2019
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Grond, Joost; Płecha, Magdalena; Hahn, Christoph; Wiig, Øystein; Bachmann, Lutz Mitochondrial genomes of ancient bowhead whales (Balaena mysticetus) from Svalbard Journal Article Mitochondrial DNA Part B, 4 (2), pp. 4152–4154, 2019, ISSN: 2380-2359. Abstract | Links | BibTeX @article{Grond2019,
title = {Mitochondrial genomes of ancient bowhead whales (Balaena mysticetus) from Svalbard},
author = {Joost Grond and Magdalena Płecha and Christoph Hahn and Øystein Wiig and Lutz Bachmann},
url = {https://www.tandfonline.com/doi/full/10.1080/23802359.2019.1693284},
doi = {10.1080/23802359.2019.1693284},
issn = {2380-2359},
year = {2019},
date = {2019-07-01},
journal = {Mitochondrial DNA Part B},
volume = {4},
number = {2},
pages = {4152--4154},
abstract = {The endangered Spitsbergen stock of bowhead whales (Balaena mysticetus) has once been large with up to estimated 100,000 individuals. Genetic diversity of the extant Spitsbergen stock is unknown. We present 10 complete mitochondrial genomes of heterochronous ancient bowhead whale samples from Svalbard (14C age estimate range: 215–8885 years) obtained via NGS of total genomic DNA extracts. The ten mitogenomes differed by nucleotide substitutions and/or indels, and there was a total of 160 variable positions. The average nucleotide diversity was π = 0.0029. There was no statistically significant correlation between genetic divergence and time.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The endangered Spitsbergen stock of bowhead whales (Balaena mysticetus) has once been large with up to estimated 100,000 individuals. Genetic diversity of the extant Spitsbergen stock is unknown. We present 10 complete mitochondrial genomes of heterochronous ancient bowhead whale samples from Svalbard (14C age estimate range: 215–8885 years) obtained via NGS of total genomic DNA extracts. The ten mitogenomes differed by nucleotide substitutions and/or indels, and there was a total of 160 variable positions. The average nucleotide diversity was π = 0.0029. There was no statistically significant correlation between genetic divergence and time. |
Płecha, Magdalena; Panagiotopoulou, Hanna; Popović, Danijela; Michalska-Parda, Aleksandra; Gromadka, Robert; Węgleński, Piotr; Stanković, Anna Microsatellite multiplexes for the genetic analyses of northern pike (Esox lucius) populations Journal Article Fisheries & Aquatic Life, 27 (1), pp. 33–40, 2019, ISSN: 2545-059X. Abstract | Links | BibTeX @article{Pecha2019,
title = {Microsatellite multiplexes for the genetic analyses of northern pike (Esox lucius) populations},
author = {Magdalena Płecha and Hanna Panagiotopoulou and Danijela Popović and Aleksandra Michalska-Parda and Robert Gromadka and Piotr Węgleński and Anna Stanković},
url = {https://content.sciendo.com/doi/10.2478/aopf-2019-0004},
doi = {10.2478/aopf-2019-0004},
issn = {2545-059X},
year = {2019},
date = {2019-03-01},
journal = {Fisheries & Aquatic Life},
volume = {27},
number = {1},
pages = {33--40},
abstract = {The northern pike (Esox lucius L.) is a commercially important fish that forms freshwater and brackish populations. While the first ecotype is still quite abundant, the second has suffered rapid declines in recent years. Populations inhabiting the Baltic coastal waters of Poland have been supported by stocking programs since the late 1990s. This study describes a multiplex microsatellite (msDNA) assay consisting of 12 loci divided conveniently into two amplification sets (Elu78, Elu87, B451, Elu37, B457, B16, B25, and Elu19, Elu76, B422, Elu2, Elu7). The assay was optimized for genetic analyses of freshwater and brackish populations. These multiplexes were successfully executed to obtain the genetic profiles of 668 individuals from 16 populations (Poland and Germany). The average number of alleles was equal to 10.4, whereas the observed heterozygosity per locus ranged from 0.18 to 0.89, with the average value of 0.64. The probability of the identity of the marker sets indicated the high power of identification of unique genotypes. Therefore, this molecular tool can be used to describe the genetic variability of populations, select the proper source of breeding material, and monitor the progress of stocking efforts in genetic conservation projects of this species.