Journal articles: 'Genome survey sequencing (GSS)'

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Beckett, Paul, Ian Bancroft, and Martin Trick. "Computational Tools forBrassica–ArabidopsisComparative Genomics." Comparative and Functional Genomics 6, no. 3 (2005): 147–52. http://dx.doi.org/10.1002/cfg.463.

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Recent advances, such as the availability of extensive genome survey sequence (GSS) data and draft physical maps, are radically transforming the means by which we can dissectBrassicagenome structure and systematically relate it to theArabidopsismodel. Hitherto, our view of the co-linearities between these closely related genomes had been largely inferred from comparative RFLP data, necessitating substantial interpolation and expert interpretation. Sequencing of theBrassica rapagenome by the MultinationalBrassicaGenome Project will, however, enable an entirely computational approach to this problem. Meanwhile we have been developing databases and bioinformatics tools to support our work inBrassicacomparative genomics, including a recently completed draft physical map ofB. rapaintegrated with anchor probes derived from theArabidopsisgenome sequence. We are also exploring new ways to display the emergingBrassica–Arabidopsissequence homology data. We have mapped all publicly available Brassica sequencesin silicoto theArabidopsisTIGR v5 genome sequence and published this in the ATIDB database that uses Generic Genome Browser (GBrowse). Thisin silicoapproach potentially identifies all paralogous sequences and so we colour-code the significance of the mappings and offer an integrated, real-time multiple alignment tool to partition them into paralogous groups. The MySQL database driving GBrowse can also be directly interrogated, using the powerful API offered by the Perl Bio∷DB∷GFF methods, facilitating a wide range of data-mining possibilities.

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Vining, Kelly J., Natalia Salinas, Jacob A. Tennessen, Jason D. Zurn, Daniel James Sargent, James Hancock, and Nahla V. Bassil. "Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families." PeerJ 5 (August 30, 2017): e3731. http://dx.doi.org/10.7717/peerj.3731.

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Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria× ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to theF. vesca‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30–65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of theFvbreference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral speciesF. vescafor each chromosome. Linkage groups that were most similar to a second ancestral species,F. iinumae, were only resolved forFvb4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolvedF.× ananassachromosomal regions derived from diploid ancestorF. vesca.

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Wang, Sui, Su Chen, Caixia Liu, Yi Liu, Xiyang Zhao, Chuanping Yang, and Guan-Zheng Qu. "Genome Survey Sequencing of Betula platyphylla." Forests 10, no. 10 (September 20, 2019): 826. http://dx.doi.org/10.3390/f10100826.

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Research Highlights: A rigorous genome survey helped us to estimate the genomic characteristics, remove the DNA contamination, and determine the sequencing scheme of Betula platyphylla. Background and Objectives: B. platyphylla is a common tree species in northern China that has high economic and medicinal value. However, there is a lack of complete genomic information for this species, which severely constrains the progress of relevant research. The objective of this study was to survey the genome of B. platyphylla and determine the large-scale sequencing scheme of this species. Materials and Methods: Next-generation sequencing was used to survey the genome. The genome size, heterozygosity rate, and repetitive sequences were estimated by k-mer analysis. After preliminary genome assembly, sequence contamination was identified and filtered by sequence alignment. Finally, we obtained sterilized plantlets of B. platyphylla by plant tissue culture, which can be used for third-generation sequencing. Results: We estimated the genome size to be 432.9 Mb and the heterozygosity rate to be 1.22%, with repetitive sequences accounting for 62.2%. Bacterial contamination was observed in the leaves taken from the field, and most of the contaminants may be from the genus Mycobacterium. A total of 249,784 simple sequence repeat (SSR) loci were also identified in the B. platyphylla genome. Among the SSRs, only 11,326 can be used as candidates to distinguish the three Betula species. Conclusions: The B. platyphylla genome is complex and highly heterozygous and repetitive. Higher-depth third-generation sequencing may yield better assembly results. Sterilized plantlets can be used for sequencing to avoid contamination.

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Zhou, Wen, Bin Li, Lin Li, Wen Ma, Yuanchu Liu, Shuchao Feng, and Zhezhi Wang. "Genome survey sequencing of Dioscorea zingiberensis." Genome 61, no. 8 (August 2018): 567–74. http://dx.doi.org/10.1139/gen-2018-0011.

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Dioscorea zingiberensis (Dioscoreceae) is the main plant source of diosgenin (steroidal sapogenins), the precursor for the production of steroid hormones in the pharmaceutical industry. Despite its large economic value, genomic information of the genus Dioscorea is currently unavailable. Here, we present an initial survey of the D. zingiberensis genome performed by next-generation sequencing technology together with a genome size investigation inferred by flow cytometry. The whole genome survey of D. zingiberensis generated 31.48 Gb of sequence data with approximately 78.70× coverage. The estimated genome size is 800 Mb, with a high level of heterozygosity based on K-mer analysis. These reads were assembled into 334 288 contigs with a N50 length of 1079 bp, which were further assembled into 92 163 scaffolds with a total length of 173.46 Mb. A total of 4935 genes, 81 tRNAs, 69 rRNAs, and 661 miRNAs were predicted by the genome analysis, and 263 484 repeated sequences were obtained with 419 372 simple sequence repeats (SSRs). Among these SSRs, the mononucleotide repeat type was the most abundant (up to 54.60% of the total SSRs), followed by the dinucleotide (29.60%), trinucleotide (11.37%), tetranucleotide (3.53%), pentanucleotide (0.65%), and hexanucleotide (0.25%) repeat types. The 1C-value of D. zingiberensis was calibrated against Salvia miltiorrhiza and calculated as 0.87 pg (851 Mb) by flow cytometry, which was very close to the result of the genome survey. This is the first report of genome-wide characterization within this taxon.

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Kirkness, E. F. "The Dog Genome: Survey Sequencing and Comparative Analysis." Science 301, no. 5641 (September 26, 2003): 1898–903. http://dx.doi.org/10.1126/science.1086432.

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Bhore, Subhash J., Amelia Kassim, and Farida H. Shah. "Insights from the GC content analysis of 76 genome survey sequences (GSS) from Elaeis oleifera." Bioinformation 5, no. 4 (September 20, 2010): 141–45. http://dx.doi.org/10.6026/97320630005141.

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Laurentino, Eliane C., Jeronimo C. Ruiz, Gholam Fazelinia, Peter J. Myler, Wim Degrave, Marcelo Alves-Ferreira, José Marcos C. Ribeiro, and Angela K. Cruz. "A survey of Leishmania braziliensis genome by shotgun sequencing." Molecular and Biochemical Parasitology 137, no. 1 (September 2004): 81–86. http://dx.doi.org/10.1016/j.molbiopara.2004.05.001.

