ABC - Department of Genomics - Agricultural Genomics and Bioinformatics

Research Interests

The primary research field of the Agricultral Genomics and Bioinformatics Group is the mammalian and honeybee (Apis Mellifera) genetics and genomics. Within this research topic our primarily goal is the genome sequencing of native domesticated and wild animals. The modern methods of gemone research, mainly genome sequencing makes it possible to find markers using bioinformatical methods. Genetic markers can be single nucleotide polymorphisms (SNPs) or bigger deletions, insertions. Firstly these markers can be used to identify specimens within the population secondly we are pairing phenotypes to the regulatory polymorhisms.

Current Research Projects

The Examination of Regulatory Polymorphisms

In cooperation with the University of Debrecen Chip-seq data was analyzed to identify regulatory regions (a region where transcription factors bind to a specific sequence) within the mouse and human genome. Then the regions were examined to see which regions were conserved amongst the various mammals. Today the genome sequences of more than 200 pig and wild boar genome sequences are available, including the 3 mangalica and a duroc genome that were sequenced here. Tests were made to search for polymorphisms in the conservated regulating regions that are specific for one breed using these genomes. The results were validated using gene bank samples. Later goals include identifying beneficial polymorphisms in the regulating regions of important genes that can prove useful during agricultural oriented breeding.

Mangalica Genome Project

Mangalica is an old Hungarian breed, its protection is a national priority supported and regulated by the Ministry of Agriculture. For the research related to the mangalica, the MANGFOOD research consortium has been established by six participants (National Agricultural Research and Innovation Center, Állattenyésztési és Takarmányozási Kutatóintézet, Central Environmental and Food Science Research Institute, Biomi Ltd., Wessling Magyarország Ltd., Olmos és Tóth Ltd.) that is supported by the National Developement Agency. The group has created and maintained a blood and tissue biobank where thousands of samples mainly from mangalica and other domesticated animals can be found. These can serve as sources for DNA and RNA isolates to help research projects for the members of the consortium. Three male mangalica and a duroc specimen has been sequenced using HiSEQ 2000 technology by our partners. 11 Gbp of mangalica sequence has been aligned on the pig genome using bioinformatic methods. According to the alignments 11 thousand structural differences have been found between the mangalica and the reference genome. The mangalica genome is compared to other breeds to identify the structural differneces. These can help to create and evaluate DNA tests that can serve as biomarkers to determine the quality and quantity of meat in food products using PCR methods. These results can be used to find markers for other pig and boar breeds.

Red Deer (Cervus Elaphus) Project

In cooperation with the University of Kaposvár the specification of the genome sequence of the red deer has been started. In the Game Management Landscape Center of the University of Kaposvár the genome of the male red deer has been sequenced using the HiSEQ 2000 technology. The 22 Gbp of acquired data was de novo assembled and while there is no red deer reference genome to be found, our sequences were rearranged to chromosome sequences using deer genome and cattle chromosome synthenia. Firstly the genome of the mitochondria has been specified and the result published. The tandem differences (and the microsatellites) in the red deer genome have been identified and new sexual chromosome marker developement is on its way at the moment.

Apiary and honeybee (Apis Mellifera) genetic and genomic research

Our team plans to benefit from the bioinformatic and laboratory experience gained so far in the field of bee genetic and genomic research. The project will be carried out with the help of experienced beekeepers, bee breeders and universities. The research is comissioned by the Bee Keeping Association of the Hungarian Beekeepers. The genome of five bee specimen have been sequenced using the Illumina HiSEQ 2000 technology. Using bioinformatic methods 22 Gbp data has been fitted on the bee reference genome. During the fitting 17 million structural differences have been found between the bee genomes. Firstly the genome of the mitochondria has been specified and the differences examined to explore the diagnostic variations between the european and asian honeybee. We are working on developing markers that can differentiate between the two honeybee species and the DNA samples produced by us using real-time PCR.

The genetic monitoring of predators

Joined to the monitoring of Hungarian big predators in cooperation with the Institute of Wildlife Conservation of Szent István University and the National Park of Bükk genetic monitoring examinations are made using various animal tissues as samples, mainly fur and fecal samples. The monitored species are 1) gray wolf/dog/golden jackal 2) wild cat/cat species complex 3) eurasiam lynx 4) brown bear. Multiplex reactions are assembled and optimised from STR markers (microsatellites) for the genotypization. The unique STR profiles gained are used to identify specimens, also the minimal population was calculated. If the needed sample quantity is reached, the genetic diversity and the kinship of various specimen will be assessed.

Bioinformatic services in the MBK

Professional relationships are maintained with multiple research groups, several bioinformatical databases are constructed and maintained and webpages developed.

