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001-es BibID:	BIBFORM118760
035-os BibID:	(cikkazonosító)219 (WoS)001163790400002 (Scopus)85185406034
Első szerző:	Laczkó Levente (biológus)
Cím:	The draft genome of Spiraea crenata L. (Rosaceae) : the frst complete genome in tribe Spiraeeae / Levente Laczkó, Sándor Jordán, Szilárd Póliska, Hanna Viktória Rácz, Nikoletta Andrea Nagy, Attila Molnár V., Gábor Sramkó
Dátum:	2024
ISSN:	2052-4463
Megjegyzések:	Spiraea crenata L. is a deciduous shrub distributed across the Eurasian steppe zone. The species is of cultural and horticultural importance and occurs in scattered populations throughout its westernmost range. Currently, there is no genomic information on the tribe of Spiraeeae. Therefore we sequenced and assembled the whole genome of S. crenata using second- and third-generation sequencing and a hybrid assembly approach to expand genomic resources for conservation and support research on this horticulturally important lineage. In addition to the organellar genomes (the plastome and the mitochondrion), we present the first draft genome of the species with an estimated size of 220 Mbp, an N50 value of 7.7 Mbp, and a BUSCO score of 96.0%. Being the first complete genome in tribe Spiraeeae, this may not only be the first step in the genomic study of a rare plant but also a contribution to genomic resources supporting the study of biodiversity and evolutionary history of Rosaceae.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk whole genome genome assembly non-model plant
Megjelenés:	Scientific Data. - 11 : 1 (2024), p.1-11. -
További szerzők:	Jordán Sándor (1992-) Póliska Szilárd (1978-) (biológus) Rácz Hanna Viktória (1994-) (biológus) Nagy Nikoletta Andrea (1990-) (biológus) Molnár V. Attila (1969-) (biológus, botanikus) Sramkó Gábor (1981-) (biológus)
Pályázati támogatás:	FK137962 OTKA ÚNKP-22-3-II-DE-172 Egyéb
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001-es BibID:	BIBFORM119954
035-os BibID:	(cikkazonosító)7545
Első szerző:	Nagy Nikoletta Andrea (biológus)
Cím:	The updated genome of the Hungarian population of Aedes koreicus / Nikoletta Andrea Nagy, Gábor Endre Tóth, Kornélia Kurucz, Gábor Kemenesi, Levente Laczkó
Dátum:	2024
ISSN:	2045-2322
Megjegyzések:	Vector-borne diseases pose a potential risk to human and animal welfare, and understanding their spread requires genomic resources. The mosquito Aedes koreicus is an emerging vector that has been introduced into Europe more than 15 years ago but only a low quality, fragmented genome was available. In this study, we carried out additional sequencing and assembled and characterized the genome of the species to provide a background for understanding its evolution and biology. The updated genome was 1.1Gbp long and consisted of 6099 contigs with an N50 value of 329,610 bp and a BUSCO score of 84%. We identifed 22,580 genes that could be functionally annotated and paid particular attention to the identifcation of potential insecticide resistance genes. The assessment of the orthology of the genes indicates a high turnover at the terminal branches of the species tree of mosquitoes with complete genomes, which could contribute to the adaptation and evolutionary success of the species. These results could form the basis for numerous downstream analyzes to develop targets for the control of mosquito populations.
Tárgyszavak:	Orvostudományok Egészségtudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk Aedes Invasive mosquito Genome assembly Tird generation sequencing Hybrid assembly Functional annotation
Megjelenés:	Scientific Reports. - 14 : 1 (2024), p.1-12. -
További szerzők:	Tóth Gábor Endre Kurucz Kornélia Kemenesi Gábor Laczkó Levente (1992-) (biológus)
Pályázati támogatás:	PD142602 OTKA FK-138563 Egyéb RRF-2.3.1-21-2022-00010 Egyéb
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001-es BibID:	BIBFORM117877
035-os BibID:	(cikkazonosító)45 (Scopus)85181689003 (WOS)001138932000001
Első szerző:	Rádai Zoltán (biológus)
Cím:	An overlooked phenomenon : complex interactions of potential error sources on the quality of bacterial de novo genome assemblies / Zoltán Rádai, Alex Váradi, Péter Takács, Nikoletta Andrea Nagy, Nicholas Schmitt, Eszter Prépost, Gábor Kardos, Levente Laczkó
Dátum:	2024
ISSN:	1471-2164
Megjegyzések:	Background: Parameters adversely affecting the contiguity and accuracy of the assemblies from Illumina next-generation sequencing (NGS) are well described. However, past studies generally focused on their additive effects, overlooking their potential interactions possibly exacerbating one another's effects in a multiplicative manner. To investigate whether or not they act interactively on de novo genome assembly quality, we simulated sequencing data for 13 bacterial reference genomes, with varying levels of error rate, sequencing depth, PCR and optical duplicate ratios. Results: We assessed the quality of assemblies from the simulated sequencing data with a number of contiguity and accuracy metrics, which we used to quantify both additive and multiplicative effects of the four parameters. We found that the tested parameters are engaged in complex interactions, exerting multiplicative, rather than additive, effects on assembly quality. Also, the ratio of non-repeated regions and GC% of the original genomes can shape how the four parameters affect assembly quality. Conclusions: We provide a framework for consideration in future studies using de novo genome assembly of bacterial genomes, e.g. in choosing the optimal sequencing depth, balancing between its positive effect on contiguity and negative effect on accuracy due to its interaction with error rate. Furthermore, the properties of the genomes to be sequenced also should be taken into account, as they might influence the effects of error sources themselves.
Tárgyszavak:	Orvostudományok Egészségtudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk Bacterial genomes Optical duplicates PCR duplicates Sequencing depth Sequencing error
Megjelenés:	BMC Genomics. - 25 : 1 (2024), p. 1-8. -
További szerzők:	Váradi Alex (1991-) (biológus) Takács Péter (1966-) (informatikus) Nagy Nikoletta Andrea (1990-) (biológus) Schmitt, Nicholas Prépost Eszter Kardos Gábor (1974-) (szakorvos, klinikai mikrobiológus) Laczkó Levente (1992-) (biológus)
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