Publikácie

@article{Strieskova20198,

title = {Ultracentrifugation enrichment protocol followed by total RNA sequencing allows assembly of the complete mitochondrial genome},

author = {L Strieskova and I Gazdaricova and M Kajsik and K Soltys and J Budis and O Pos and M Lickova and B Klempa and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064954323&doi=10.1016%2fj.jbiotec.2019.04.019&partnerID=40&md5=90856f6a0fd40fd7eeaf877edfdbdeb3},

doi = {10.1016/j.jbiotec.2019.04.019},

issn = {01681656},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Biotechnology},

volume = {299},

pages = {8-12},

publisher = {Elsevier B.V.},

abstract = {The mitochondrial genome is an independent genetic system in each eukaryotic cell outside the nuclear genome. Mitochondrial DNA (mtDNA) appears in high copy number within one cell, unlike nuclear DNA, which exists in two copies. But nevertheless, mtDNA represent only small part of total cellular DNA what causes problematic analysis and identification of relevant mutations. While most researchers tend to overlook it because of its small size, the mitochondrial genome contains genes that are essential for cellular energetics and survival. Because of the increased awareness on the importance of metabolism and bioenergetics in a wide variety of human diseases, more and more mtDNA studies were performed. Mitochondrial genome research has established the connection between mtDNA and a wide variety of diseases such as cancer or neurodegenerative disorders. At the present time, several methods are known, that allow sequencing of mtDNA. However, genomic analysis is often complicated due to the low content of mtDNA compared to nuclear DNA. For this reason, we have designed a new approach to obtaining the genomic mitochondrial sequence. We chose RNA based sequencing. Since human mtDNA does not contain introns, the reconstruction of whole mitochondrial genome through RNA sequencing seems to be effective. Our method is based on total RNA sequencing coupled with simple ultracentrifugation protocol and de novo assembly. Following our protocol, we were able to assemble a complete mammalian mitochondrial genome with a length of 16,505 bp and an average coverage of 156. The method is a relatively simple and inexpensive which could help in the further research or diagnostics of mtDNA-based diseases. © 2019 Elsevier B.V.},

keywords = {Assembly, Mitochondria, Single nucleotide variants, Transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{Soltys2018,

title = {Draft genome sequence of Escherichia coli KL53},

author = {K Soltys and S Vavrova and J Budis and L Palkova and G Minarik and J Grones},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85044840002&doi=10.1128%2fgenomeA.00220-18&partnerID=40&md5=b7145569beb42e97a74d2c434287004d},

doi = {10.1128/genomeA.00220-18},

issn = {21698287},

year  = {2018},

date = {2018-01-01},

journal = {Genome Announcements},

volume = {6},

number = {13},

publisher = {American Society for Microbiology},

abstract = {Here, we report the draft genome sequence of a clinical isolate of the uropathogenic strain Escherichia coli KL53. A total of 5,083,632 bp was de novo assembled into 170 contigs containing 89 RNAs and 5,034 protein-coding genes. Remarkable is the presence of the tellurite resistance (ter) operon on a plasmid. © 2018 Soltys et al.},

keywords = {Assembly, Bacteria},

pubstate = {published},

tppubtype = {article}

}

@article{Sulo2017571,

title = {The evolutionary history of Saccharomyces species inferred fromcompleted mitochondrial genomes and revision in the 'yeast mitochondrial genetic code'},

author = {P Sulo and D Szabóová and P Bielik and S Poláková and K Soltys and K Jatzová and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85043997344&doi=10.1093%2fdnares%2fdsx026&partnerID=40&md5=06765f8bce0a85c0d5b881f73efb11f8},

doi = {10.1093/dnares/dsx026},

issn = {13402838},

year  = {2017},

date = {2017-01-01},

journal = {DNA Research},

volume = {24},

number = {6},

pages = {571-583},

publisher = {Oxford University Press},

abstract = {The yeast Saccharomyces are widely used to test ecological and evolutionary hypotheses. A large number of nuclear genomic DNA sequences are available, but mitochondrial genomic data are insufficient. We completed mitochondrial DNA (mtDNA) sequencing from Illumina MiSeq reads for all Saccharomyces species. All are circularly mapped molecules decreasing in size with phylogenetic distance from Saccharomyces cerevisiae but with similar gene content including regulatory and selfish elements like origins of replication, introns, free-standing open reading frames or GC clusters. Their most profound feature is species-specific alteration in gene order. The genetic code slightly differs from well-established yeast mitochondrial code as GUG is used rarely as the translation start and CGA and CGC code for arginine. The multilocus phylogeny, inferred from mtDNA, does not correlate with the trees derived from nuclear genes. mtDNA data demonstrate that Saccharomyces cariocanus should be assigned as a separate species and Saccharomyces bayanus CBS 380T should not be considered as a distinct species due to mtDNA nearly identical to Saccharomyces uvarum mtDNA. Apparently, comparison of mtDNAs should not be neglected in genomic studies as it is an important tool to understand the origin and evolutionary history of some yeast species. © The Author 2017.},

keywords = {Assembly, Fungi, Mitochondria, Phylogeny},

pubstate = {published},

tppubtype = {article}

}