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Janssen, Christoph S., Michael P. Barrett, Daniel Lawson, Michael A. Quail, David Harris, Sharen Bowman, R. Stephen Phillips, and C. Michael R. Turner. "Gene discovery in Plasmodium chabaudi by genome survey sequencing." Molecular and Biochemical Parasitology 113, no. 2 (April 2001): 251–60. http://dx.doi.org/10.1016/s0166-6851(01)00224-9.

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Shi, Linlin, Shaokui Yi, and Yanhe Li. "Genome survey sequencing of red swamp crayfish Procambarus clarkii." Molecular Biology Reports 45, no. 5 (June 21, 2018): 799–806. http://dx.doi.org/10.1007/s11033-018-4219-3.

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Sun, Kuo, De-Long Guan, Hua-Teng Huang, and Sheng-Quan Xu. "Genome Survey Sequencing of the Mole Cricket Gryllotalpa orientalis." Genes 14, no. 2 (January 18, 2023): 255. http://dx.doi.org/10.3390/genes14020255.

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The mole cricket Gryllotalpa orientalis is an evolutionarily, medicinal, and agriculturally significant insect that inhabits underground environments and is distributed globally. This study measured genome size by flow cytometry and k-mer based on low-coverage sequencing, and nuclear repetitive elements were also identified. The haploid genome size estimate is 3.14 Gb by flow cytometry, 3.17 Gb, and 3.77 Gb-based two k-mer methods, respectively, which is well within the range previously reported for other species of the suborder Ensifera. 56% of repetitive elements were found in G. orientalis, similar to 56.83% in Locusta migratoria. However, the great size of repetitive sequences could not be annotated to specific repeat element families. For the repetitive elements that were annotated, Class I-LINE retrotransposon elements were the most common families and more abundant than satellite and Class I-LTR. These results based on the newly developed genome survey could be used in the taxonomic study and whole genome sequencing to improve the understanding of the biology of G. orientalis.

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Zhou, Peng, Jiao Li, Jing Huang, Fei Li, Qiang Zhang, and Min Zhang. "Genome Survey Sequencing and Genetic Background Characterization of Ilex chinensis Sims (Aquifoliaceae) Based on Next-Generation Sequencing." Plants 11, no. 23 (December 1, 2022): 3322. http://dx.doi.org/10.3390/plants11233322.

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Ilex chinensis Sims. is an evergreen arbor species with high ornamental and medicinal value that is widely distributed in China. However, there is a lack of molecular and genomic data for this plant, which severely restricts the development of its relevant research. To obtain the whole reference genome, we first conducted a genome survey of I. chinensis by next-generation sequencing (NGS) to perform de novo whole-genome sequencing. As a result, our estimates using k-mer and flow cytometric analysis suggested the genome size of I. chinensis to be around 618–655 Mb, with the GC content, heterozygous rate, and repeat sequence rate of 37.52%, 1.1%, and 38%, respectively. A total of 334,649 microsatellite motifs were detected from the I. chinensis genome data, which will provide basic molecular markers for germplasm characterization, genetic diversity, and QTL mapping studies for I. chinensis. In summary, the I. chinensis genome is complex with high heterozygosity and few repeated sequences. Overall, this is the first report on the genome features of I. chinensis, and the information may lay a strong groundwork for future whole-genome sequencing and molecular breeding studies of this species.

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Jia, Chenghao, Tianyan Yang, Takashi Yanagimoto, and Tianxiang Gao. "Comprehensive Draft Genome Analyses of Three Rockfishes (Scorpaeniformes, Sebastiscus) via Genome Survey Sequencing." Current Issues in Molecular Biology 43, no. 3 (November 18, 2021): 2048–58. http://dx.doi.org/10.3390/cimb43030141.

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Sebastiscus species, marine rockfishes, are of essential economic value. However, the genomic data of this genus is lacking and incomplete. Here, whole genome sequencing of all species of Sebastiscus was conducted to provide fundamental genomic information. The genome sizes were estimated to be 802.49 Mb (S. albofasciatus), 786.79 Mb (S. tertius), and 776.00 Mb (S. marmoratus) by using k-mer analyses. The draft genome sequences were initially assembled, and genome-wide microsatellite motifs were identified. The heterozygosity, repeat ratios, and numbers of microsatellite motifs all suggested possibly that S. tertius is more closely related to S. albofasciatus than S. marmoratus at the genetic level. Moreover, the complete mitochondrial genome sequences were assembled from the whole genome data and the phylogenetic analyses genetically supported the validation of Sebastiscus species. This study provides an important genome resource for further studies of Sebastiscus species.

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Bai, Yu, Lin Ye, Kang Yang, and Hui Wang. "Genome Survey and SSR Analysis of Camellia nitidissima Chi (Theaceae)." Genetics Research 2022 (November 2, 2022): 1–8. http://dx.doi.org/10.1155/2022/5417970.

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Camellia nitidissima Chi (CNC), a species of golden Camellia, is well known as “the queen of camellias.” It is an ornamental, medicinal, and edible plant grown in China. In this study, we conducted a genome survey sequencing analysis and simple sequence repeat (SSR) identification of CNC using the Illumina sequencing platform. The 21-mer analysis predicted its genome size to be 2,778.82 Mb, with heterozygosity and repetition rates of 1.42% and 65.27%, respectively. The CNC genome sequences were assembled into 9,399,197 scaffolds, covering ∼2,910 Mb and an N50 of 869 base pair. Its genomic characteristics were found to be similar to those of Camellia oleifera. In addition, 1,940,616 SSRs were identified from the genome data, including mono-(61.85%), di-(28.71%), tri-(6.51%), tetra-(1.85%), penta-(0.57%), and hexanucleotide motifs (0.51%). We believe these data will provide a useful foundation for the development of novel molecular markers for CNC as well as for further whole-genome sequencing of CNC.

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Sakurai, Aki, An Q. Dinh, Blake Hanson, William C. Shropshire, Truc T. Tran, Audrey Wanger, Cesar A. Arias, and William R. Miller. "481. Evolution of Carbapenem-Resistant Pseudomonas aeruginosa (CR-PA) Genetic Lineages and Acquisition of β-Lactamase Enzymes." Open Forum Infectious Diseases 6, Supplement_2 (October 2019): S235—S236. http://dx.doi.org/10.1093/ofid/ofz360.554.