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The northern pike (Esox lucius L.) is a commercially important fish that forms freshwater and brackish populations. While the first ecotype is still quite abundant, the second has suffered rapid declines in recent years. Populations inhabiting the Baltic coastal waters of Poland have been supported by stocking programs since the late 1990s. This study describes a multiplex microsatellite (msDNA) assay consisting of 12 loci divided conveniently into two amplification sets (Elu78, Elu87, B451, Elu37, B457, B16, B25, and Elu19, Elu76, B422, Elu2, Elu7). The assay was optimized for genetic analyses of freshwater and brackish populations. These multiplexes were successfully executed to obtain the genetic profiles of 668 individuals from 16 populations (Poland and Germany). The average number of alleles was equal to 10.4, whereas the observed heterozygosity per locus ranged from 0.18 to 0.89, with the average value of 0.64. The probability of the identity of the marker sets indicated the high power of identification of unique genotypes. Therefore, this molecular tool can be used to describe the genetic variability of populations, select the proper source of breeding material, and monitor the progress of stocking efforts in genetic conservation projects of this species. |
2018
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Gumińska, Natalia; Płecha, Magdalena; Walkiewicz, Halszka; Hałakuc, Paweł; Zakryś, Bożena; Milanowski, Rafał Culture purification and DNA extraction procedures suitable for next-generation sequencing of euglenids Journal Article Journal of Applied Phycology, 30 (6), pp. 3541–3549, 2018, ISSN: 1573-5176. Abstract | Links | BibTeX @article{Guminska2018,
title = {Culture purification and DNA extraction procedures suitable for next-generation sequencing of euglenids},
author = {Natalia Gumińska and Magdalena Płecha and Halszka Walkiewicz and Paweł Hałakuc and Bożena Zakryś and Rafał Milanowski},
url = {https://doi.org/10.1007/s10811-018-1496-0},
doi = {10.1007/s10811-018-1496-0},
issn = {1573-5176},
year = {2018},
date = {2018-01-01},
journal = {Journal of Applied Phycology},
volume = {30},
number = {6},
pages = {3541--3549},
abstract = {In the present study, five different DNA extraction procedures were examined to determine their effectiveness for extracting DNA suitable for NGS applications. This included two silica-membrane spin column kits, phenol:chloroform, and two CTAB-based methods. Spectrophotometric and fluorimetric measurements as well as standard gel electrophoresis were used as criteria for evaluating the quantity and quality of the isolated DNA prior to the sequencing. Herein, the method of establishing and maintaining axenic Euglena cultures is also presented. The modified CTAB-based method proved to be highly efficient. In terms of DNA quantity and purity (according to the absorbance ratios), the chosen method resulted in DNA of high molecular weight and quality, which fulfills the library construction requirements. Genomic DNA of Euglena hiemalis (CCAP 1224/35) and E. longa (CCAP 1204-17a) isolated using the suggested protocol had been successfully sequenced on the Illumina HiSeq platform. A modified, rapid CTAB-based method of total DNA isolation from Euglena has been described. In terms of the DNA quantity and quality, the protocol devised involving the washing step with DMSO:acetonitrile proved superior to the commonly used, commercially manufactured kits and isolation with phenol:chloroform. The method is also less labor-intensive and time-consuming than the traditional CTAB-based protocol.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In the present study, five different DNA extraction procedures were examined to determine their effectiveness for extracting DNA suitable for NGS applications. This included two silica-membrane spin column kits, phenol:chloroform, and two CTAB-based methods. Spectrophotometric and fluorimetric measurements as well as standard gel electrophoresis were used as criteria for evaluating the quantity and quality of the isolated DNA prior to the sequencing. Herein, the method of establishing and maintaining axenic Euglena cultures is also presented. The modified CTAB-based method proved to be highly efficient. In terms of DNA quantity and purity (according to the absorbance ratios), the chosen method resulted in DNA of high molecular weight and quality, which fulfills the library construction requirements. Genomic DNA of Euglena hiemalis (CCAP 1224/35) and E. longa (CCAP 1204-17a) isolated using the suggested protocol had been successfully sequenced on the Illumina HiSeq platform. A modified, rapid CTAB-based method of total DNA isolation from Euglena has been described. In terms of the DNA quantity and quality, the protocol devised involving the washing step with DMSO:acetonitrile proved superior to the commonly used, commercially manufactured kits and isolation with phenol:chloroform. The method is also less labor-intensive and time-consuming than the traditional CTAB-based protocol. |