Staff

Munkakör: főosztályvezető, csoportvezető, tudományos főmunkatárs
Munkavégzés helye: 2100 Gödöllő, Szent-Györgyi Albert utca 4.
Telephone: +36 28526144
Fax: +36 28526101
Mobil: +36 703206881
E-mail: barta.endre[at]abc.naik.hu
Levente Kontra
Munkakör: tudományos munkatárs
Munkavégzés helye: 2100 Gödöllő, Szent-Györgyi Albert utca 4.
Fax: +36 28526101
E-mail: kontra.levente[at]abc.naik.hu
Ferenc Marincs PhD
Munkakör: Önkéntes, tudományos főmunkatárs
Munkavégzés helye: 2100 Gödöllő, Szent-Györgyi Albert utca 4.
Fax: +36 28526101
E-mail: marincs.ferenc[at]abc.naik.hu
Tibor Nagy
Munkakör: tudományos munkatárs
E-mail: nagy.tibor[at]abc.naik.hu
Mátyás Schiller
Munkakör: tudományos segédmunkatárs
Munkavégzés helye: 2100 Gödöllő, Szent-Györgyi Albert utca 4.
Fax: +36 28526101
E-mail: schiller.matyas[at]abc.naik.hu

Publications

Publications (2007 – present)


2017

Kalapos B, Novák A, Dobrev P, Vítámvás P, Marincs F, Galiba G and Vanková R (2017) Effect of the Winter Wheat Cheyenne 5A Substituted Chromosome on Dynamics of Abscisic Acid and Cytokinins in Freezing-Sensitive Chinese Spring Genetic Background. Frontiers in Plant Science 8:2033. Link

Krisztián Frank, János Molnár, Endre Barta and Ferenc Marincs (2017) The full mitochondrial genomes of Mangalica pig breeds and their possible origin. Mitochondrial DNA Part B 2:730-734. Link

Krisztián Frank, Krisztina Miró, Tibor Nagy, Ferenc Marincs (2017) Development of a PCR-based DNA marker for Glu-1By alleles in the old Hungarian Bánkúti wheat. Molecular Breeding 37:120. Link

Krisztina Miró, Tibor Nagy, Edit Korom, Ferenc Marincs (2017) Discrimination of grape varieties by Start Codon Targeted genotyping using partially degenerate primers. Acta Biologica Szegediensis 61:77-83.

Ferenc Marincs, Tibor Nagy, Krisztina Miró, Zsuzsanna Kollár, Endre Barta, Péter Kaló (2017) Large‑scale amplicon sequencing of the SP3D gene responsible for fruit-yield heterosis in tomato. Plant Gene 9:45‑49. Link

 

2016

Balázs Kalapos, Petre Dobrev, Tibor Nagy, Pavel Vítámvás, János Györgyey, Gábor Kocsy, Ferenc Marincs, Gábor Galiba (2016) Transcript and hormone analyses reveal the involvement of ABA signalling, hormone crosstalk and genotype-specific biological processes in cold-shock response in wheat. Plant Science 253:86‑97. Link

Endre Barta, Zsófia Bánfalvi, Zoltán Havelda, László Hiripi, Zsigmond Jeney, János Kiss, Balázs Kolics, Ferenc Marincs, Dániel Silhavy, Viktor Stéger, Éva Várallyay (2016) Agricultural genomics: an overview of the Next Generation Sequencing projects at the NARIC-Agricultural Biotechnology Institute in Gödöllő. Hungarian Agricultural Research 25:10-21.

Nagy, Gergely, Erik Czipa, László Steiner, Tibor Nagy, Sándor Pongor, László Nagy, and Endre Barta. “Motif Oriented High-Resolution Analysis of ChIP-Seq Data Reveals the Topological Order of CTCF and Cohesin Proteins on DNA.” BMC Genomics 17, no. 1 (2016): 1–9. doi:10.1186/s12864-016-2940-7. Link

Nagy T, Kis A, Poliska Sz, Barta E, Havelda Z, Marincs F (2016) Comparison of small RNA next-generation sequencing with and without isolation of small RNA fraction. BioTechniques 60:(6) 273-278. Link

Frank K, Barta E, Bana ÁN, Nagy J, Horn P, Orosz L, Stéger V (2016) Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae. Acta Biologica Hungarica 67:(2) 133-147. Link

 

2015

Bálint Jeannette, Kis András, Taller Dénes, Nagy Tibor, Barta Endre, Molnár János, Tusnády E. Gábor, Marincs Ferenc és Havelda Zoltán (2015) Az RNS interferencia szerepe a növények patogénekkel szembeni védekezésében és a fejlődésbiológiai folyamatokban. Növényvédelem 51:539-549.

