (2017). http://dx.doi.org/10.1128/genomea.00658-17.

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ABSTRACT Acinetobacter pittii strain HUMV-6483 was obtained from urine from an adult patient. We report here its complete genome assembly using PacBio single-molecule real-time sequencing, which resulted in a chromosome with 4.07 Mb and a circular contig of 112 kb. About 3,953 protein-coding genes are predicted from this assembly.

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Tvedte, Eric S., Mark Gasser, Benjamin C. Sparklin, et al. "Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes." G3 Genes|Genomes|Genetics 11, no. 6 (2021). http://dx.doi.org/10.1093/g3journal/jkab083.

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Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit f

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Augelletti, Floriana, Julien Tremblay, Spiros N. Agathos, Alexandre Jousset, and Ben Stenuit. "Draft Whole-Genome Sequence of the Anthracene-Degrading Strain Mycolicibacterium frederiksbergense LB501T, Isolated from a Polycyclic Aromatic Hydrocarbon-Contaminated Soil." Microbiology Resource Announcements 9, no. 43 (2020). http://dx.doi.org/10.1128/mra.00671-20.

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ABSTRACT Here, we report the draft whole-genome sequence of an anthracene-degrading bacterium, Mycolicibacterium frederiksbergense strain LB501T, using the PacBio and Illumina sequencing platforms. The complete genome sequence of strain LB501T consists of 6,713,618 bp and provides new insights into its metabolic capabilities, including aromatic conversion pathways with promiscuous activities.

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Zhu, Liya, Céline Lopez-Roques, Marine Sallaberry, et al. "Whole-genome sequences of 38 siderophore-producing isolates from root systems of two pea and one wheat varieties." Microbiology Resource Announcements, July 23, 2025. https://doi.org/10.1128/mra.00570-25.

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ABSTRACT Here, we report the whole-genome sequencing of 38 siderophore-producing bacterial strains isolated from the root systems of two pea and one wheat varieties. High-quality genomic data for each isolate was generated using PacBio HiFi sequencing, producing 6.1 Gb of HiFi reads and achieving an average assembly completeness of 98.85%.

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Zhu, Ying, Xiaoliang Shan, Jianping Zhou, et al. "Complete Genome Sequence of Pythium oligandrum, Isolated from Rhizosphere Soils of Chinese Angelica sinensis." Molecular Plant-Microbe Interactions®, November 16, 2022. http://dx.doi.org/10.1094/mpmi-04-22-0091-a.

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Most of the Pythium species are pathogenic to a wide range of economically important crops and, sometimes, can even cause diseases in animals and humans. An exception is that the soil-inhabiting P. oligandrum is an effective biocontrol agent against a diverse suite of pathogens and promotes plant growth. In this work, we sequenced the whole genome of P. oligandrum PO-1, isolated from rhizosphere soils of Chinese Angelica sinensis, using a combination of long-read single-molecule real-time sequencing technology (Pacific Biosciences [PacBio]) and Illumina sequencing. The 2.5-Gb and 5.2-Gb bases

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Gaber, Alhussien M., John C. Blazier, and Artem S. Rogovskyy. "Whole-genome sequences of six Borrelia recurrentis strains obtained via PacBio sequencing." Microbiology Resource Announcements, January 13, 2025. https://doi.org/10.1128/mra.01026-24.

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ABSTRACT Provided are whole-genome sequences of six Borrelia recurrentis strains that had been earlier isolated from louse-borne relapsing fever patients. The sequences of each genome presented here included one linear chromosome and 5 linear plasmids, whose average size was 1,284,895 bp with the mean GC content being 27.5%.

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Chen, Jinfeng, Jingfei Cheng, Xiufei Chen, Masato Inoue, Yibin Liu, and Chun-Xiao Song. "Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology." Nucleic Acids Research, July 18, 2022. http://dx.doi.org/10.1093/nar/gkac612.

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Abstract Long-read sequencing provides valuable information on difficult-to-map genomic regions, which can complement short-read sequencing to improve genome assembly, yet limited methods are available to accurately detect DNA methylation over long distances at a whole-genome scale. By combining our recently developed TET-assisted pyridine borane sequencing (TAPS) method, which enables direct detection of 5-methylcytosine and 5-hydroxymethylcytosine, with PacBio single-molecule real-time sequencing, we present here whole-genome long-read TAPS (wglrTAPS). To evaluate the performance of wglrTAPS

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Karin, Benjamin R., Selene Arellano, Laura Wang, et al. "Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes." BMC Genomics 24, no. 1 (2023). http://dx.doi.org/10.1186/s12864-023-09277-6.

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Abstract Background Mitochondrial genome sequences have become critical to the study of biodiversity. Genome skimming and other short-read based methods are the most common approaches, but they are not well-suited to scale up to multiplexing hundreds of samples. Here, we report on a new approach to sequence hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing. We amplified the mitochondrial genome of 677 specimens in two partially overlapping amplicons and implemented an asymmetric PCR-based indexing approach to multiplex 1,159 long amplicons toget

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Al-Harbi, Ahmed H. "Whole-genome sequence of Staphylococcus epidermidis strain AH3, isolated from Nile tilapia ( Oreochromis niloticus )." Microbiology Resource Announcements, October 6, 2023. http://dx.doi.org/10.1128/mra.00682-23.

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ABSTRACT The whole-genome sequence of Staphylococcus epidermidis strain AH3 isolated from moribund farmed Nile tilapia ( Oreochromis niloticus ) was performed using a combination of the Illumina and Pacific Biosciences (PacBio) sequencing platforms. The genome sequence is composed of a single chromosome of 2,464,380 bp with a GC content of 32.2% and 2,220 predicted protein-coding genes.

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