Gumińska, Natalia; Płecha, Magdalena; Zakryś, Bożena; Milanowski, Rafał Order of removal of conventional and nonconventional introns from nuclear transcripts of Euglena gracilis Journal Article PLoS Genetics, 14 (10), pp. e1007761, 2018, ISSN: 15537404. Abstract | Links | BibTeX @article{Guminska2018b,
title = {Order of removal of conventional and nonconventional introns from nuclear transcripts of Euglena gracilis},
author = {Natalia Gumińska and Magdalena Płecha and Bożena Zakryś and Rafał Milanowski},
doi = {10.1371/journal.pgen.1007761},
issn = {15537404},
year = {2018},
date = {2018-01-01},
journal = {PLoS Genetics},
volume = {14},
number = {10},
pages = {e1007761},
abstract = {Nuclear genes of euglenids and marine diplonemids harbor atypical, nonconventional introns which are not observed in the genomes of other eukaryotes. Nonconventional introns do not have the conserved borders characteristic for spliceosomal introns or the sequence complementary to U1 snRNA at the 5' end. They form a stable secondary structure bringing together both exon/intron junctions, nevertheless, this conformation does not resemble the form of self-splicing or tRNA introns. In the genes studied so far, frequent nonconventional introns insertions at new positions have been observed, whereas conventional introns have been either found at the conserved positions, or simply lost. In this work, we examined the order of intron removal from Euglena gracilis transcripts of the tubA and gapC genes, which contain two types of introns: nonconventional and spliceosomal. The relative order of intron excision was compared for pairs of introns belonging to different types. Furthermore, intermediate products of splicing were analyzed using the PacBio Next Generation Sequencing system. The analysis led to the main conclusion that nonconventional introns are removed in a rapid way but later than spliceosomal introns. Moreover, the observed accumulation of transcripts with conventional introns removed and nonconventional present may suggest the existence of a time gap between the two types of splicing.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nuclear genes of euglenids and marine diplonemids harbor atypical, nonconventional introns which are not observed in the genomes of other eukaryotes. Nonconventional introns do not have the conserved borders characteristic for spliceosomal introns or the sequence complementary to U1 snRNA at the 5' end. They form a stable secondary structure bringing together both exon/intron junctions, nevertheless, this conformation does not resemble the form of self-splicing or tRNA introns. In the genes studied so far, frequent nonconventional introns insertions at new positions have been observed, whereas conventional introns have been either found at the conserved positions, or simply lost. In this work, we examined the order of intron removal from Euglena gracilis transcripts of the tubA and gapC genes, which contain two types of introns: nonconventional and spliceosomal. The relative order of intron excision was compared for pairs of introns belonging to different types. Furthermore, intermediate products of splicing were analyzed using the PacBio Next Generation Sequencing system. The analysis led to the main conclusion that nonconventional introns are removed in a rapid way but later than spliceosomal introns. Moreover, the observed accumulation of transcripts with conventional introns removed and nonconventional present may suggest the existence of a time gap between the two types of splicing. |
2017
|
Panagiotopoulou, Hanna; Austin, James D; Zalewska, Katarzyna; Gonciarz, Magdalena; Czarnogórska, Kinga; Gawor, Jan; Weglenski, Piotr; Popović, Danijela Microsatellite Mutation Rate in Atlantic Sturgeon (Acipenser oxyrinchus) Journal Article Journal of Heredity, 108 (6), pp. 686-692, 2017, ISSN: 0022-1503. Abstract | Links | BibTeX @article{10.1093/jhered/esx057,
title = {Microsatellite Mutation Rate in Atlantic Sturgeon (Acipenser oxyrinchus)},
author = {Hanna Panagiotopoulou and James D Austin and Katarzyna Zalewska and Magdalena Gonciarz and Kinga Czarnogórska and Jan Gawor and Piotr Weglenski and Danijela Popović},
url = {https://doi.org/10.1093/jhered/esx057},
doi = {10.1093/jhered/esx057},
issn = {0022-1503},
year = {2017},
date = {2017-01-01},
journal = {Journal of Heredity},
volume = {108},
number = {6},
pages = {686-692},