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Abstract Background Nosocomial infections due to CR-PA are associated with significant morbidity and mortality, and knowledge of epidemiology and underlying mechanisms of antimicrobial resistance is critical to addressing this threat. Recently, we identified a CR-PA of sequence type (ST) 309 resistant to all available β-lactams due to acquired β-lactamases as a potential emerging clone. To assess the evolving landscape of resistance in CR-PA we performed a cross-sectional survey of historical and contemporary isolates utilizing phenotypic testing and whole-genome sequencing (WGS). Methods Historical CR-PA isolates (n = 61, collected from 1999 to 2015) and contemporary isolates (n = 110, collected from 2017 to 2018) from a large urban hospital network in Houston, TX were tested for susceptibility to meropenem, aztreonam (ATM), ceftolozane/tazobactam (C/T), and ceftazidime/avibactam (CZA) using E-test on Mueller–Hinton (MH) agar. WGS for all isolates was performed on a MiSeq platform (Illumina). Data analysis was performed using a custom analysis pipeline, including Tseemann MLST tool, Resfinder, and Abricate using the CARD database. Results The prevalence of resistance across all β-lactams tested increased in contemporary strains as compared with that of historical strains (Figure 1). Among important contemporary antipseudomonal antibiotics C/T, ATM, and CZA, resistance increased from 0%, 22%, and 5% to 15%, 44%, and 16%, respectively (Figure 1). WGS revealed that ST235 was the most common sequence type, followed by ST111 in the historical collection (Figure 2). In contrast, a larger degree of genetic diversity was found in contemporary isolates, with the emergence of multidrug-resistant clones such as ST308 (2%) and ST309 (3%). Resistance to C/T was associated with acquired β-lactamases in 88% (14/16) of isolates, including VIM-2, GES-19/GES-26, VEB-1, NMD-1, and OXA enzymes. Conclusion Resistance to newer agents C/T and CZA markedly increased in contemporary CR-PA strains. While the epidemic clones ST235 and ST111 were the most frequent STs, ST308 and 309 have emerged among contemporary MDR isolates. Most concerning was the association of C/T resistance and the acquisition of β-lactamases, due to the potential for further dissemination. Disclosures All authors: No reported disclosures.

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Hong, Yongfeng, Xia Huang, Chunmei Li, Xiaoxian Ruan, Zhen Wang, Yingjuan Su, and Ting Wang. "Genome Survey Sequencing of In Vivo Mother Plant and In Vitro Plantlets of Mikania cordata." Plants 9, no. 12 (November 27, 2020): 1665. http://dx.doi.org/10.3390/plants9121665.

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Mikania cordata, the only native congener of the invasive weed Mikania micrantha in China, is an ideal species for comparative study to reveal the invasion mechanism. However, its genome resources are lagging far behind its congener, which limits the comparative genomic analysis. Our goal is to characterize the genome of M. cordata by next-generation sequencing and propose a scheme for long-read genome sequencing. Previous studies have shown that the genomic resources of the host plant would be affected by the endophytic microbial DNA. An aseptic sample of M. cordata will ensure the proper genome in downstream analysis. Because endophytes are ubiquitous in the greenhouse-grown M. cordata, the in vitro culture with cefotaxime or timentin treatment was undertaken to obtain the aseptic plantlets. The in vivo mother plant and in vitro plantlets were used to survey the genome. The microbial contamination in M. cordata was recognized by blast search and eliminated from the raw reads. The decontaminated sequencing reads were used to predict the genome size, heterozygosity, and repetitive rate. The in vivo plant was so contaminated that microbes occupied substantial sequencing resources and misled the scaffold assembly. Compared with cefotaxime, treatment with timentin performed better in cultivating robust in vitro plantlets. The survey result from the in vitro plantlets was more accurate due to low levels of contamination. The genome size was estimated to be 1.80 Gb with 0.50% heterozygosity and 78.35% repetitive rate. Additionally, 289,831 SSRs were identified in the genome. The genome is heavily contaminated and repetitive; therefore, the in vitro culture technique and long-read sequencing technology are recommended to generate a high-quality and highly contiguous genome.

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Etchegary, Holly, Brenda Wilson, Proton Rahman, Charlene Simmonds, and Daryl Pullman. "Public interest in whole genome sequencing and information needs: an online survey study." Personalized Medicine 17, no. 4 (July 1, 2020): 283–93. http://dx.doi.org/10.2217/pme-2019-0136.

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Aim: To survey the general public about whole genome sequencing interest, including pharmacogenomic testing, and to identify information important for sequencing decisions. Patients & methods: An online survey of 901 members of the general public in an eastern Canadian province. Results: Interest in whole genome sequencing, including pharmacogenomic testing, was high with few differences among demographic variables. Issues identified as very important to sequencing decisions included familial implications of testing, whether treatment was available for conditions tested and knowing who could access genomic information. Most respondents would value support when interpreting sequencing results. Conclusion: Findings reveal the kind of information and support users of sequencing services would value and could inform the implementation of sequencing into care in ways that accord with public preferences and needs.

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Sperling, Linda, Philippe Dessen, Marek Zagulski, Ron E. Pearlman, Andrzey Migdalski, Robert Gromadka, Marine Froissard, Anne-Marie Keller, and Jean Cohen. "Random Sequencing of Paramecium Somatic DNA." Eukaryotic Cell 1, no. 3 (June 2002): 341–52. http://dx.doi.org/10.1128/ec.1.3.341-352.2002.

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ABSTRACT We report a random survey of 1 to 2% of the somatic genome of the free-living ciliate Paramecium tetraurelia by single-run sequencing of the ends of plasmid inserts. As in all ciliates, the germ line genome of Paramecium (100 to 200 Mb) is reproducibly rearranged at each sexual cycle to produce a somatic genome of expressed or potentially expressed genes, stripped of repeated sequences, transposons, and AT-rich unique sequence elements limited to the germ line. We found the somatic genome to be compact (>68% coding, estimated from the sequence of several complete library inserts) and to feature uniformly small introns (18 to 35 nucleotides). This facilitated gene discovery: 722 open reading frames (ORFs) were identified by similarity with known proteins, and 119 novel ORFs were tentatively identified by internal comparison of the data set. We determined the phylogenetic position of Paramecium with respect to eukaryotes whose genomes have been sequenced by the distance matrix neighbor-joining method by using random combined protein data from the project. The unrooted tree obtained is very robust and in excellent agreement with accepted topology, providing strong support for the quality and consistency of the data set. Our study demonstrates that a random survey of the somatic genome of Paramecium is a good strategy for gene discovery in this organism.

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Bhatia, Vandanajay, Mala Sinha, Bruce Luxon, and Nisha Garg. "Utility of the Trypanosoma cruzi Sequence Database for Identification of Potential Vaccine Candidates by In Silico and In Vitro Screening." Infection and Immunity 72, no. 11 (November 2004): 6245–54. http://dx.doi.org/10.1128/iai.72.11.6245-6254.2004.

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ABSTRACT Glycosylphosphatidylinositol (GPI)-anchored proteins are abundantly expressed in the infective and intracellular stages of Trypanosoma cruzi and are recognized as antigenic targets by both the humoral and cellular arms of the immune system. Previously, we demonstrated the efficacy of genes encoding GPI-anchored proteins in eliciting partially protective immunity to T. cruzi infection and disease, suggesting their utility as vaccine candidates. For the identification of additional vaccine targets, in this study we screened the T. cruzi expressed sequence tag (EST) and genomic sequence survey (GSS) databases. By applying a variety of web-based genome-mining tools to the analysis of ∼2,500 sequences, we identified 348 (37.6%) EST and 260 (17.4%) GSS sequences encoding novel parasite-specific proteins. Of these, 19 sequences exhibited the characteristics of secreted and/or membrane-associated GPI proteins. Eight of the selected sequences were amplified to obtain genes TcG1, TcG2, TcG3, TcG4, TcG5, TcG6, TcG7, and TcG8 (TcG1-TcG8) which are expressed in different developmental stages of the parasite and conserved in the genome of a variety of T. cruzi strains. Flow cytometry confirmed the expression of the antigens encoded by the cloned genes as surface proteins in trypomastigote and/or amastigote stages of T. cruzi. When delivered as a DNA vaccine, genes TcG1-TcG6 elicited a parasite-specific antibody response in mice. Except for TcG5, antisera to genes TcG1-TcG6 exhibited trypanolytic activity against the trypomastigote forms of T. cruzi, a property known to correlate with the immune control of T. cruzi. Taken together, our results validate the applicability of bioinformatics in genome mining, resulting in the identification of T. cruzi membrane-associated proteins that are potential vaccine candidates.

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Bi, Quanxin, Yang Zhao, Yifan Cui, and Libing Wang. "Genome survey sequencing and genetic background characterization of yellow horn based on next-generation sequencing." Molecular Biology Reports 46, no. 4 (May 21, 2019): 4303–12. http://dx.doi.org/10.1007/s11033-019-04884-7.

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Berent, Linda M., and Joanne B. Messick. "Physical Map and Genome Sequencing Survey of Mycoplasma haemofelis (Haemobartonella felis)." Infection and Immunity 71, no. 6 (June 2003): 3657–62. http://dx.doi.org/10.1128/iai.71.6.3657-3662.2003.

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ABSTRACT Mycoplasma haemofelis is an uncultivable red-cell pathogen of cats. Isolated M. haemofelis DNA was used to create a bacterial artificial chromosome library and physical map. Random sequencing of this material revealed 75 genes that had not been previously reported for M. haemofelis or any other hemotrophic mycoplasma.

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Woolfit, Megan, Elżbieta Rozpędowska, Jure Piškur, and Kenneth H. Wolfe. "Genome Survey Sequencing of the Wine Spoilage Yeast Dekkera (Brettanomyces) bruxellensis." Eukaryotic Cell 6, no. 4 (February 2, 2007): 721–33. http://dx.doi.org/10.1128/ec.00338-06.

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ABSTRACT The hemiascomycete yeast Dekkera bruxellensis, also known as Brettanomyces bruxellensis, is a major cause of wine spoilage worldwide. Wines infected with D. bruxellensis develop distinctive, unpleasant aromas due to volatile phenols produced by this species, which is highly ethanol tolerant and facultatively anaerobic. Despite its importance, however, D. bruxellensis has been poorly genetically characterized until now. We performed genome survey sequencing of a wine strain of D. bruxellensis to obtain 0.4× coverage of the genome. We identified approximately 3,000 genes, whose products averaged 49% amino acid identity to their Saccharomyces cerevisiae orthologs, with similar intron contents. Maximum likelihood phylogenetic analyses suggest that the relationship between D. bruxellensis, S. cerevisiae, and Candida albicans is close to a trichotomy. The estimated rate of chromosomal rearrangement in D. bruxellensis is slower than that calculated for C. albicans, while its rate of amino acid evolution is somewhat higher. The proteome of D. bruxellensis is enriched for transporters and genes involved in nitrogen and lipid metabolism, among other functions, which may reflect adaptations to its low-nutrient, high-ethanol niche. We also identified an adenyl deaminase gene that has high similarity to a gene in bacteria of the Burkholderia cepacia species complex and appears to be the result of horizontal gene transfer. These data provide a resource for further analyses of the population genetics and evolution of D. bruxellensis and of the genetic bases of its physiological capabilities.

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Hitte, Christophe, Jennifer Madeoy, Ewen F. Kirkness, Catherine Priat, Travis D. Lorentzen, Fabrice Senger, Dan Thomas, et al. "Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping." Nature Reviews Genetics 6, no. 8 (July 12, 2005): 643–48. http://dx.doi.org/10.1038/nrg1658.

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Peterson, S. N., P. C. Hu, K. F. Bott, and C. A. Hutchison. "A survey of the Mycoplasma genitalium genome by using random sequencing." Journal of Bacteriology 175, no. 24 (1993): 7918–30. http://dx.doi.org/10.1128/jb.175.24.7918-7930.1993.

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Liu, Chang, Vladimir Vigdorovich, Vivek Kapur, and Mitchell S. Abrahamsen. "A Random Survey of the Cryptosporidium parvum Genome." Infection and Immunity 67, no. 8 (August 1, 1999): 3960–69. http://dx.doi.org/10.1128/iai.67.8.3960-3969.1999.