abstract = {Understanding mutation rates can greatly extend the utility of population and conservation genetic analyses. Herein, we present an estimate of genome-wide microsatellite mutation rate in Atlantic sturgeon (Acipenser oxyrinchus) based on parent–offspring transmission patterns. We screened 307 individuals for parentage and mutation-rate analysis applying 43 variable markers. Out of 13228 allele transfers, 11 mutations were detected, producing a mutation rate of 8.3 × 10−4 per locus per generation (95% confidence interval: 1.48 × 10−3, 4.15 × 10−4). Single-step mutations predominated and there were trends toward mutations in loci with greater polymorphism and allele length. Two of the detected mutations were most probably cluster mutations, being identified in 12 and 28 sibs, respectively. Finally, we observed evidences of polyploidy based on the sporadic presence of 3 or 4 alleles per locus in the genotyped individuals, supporting previous reports of incomplete diploidization in Atlantic sturgeon.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Understanding mutation rates can greatly extend the utility of population and conservation genetic analyses. Herein, we present an estimate of genome-wide microsatellite mutation rate in Atlantic sturgeon (Acipenser oxyrinchus) based on parent–offspring transmission patterns. We screened 307 individuals for parentage and mutation-rate analysis applying 43 variable markers. Out of 13228 allele transfers, 11 mutations were detected, producing a mutation rate of 8.3 × 10−4 per locus per generation (95% confidence interval: 1.48 × 10−3, 4.15 × 10−4). Single-step mutations predominated and there were trends toward mutations in loci with greater polymorphism and allele length. Two of the detected mutations were most probably cluster mutations, being identified in 12 and 28 sibs, respectively. Finally, we observed evidences of polyploidy based on the sporadic presence of 3 or 4 alleles per locus in the genotyped individuals, supporting previous reports of incomplete diploidization in Atlantic sturgeon. |
2014
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Gonciarz, Magdalena; Wiktor, Józef; Tatarek, Agnieszka; Węgleński, Piotr; Stanković, Anna Genetic characteristics of three Baltic Zostera marina populations Journal Article Oceanologia, 56 (3), pp. 549-564, 2014, ISSN: 0078-3234. Abstract | Links | BibTeX @article{GONCIARZ2014549,
title = {Genetic characteristics of three Baltic Zostera marina populations},
author = {Magdalena Gonciarz and Józef Wiktor and Agnieszka Tatarek and Piotr Węgleński and Anna Stanković},
url = {https://www.sciencedirect.com/science/article/pii/S0078323414500309},
doi = {https://doi.org/10.5697/oc.55-3.549},
issn = {0078-3234},
year = {2014},
date = {2014-01-01},
journal = {Oceanologia},
volume = {56},
number = {3},
pages = {549-564},
abstract = {We performed genetic analyses of three Baltic eelgrass (Zostera marina) populations in Puck Bay (PB), Cudema Bay (CB) and Greifswalder Bodden (GB). The aim of this study was to identify the eelgrass population genetically closest to that from the PB, which could potentially serve as a reservoir for the restoration of the underwater meadows in this bay, seriously degraded in the past. We applied a 12-microsatellite assay to test the genetic distance between the target eelgrass populations. We found that the allelic richness values of the GB, PB and CB populations were 2.25, 3.77 and 3.50 respectively. The genetic diversity found in GB was low and could be explained by the population’s history, whereas the diversity of CB was higher than expected in a population located at the edge of the species’ range. Analyses of genetic differentiation and structure showed that of the three populations studied, PB and CB were closer to each other than to the GB population. The reasons for this differentiation in eelgrass populations and the implications of the results of their genetic analysis on the planned restoration of the PB populations are discussed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We performed genetic analyses of three Baltic eelgrass (Zostera marina) populations in Puck Bay (PB), Cudema Bay (CB) and Greifswalder Bodden (GB). The aim of this study was to identify the eelgrass population genetically closest to that from the PB, which could potentially serve as a reservoir for the restoration of the underwater meadows in this bay, seriously degraded in the past. We applied a 12-microsatellite assay to test the genetic distance between the target eelgrass populations. We found that the allelic richness values of the GB, PB and CB populations were 2.25, 3.77 and 3.50 respectively. The genetic diversity found in GB was low and could be explained by the population’s history, whereas the diversity of CB was higher than expected in a population located at the edge of the species’ range. Analyses of genetic differentiation and structure showed that of the three populations studied, PB and CB were closer to each other than to the GB population. The reasons for this differentiation in eelgrass populations and the implications of the results of their genetic analysis on the planned restoration of the PB populations are discussed. |