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ABSTRACT Cryptosporidium parvum is an obligate intracellular pathogen responsible for widespread infections in humans and animals. The inability to obtain purified samples of this organism’s various developmental stages has limited the understanding of the biochemical mechanisms important for C. parvum development or host-parasite interaction. To identify C. parvum genes independent of their developmental expression, a random sequence analysis of the 10.4-megabase genome of C. parvum was undertaken. Total genomic DNA was sheared by nebulization, and fragments between 800 and 1,500 bp were gel purified and cloned into a plasmid vector. A total of 442 clones were randomly selected and subjected to automated sequencing by using one or two primers flanking the cloning site. In this way, 654 genomic survey sequences (GSSs) were generated, corresponding to >320 kb of genomic sequence. These sequences were assembled into 408 contigs containing >250 kb of unique sequence, representing ∼2.5% of the C. parvum genome. Comparison of the GSSs with sequences in the public DNA and protein databases revealed that 107 contigs (26%) displayed similarity to previously identified proteins and rRNA and tRNA genes. These included putative genes involved in the glycolytic pathway, DNA, RNA, and protein metabolism, and signal transduction pathways. The repetitive sequence elements identified included a telomere-like sequence containing hexamer repeats, 57 microsatellite-like elements composed of dinucleotide or trinucleotide repeats, and a direct repeat sequence. This study demonstrates that large-scale genomic sequencing is an efficient approach to analyze the organizational characteristics and information content of the C. parvum genome.

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Ma, Xinyuan, Paula Agudelo, Vincent P. Richards, and J. Antonio Baeza. "Genome survey sequencing of the phyto-parasitic nematode Hoplolaimus galeatus." PeerJ 10 (January 18, 2022): e12749. http://dx.doi.org/10.7717/peerj.12749.

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Background Hoplolaimus galeatus is a plant-parasite nematode with a broad range of hosts. This nematode is known to damage cotton, corn, and soybean crops. Hoplolaimus galeatus is also an economically important pest of turfgrasses. Despite its economical importance, no genomic resources exist for this parasite. Methods Using 300 bp paired-end short read sequencing, this study estimated genome size, analyzed a nearly complete mitochondrial chromosome, and explored nuclear repetitive elements, including microsatellites, in H. galeatus for the first time. The phylogenetic placement of H. galeatus in the superfamily Tylenchoidea was also examined. Results The average haploid genome size estimated using a k-mer approach was 517.69 Mbp. The partially assembled mitochondrial genome of H. galeatus is 16,578 bp in length and comprised of 11 protein-coding genes, two ribosomal RNA genes, and 16 transfer RNA genes. A maximum likelihood phylogenetic analysis confirmed the monophyly of the genus Hoplolaimus and the superfamily Tylenchoidea. Repetitive elements constituted 50% of the nuclear genome while half of the genome represented single- or low-copy sequences. A large portion of repetitive sequences could not be assigned to known repeat element families. Considering only annotated repetitive elements, the most ubiquitous belonged to Class II- Subclass 2-Maverick elements, Class I-LTR-Ty-3/Bel-Pao elements, and satellites. 45S ribosomal DNA was also abundant and a total of 36 SSRs were identified.This study developed genomic resources for the plant-parasitic nematode Hoplolaimus galeatus that will contribute to the better understanding of meta-population connectivity and putative genomic mechanisms involved in the exploitation of the broad range of host plants used by H. galeatus.

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Adelyna, M. A. Noor, H. Jung, V. Chand, P. B. Mather, and M. N. Siti Azizah. "A genome survey sequence (GSS) analysis and microsatellite marker development for Indian mackerel, Rastrelliger kanagurta , using Ion Torrent technology." Meta Gene 10 (December 2016): 67–72. http://dx.doi.org/10.1016/j.mgene.2016.10.005.

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Zhou, Wei, Yiyi Hu, Zhenghong Sui, Feng Fu, Jinguo Wang, Lianpeng Chang, Weihua Guo, and Binbin Li. "Genome Survey Sequencing and Genetic Background Characterization of Gracilariopsis lemaneiformis (Rhodophyta) Based on Next-Generation Sequencing." PLoS ONE 8, no. 7 (July 16, 2013): e69909. http://dx.doi.org/10.1371/journal.pone.0069909.

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Yu, Liansheng, Zhigang Qian, Jingping Ge, and Renpeng Du. "Glucansucrase Produced by Lactic Acid Bacteria: Structure, Properties, and Applications." Fermentation 8, no. 11 (November 11, 2022): 629. http://dx.doi.org/10.3390/fermentation8110629.

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Glucansucrase (GS) belongs to the GH70 family, which not only can synthesize exopolysaccharides (EPSs) with different physicochemical properties through glucosyl transglycosylation (by hydrolyzing sucrose) but can also produce oligosaccharides. Different strains produce different GSs, which catalyze the synthesis of EPS with different glycosidic bond structures; these EPSs have different biological functions. As an important enzymatic tool, GS has great potential in health care medicine, biological materials, ecological protection, the food chemical industry, etc. GS is mainly produced by lactic acid bacteria (LAB), including Leuconostoc, Streptococcus, Lactobacillus, and Weissella species. With the elucidation of the crystal structure of GS and the advancement of genome sequencing technology, its synthesis reaction mechanism and specific structural characteristics are gradually becoming clear. This review summarizes the isolation, purification, physical and chemical properties, detection methods, sources, and applications of GS in order to provide a reference for the research and development of GS.

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Li, Tian, Huang, Lin, Wang, Jiang, Zhu, Chen, and Li. "A First Insight into a Draft Genome of Silver Sillago (Sillago sihama) via Genome Survey Sequencing." Animals 9, no. 10 (October 1, 2019): 756. http://dx.doi.org/10.3390/ani9100756.

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Sillago sihama has high economic value and is one of the most attractive aquaculture species in China. Despite its economic importance, studies of its genome have barely been performed. In this study, we conducted a first genomic survey of S. sihama using next-generation sequencing (NGS). In total, 45.063 Gb of high-quality sequence data were obtained. For the 17-mer frequency distribution, the genome size was estimated to be 508.50 Mb. The sequence repeat ratio was calculated to be 21.25%, and the heterozygosity ratio was 0.92%. Reads were assembled into 1,009,363 contigs, with a N50 length of 1362 bp, and then into 814,219 scaffolds, with a N50 length of 2173 bp. The average Guanine and Cytosine (GC) content was 45.04%. Dinucleotide repeats (56.55%) were the dominant form of simple sequence repeats (SSR).

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Lu, Xia, Sheng Luan, Jie Kong, Longyang Hu, Yong Mao, and Shengping Zhong. "Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing." Chinese Journal of Oceanology and Limnology 35, no. 1 (December 28, 2015): 203–14. http://dx.doi.org/10.1007/s00343-016-5250-7.

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Choi, Eunkyung, Sun Hee Kim, Seung Jae Lee, Euna Jo, Jinmu Kim, Jeong-Hoon Kim, Steven J. Parker, Young-Min Chi, and Hyun Park. "A First Genome Survey and Genomic SSR Marker Analysis of Trematomus loennbergii Regan, 1913." Animals 11, no. 11 (November 8, 2021): 3186. http://dx.doi.org/10.3390/ani11113186.

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Trematomus loennbergii Regan, 1913, is an evolutionarily important marine fish species distributed in the Antarctic Ocean. However, its genome has not been studied to date. In the present study, whole genome sequencing was performed using next-generation sequencing (NGS) technology to characterize its genome and develop genomic microsatellite markers. The 25-mer frequency distribution was estimated to be the best, and the genome size was predicted to be 815,042,992 bp. The heterozygosity, average rate of read duplication, and sequencing error rates were 0.536%, 0.724%, and 0.292%, respectively. These data were used to analyze microsatellite markers, and a total of 2,264,647 repeat motifs were identified. The most frequent repeat motif was di-nucleotide with 87.00% frequency, followed by tri-nucleotide (10.45%), tetra-nucleotide (1.94%), penta-nucleotide (0.34%), and hexa-nucleotide (0.27%). The AC repeat motif was the most abundant motif among di-nucleotides and among all repeat motifs. Among microsatellite markers, 181 markers were selected and PCR technology was used to validate several markers. A total of 15 markers produced only one band. In summary, these results provide a good basis for further studies, including evolutionary biology studies and population genetics of Antarctic fish species.

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Choi, Eunkyung, Seung Jae Lee, Euna Jo, Jinmu Kim, Steven J. Parker, Jeong-Hoon Kim, and Hyun Park. "Genomic Survey and Microsatellite Marker Investigation of Patagonian Moray Cod (Muraenolepis orangiensis)." Animals 12, no. 13 (June 22, 2022): 1608. http://dx.doi.org/10.3390/ani12131608.

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The Muraenolepididae family of fishes, known as eel cods, inhabits continental slopes and shelves in the Southern Hemisphere. This family belongs to the Gadiformes order, which constitutes one of the most important commercial fish resources worldwide, but the classification of the fish species in this order is ambiguous because it is only based on the morphological and habitat characteristics of the fishes. Here, the genome of Patagonian moray cod was sequenced using the Illumina HiSeq platform, and screened for microsatellite motifs. The genome was predicted to be 748.97 Mb, with a heterozygosity rate of 0.768%, via K-mer analysis (K = 25). The genome assembly showed that the total size of scaffolds was 711.92 Mb and the N50 scaffold length was 1522 bp. Additionally, 4,447,517 microsatellite motifs were identified from the genome survey assembly, and the most abundant motif type was found to be AC/GT. In summary, these data may facilitate the identification of molecular markers in Patagonian moray cod, which would be a good basis for further whole-genome sequencing with long read sequencing technology and chromosome conformation capture technology, as well as population genetics.

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Hong, Jenny, Annalijn Conklin, Nick Dragojlovic, Alison Elliott, Jan Friedman, and Larry Lynd. "PP48 Caregiver Perceptions And Experiences Of Diagnostic Genome-Wide Sequencing." International Journal of Technology Assessment in Health Care 34, S1 (2018): 84. http://dx.doi.org/10.1017/s0266462318002106.

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Introduction:The objective of this qualitative analysis was to explore caregiver perceptions and experiences of receiving or not receiving a genetic diagnosis following genome-wide sequencing (GWS) in children with suspected genetic disorders.Methods:One caregiver for each child completed an online survey two weeks after enrolling in the Clinical Assessment of the Utility of Sequencing and Evaluation as a Service (CAUSES) study, beginning in January 2016, and again about six months after receiving the GWS results. The survey covered the caregivers' experiences and quality of life and children's healthcare resource utilization, and provided open-ended questions for comments. The follow-up survey was completed by twenty families who had received a diagnosis with their GWS results and by twenty-two families who had not received a diagnosis. A thematic analysis of the free-text comments from both groups was performed using NVivo 11.4.2.Results:Caregivers from both groups expressed similar experiences of negative socioeconomic effects of caregiving, particularly related to employment and time burden. Caregivers who did not receive a diagnosis with the GWS results were generally hopeful of receiving a diagnosis in the future and reported expectations of a positive benefit from receiving a diagnosis, both in terms of access to additional resources and of positive psychological effects. The absence of a diagnosis was a source of anxiety for many caregivers. By contrast, caregivers who had received a diagnosis reported positive, neutral, and negative psychological effects from the knowledge gained; no participants commented on the consequences for access to additional services or other socioeconomic effects.Conclusions:Our findings suggest that caregivers may have high expectations for what a diagnosis can provide to them and their families, which may not be fully met once a diagnosis is obtained. The study underpins the importance of patient-centered communication of genomic testing results so that families can set realistic expectations of what having a diagnosis will achieve.

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Hill, Emily J., Laurie A. Robak, Rami Al-Ouran, Jennifer Deger, Jamie C. Fong, Paul Jerrod Vandeventer, Emily Schulman, et al. "Genome Sequencing in the Parkinson Disease Clinic." Neurology Genetics 8, no. 4 (June 20, 2022): e200002. http://dx.doi.org/10.1212/nxg.0000000000200002.

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Background and ObjectivesGenetic variants affect both Parkinson disease (PD) risk and manifestations. Although genetic information is of potential interest to patients and clinicians, genetic testing is rarely performed during routine PD clinical care. The goal of this study was to examine interest in comprehensive genetic testing among patients with PD and document reactions to possible findings from genome sequencing in 2 academic movement disorder clinics.MethodsIn 203 subjects with PD (age = 63 years, 67% male), genome sequencing was performed and filtered using a custom panel, including 49 genes associated with PD, parkinsonism, or related disorders, as well as a 90-variant PD genetic risk score. Based on the results, 231 patients (age = 67 years, 63% male) were surveyed on interest in genetic testing and responses to vignettes covering (1) familial risk of PD (LRRK2); (2) risk of PD dementia (GBA); (3) PD genetic risk score; and (4) secondary, medically actionable variants (BRCA1).ResultsGenome sequencing revealed a LRRK2 variant in 3% and a GBA risk variant in 10% of our clinical sample. The genetic risk score was normally distributed, identifying 41 subjects with a high risk of PD. Medically actionable findings were discovered in 2 subjects (1%). In our survey, the majority (82%) responded that they would share a LRRK2 variant with relatives. Most registered unchanged or increased interest in testing when confronted with a potential risk for dementia or medically actionable findings, and most (75%) expressed interest in learning their PD genetic risk score.DiscussionOur results highlight broad interest in comprehensive genetic testing among patients with PD and may facilitate integration of genome sequencing in clinical practice.

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Venkatesh, Byrappa, Ewen F. Kirkness, Yong-Hwee Loh, Aaron L. Halpern, Alison P. Lee, Justin Johnson, Nidhi Dandona, et al. "Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome." PLoS Biology 5, no. 4 (April 3, 2007): e101. http://dx.doi.org/10.1371/journal.pbio.0050101.

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Nunberg, Andrew, Joseph A. Bedell, Mohammad A. Budiman, Robert W. Citek, Sandra W. Clifton, Lucinda Fulton, Deana Pape, et al. "Survey sequencing of soybean elucidates the genome structure, composition and identifies novel repeats." Functional Plant Biology 33, no. 8 (2006): 765. http://dx.doi.org/10.1071/fp06106.

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In order to expand our knowledge of the soybean genome and to create a useful DNA repeat sequence database, over 24 000 DNA fragments from a soybean [Glycine max (L.) Merr.] cv. Williams 82 genomic shotgun library were sequenced. Additional sequences came from over 29 000 bacterial artificial chromosome (BAC) end sequences derived from a BstI library of the cv. Williams 82 genome. Analysis of these sequences identified 348 different DNA repeats, many of which appear to be novel. To extend the utility of the work, a pilot study was also conducted using methylation filtration to estimate the hypomethylated, soybean gene space. A comparison between 8366 sequences obtained from a filtered library and 23 788 from an unfiltered library indicate a gene-enrichment of ~3.2-fold in the hypomethylated sequences. Given the 1.1-Gb soybean genome, our analysis predicts a ~343-Mb hypomethylated, gene-rich space.

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Mishra, Rukmini. "Analysis of microRNAs and their targets from onion (Allium cepa) using genome survey sequences (GSS) and expressed sequence tags (ESTs)." Bioinformation 15, no. 12 (December 31, 2019): 907–17. http://dx.doi.org/10.6026/97320630015907.

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Baeza, Juan Antonio, Mei Lin Neo, and Danwei Huang. "Genomic Survey and Resources for the Boring Giant Clam Tridacna crocea." Genes 13, no. 5 (May 18, 2022): 903. http://dx.doi.org/10.3390/genes13050903.

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The boring giant clam Tridacna crocea is an evolutionary, ecologically, economically, and culturally important reef-dwelling bivalve targeted by a profitable ornamental fishery in the Indo-Pacific Ocean. In this study, we developed genomic resources for T. crocea. Using low-pass (=low-coverage, ~6×) short read sequencing, this study, for the first time, estimated the genome size, unique genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon, in T. crocea. Furthermore, we tested if the mitochondrial genome can be assembled from RNA sequencing data. The haploid genome size estimated using a k-mer strategy was 1.31–1.39 Gbp, which is well within the range reported before for other members of the family Cardiidae. Unique genome content estimates using different k-mers indicated that nearly a third and probably at least 50% of the genome of T. crocea was composed of repetitive elements. A large portion of repetitive sequences could not be assigned to known repeat element families. Taking into consideration only annotated repetitive elements, the most common were classified as Satellite DNA which were more common than Class I-LINE and Class I-LTR Ty3-gypsy retrotransposon elements. The nuclear ribosomal operon in T. crocea was partially assembled into two contigs, one encoding the complete ssrDNA and 5.8S rDNA unit and a second comprising a partial lsrDNA. A nearly complete mitochondrial genome (92%) was assembled from RNA-seq. These newly developed genomic resources are highly relevant for improving our understanding of the biology of T. crocea and for the development of conservation plans and the fisheries management of this iconic reef-dwelling invertebrate.

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Wang, Rongkai, Jinshuan Fan, Pan Chang, Ling Zhu, Mengran Zhao, and Lingli Li. "Genome Survey Sequencing of Acer truncatum Bunge to Identify Genomic Information, Simple Sequence Repeat (SSR) Markers and Complete Chloroplast Genome." Forests 10, no. 2 (January 23, 2019): 87. http://dx.doi.org/10.3390/f10020087.

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The Acer truncatum Bunge is a particular forest tree species found in the north of China. Due to the recent discovery that its seeds contain a considerable amount of nervonic acid, this species has received more and more attention. However, there have been no reports of the genome in this species. In this study, we report on the Acer truncatum genome sequence produced by genome survey sequencing. In total, we obtained 61.90 Gbp of high-quality data, representing approximately 116x coverage of the Acer truncatum genome. The genomic characteristics of Acer truncatum include a genome size of 529.88 Mbp, a heterozygosis rate of 1.06% and a repeat rate of 48.8%. A total of 392,961 high-quality genomic SSR markers were developed and a graphical map of the annotated circular chloroplast genome was generated. Thus far, this is the first report of de novo whole genome sequencing and assembly of Acer truncatum. We believe that this genome sequence dataset may provide a new resource for future genomic analysis and molecular breeding studies of Acer truncatum.

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Ma, Yaping, Mura Jyostna Devi, Lihua Song, Handong Gao, and Bing Cao. "Genome survey sequencing of Ailanthus altissima and identification of simple sequence repeat (SSR) markers." Silvae Genetica 71, no. 1 (January 1, 2022): 47–53. http://dx.doi.org/10.2478/sg-2022-0006.

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Abstract Ailanthus altissima is a deciduous tree native to China and introduced to other parts of the world as an ornamental plant. It exhibits resistance to both abiotic and biotic stress factors and has various pharmacological effects and strong allelopathy, generating significant research interests. However, the genome sequence of this species has not been reported, limiting its research development. The purpose of the study was to determine the genome size and characteristics of A. altissima to conduct its genomic survey. Next-generation sequencing and K-mer analysis were employed to measure the genome size of A. altissima. Overall, a total of 61.93 Gb high-quality clean data were acquired, representing approximately 64.09× coverage of the A. altissima genome. The genomic characteristics of A. altissima include a genome size of 966.38 Mbp, a heterozygosis rate of 0.78 %, and a repeat rate of 41.22 %. A total of 735,179 genomic SSRs markers were identified based on genome survey sequences. Alignment analysis showed that A. altissima was closely related to Citrus sinensis and Leitneria florida-na. This study provides basic information for future whole-genomic sequencing of A. altissima. This will facilitate a knowledge of the population structure, genetic diversity, long distance-gene transfer, and pollen-based gene flow analyses of A. altissima populations from its known distribution ranges in China, focusing on planted and natural forest stands.

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Yang, Tianyan, Xinxin Huang, Zijun Ning, and Tianxiang Gao. "Genome-Wide Survey Reveals the Microsatellite Characteristics and Phylogenetic Relationships of Harpadon nehereus." Current Issues in Molecular Biology 43, no. 3 (September 25, 2021): 1282–92. http://dx.doi.org/10.3390/cimb43030091.

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Harpadon nehereus forms one of the most important commercial fisheries along the Bay of Bengal and the southeast coast of China. In this study, the genome-wide survey dataset first produced using next-generation sequencing (NGS) was used to provide general information on the genome size, heterozygosity and repeat sequence ratio of H. nehereus. About 68.74 GB of high-quality sequence data were obtained in total and the genome size was estimated to be 1315 Mb with the 17-mer frequency distribution. The sequence repeat ratio and heterozygosity were calculated to be 52.49% and 0.67%, respectively. A total of 1,027,651 microsatellite motifs were identified and dinucleotide repeat was the most dominant simple sequence repeat (SSR) motif with a frequency of 54.35%. As a by-product of whole genome sequencing, the mitochondrial genome is a powerful tool to investigate the evolutionary relationships between H. nehereus and its relatives. The maximum likelihood (ML) phylogenetic tree was constructed according to the concatenated matrix of amino acids translated from the 13 protein-coding genes (PCGs). Monophyly of two species of the genus Harpadon was revealed in the present study and they formed a monophyletic clade with Saurida with a high bootstrap value of 100%. The results would help to push back the frontiers of genomics and open the doors of molecular diversity as well as conservation genetics studies on this species.

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Scally, Aylwyn, Bryndis Yngvadottir, Yali Xue, Qasim Ayub, Richard Durbin, and Chris Tyler-Smith. "A Genome-Wide Survey of Genetic Variation in Gorillas Using Reduced Representation Sequencing." PLoS ONE 8, no. 6 (June 4, 2013): e65066. http://dx.doi.org/10.1371/journal.pone.0065066.

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Lim, Jong-Sung, Beom-Soon Choi, Jeong-Soo Lee, Chanseok Shin, Tae-Jin Yang, Jae-Sung Rhee, Jae-Seong Lee, and Ik-Young Choi. "Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling." Genomics & Informatics 10, no. 1 (2012): 1. http://dx.doi.org/10.5808/gi.2012.10.1.1.

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Akpinar, Bala Ani, Sezgi Biyiklioglu, Burcu Alptekin, Miroslava Havránková, Jan Vrána, Jaroslav Doležel, Assaf Distelfeld, Pilar Hernandez, and Hikmet Budak. "Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitorTriticum dicoccoides." Plant Biotechnology Journal 16, no. 12 (June 13, 2018): 2077–87. http://dx.doi.org/10.1111/pbi.12940.

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Pabinger, S., A. Dander, M. Fischer, R. Snajder, M. Sperk, M. Efremova, B. Krabichler, M. R. Speicher, J. Zschocke, and Z. Trajanoski. "A survey of tools for variant analysis of next-generation genome sequencing data." Briefings in Bioinformatics 15, no. 2 (January 21, 2013): 256–78. http://dx.doi.org/10.1093/bib/bbs086.

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Serre, David, Byron H. Lee, and Angela H. Ting. "MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome." Nucleic Acids Research 38, no. 2 (November 11, 2009): 391–99. http://dx.doi.org/10.1093/nar/gkp992.

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Keel, B. N., D. J. Nonneman, and G. A. Rohrer. "A survey of single nucleotide polymorphisms identified from whole-genome sequencing and their functional effect in the porcine genome,." Animal Genetics 48, no. 4 (May 8, 2017): 404–11. http://dx.doi.org/10.1111/age.12557.

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Sahin-Tóth, Judit, Eszter Kovács, Adrienn Tóthpál, János Juhász, Barbara Forró, Krisztián Bányai, Kata Havril, Andrea Horváth, Ágoston Ghidán, and Orsolya Dobay. "Whole genome sequencing of coagulase positive staphylococci from a dog-and-owner screening survey." PLOS ONE 16, no. 1 (January 11, 2021): e0245351. http://dx.doi.org/10.1371/journal.pone.0245351.

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Background Staphylococcus aureus and S. pseudintermedius are the two most common coagulase positive staphylococci (CPS). S. aureus is more prevalent among humans, whereas S. pseudintermedius is more commonly isolated from dogs, however, both can cause various community and hospital acquired diseases in humans. Methods In the current study we screened 102 dogs and 84 owners in Hungary. We tested the antibiotic susceptibility of the strains and in order to get a better picture of the clonal relationship of the strains, we used pulsed-field gel electrophoresis. In addition, three pairs of isolates with identical PFGE patterns were whole genome sequenced, MLST and spa types were established. Results Carriage rate of S. aureus was 23.8% in humans and 4.9% in dogs and two cases of co-carriage were found among dogs and owners. S. pseudintermedius carriage rate was 2.4% and 34.3%, respectively, with only one co-carriage. The isolates were generally rather susceptible to the tested antibiotics, but high tetracycline resistance of S. pseudintermedius strains was noted. The co-carried isolates shared almost the same resistance genes (including tet(K), bla(Z), norA, mepR, lmrS, fosB) and virulence gene pattern. Apart from the common staphylococcal enzymes and cytotoxins, we found enterotoxins and exfoliative toxins as well. The two S. aureus pairs belonged to ST45-t630, ST45-t671 and ST15-t084, ST15-t084, respectively. The co-carried S. pseudintermedius isolates shared the same housekeeping gene alleles determining a novel sequence type ST1685. Conclusions Based on the genomic data, dog-owner co-carried strains displayed only insignificant differences therefore provided evidence for potential human-to-dog and dog-to-human transmission.

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Yang, Shuqiong, Jibao Chen, Jun Zhang, Jiafei Liu, Jingjing Yu, Debao Cai, Lunguang Yao, and Pengfei Duan. "First genome survey and repeatome analysis of Chrysopogon zizanioides based on next-generation sequencing." Biologia 75, no. 9 (August 4, 2020): 1273–82. http://dx.doi.org/10.2478/s11756-020-00517-8.

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Lemke, AA, D. Bick, D. Dimmock, P. Simpson, and R. Veith. "Perspectives of clinical genetics professionals toward genome sequencing and incidental findings: a survey study." Clinical Genetics 84, no. 3 (December 7, 2012): 230–36. http://dx.doi.org/10.1111/cge.12060.

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Journal articles on the topic 'Genome survey sequencing (GSS)'

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