Juhász Zs, Boldizsár Á, Nagy T, Kocsy G, Marincs F, Galiba G, Bánfalvi Zs (2015) Pleiotropic effect of chromosome 5A and the mvp mutation on the metabolite profile during cold acclimation and the vegetative/generative transition in wheat. BMC Plant Biology 15:(57) Link

Olasz F, Nagy T, Szabo M, Kiss J, Szmolka A, Barta E, van Tonder A, Thomson N, Barrow P, Nagy B (2015) Genome Sequences of Three Salmonella enterica subsp. enterica Serovar Infantis Strains from Healthy Broiler Chicks in Hungary and in the United Kingdom. GENOME ANNOUNCEMENTS 3:(1) Paper e01468-14. 2 p. Link

Nemet Z, Albert E, Nagy T, Olasz F, Barta E, Kiss J, Dan A, Banyai K, Hermans K, Biksi I (2015) Draft Genome Sequence of a Highly Virulent Rabbit Staphylococcus aureus Strain. GENOME ANNOUNCEMENTS 3:(4) Paper e00461-15. 2 p. Link

 

2014

Juhász Z, Dancs G, Marincs F, Vossen M, Allefs S, Bánfalvi Z (2014) Vitamin C, B5, and B6 contents of segregating potato populations detected by GC-MS: a method facilitating breeding potatoes with improved vitamin content. Plant Breeding 133: 515-520. Link

Molnar J, Nagy T, Steger V, Toth G, Marincs F, Barta E (2014) Genome sequencing and analysis of Mangalica, a fatty local pig of Hungary. BMC GENOMICS 15:(1) p. 761. Link

Szabolcsi Z, Egyed B, Zenke P, Padar Zs, Borsy A, Steger V, Pasztor E, Csanyi S, Buzas Zs, Orosz L (2014) Constructing STR Multiplexes for Individual Identification of Hungarian Red Deer. JOURNAL OF FORENSIC SCIENCES 59: pp. 1090-1099.

 

2013

Koppányné Sz E, Ujhelyi G, Jánosi A, Mohr A, Szántó-Egész R, Dallmann K, Micsinai A, Zsolnai A, Egerszegi I, Anton I, Tóth G, Molnár J, Stéger V, Marincs F Tóth P, Rátky J (2013) PCR sokszorozásra alkalmas DNS kivonása különböző mangalica termékekből. ÉLELMISZER - TUDOMÁNY TECHNOLÓGIA 1: pp. 12-17.

Koppányné Sz E, Ujhelyi G, Jánosi A, Mohr A, Szántó-Egész R, Dallmann K, Micsinai A, Zsolnai A, Egerszegi I, Anton I, Tóth G, Molnár J, Stéger V, Marincs F, Tóth P, Rátky J (2013) Mangalica termékek kimutatására alkalmas real-time PCR módszer fejlesztése. ÉLELMISZER - TUDOMÁNY TECHNOLÓGIA 3: pp. 14-20.

Marincs F, Molnár J, Tóth G, Stéger V, Barta E (2013)Introgression and isolation contributed to the development of Hungarian Mangalica pigs from a particular European ancient bloodline.GENETICS SELECTION EVOLUTION 45: Paper 22. Link

Molnár J, Tóth G, Stéger V, Zsolnai A, Jánosi A, Mohr A, Szántó-Egész R, Tóth P, Micsinai A, Rátky J, Marincs F (2013) Mitochondrial D-loop analysis reveals low diversity in Mangalica pigs and their relationship to historical specimens. JOURNAL OF ANIMAL BREEDING AND GENETICS-ZEITSCHRIFT FÜR TIERZUCHTUNG UND ZUCHTUNGSBIOLOGIE 130:(4) pp. 312-320. Link

Nyiko T, Kerenyi F, Szabadkai L, Benkovics AH, Major P, Sonkoly B, Merai Z, Barta E, Niemiec E, Kufel J, Silhavy D (2013) Plant nonsense-mediated mRNA decay is controlled by different autoregulatory circuits and can be induced by an EJC-like complex. NUCLEIC ACIDS RESEARCH 41:(13) pp. 6715-6728.

Semsey S, Jauffred L, Csiszovszki Z, Erdossy J, Stéger V, Hansen S, Krishna S (2013) The effect of LacI autoregulation on the performance of the lactose utilization system in Escherichia coli. NUCLEIC ACIDS RESEARCH 41:(13) pp. 6381-6390.

Zsolnai A, Tóth G, Molnár J, Stéger V, Marincs F, Jánosi A, Ujhelyi G, Koppányné Szabó E, Mohr A, Anton I, Szántó-Egész R, Egerszegi I, Sipos R, Dallmann K, Tóth P, Micsinai A, Brüssow K-P, Rátky J (2013)  Looking for breed differentiating SNP loci and for a SNP set for parentage testing in Mangalica. ARCHIV FÜR TIERZUCHT-ARCHIVES OF ANIMAL BREEDING 56:(19) pp. 200-207. Link

 

2012

Gáspári Z, Süveges D, Perczel A, Nyitray L, Tóth G (2012) Charged single alpha-helices in proteomes revealed by a consensus prediction approach. BBA - Proteins Proteom 1824: 637-646.

Kondrák M, Marincs F, Antal F, Juhász Zs, Bánfalvi Zs (2012) Effects of yeast trehalose-6-phosphate synthase 1 on gene expression and carbohydrate contents of potato leaves under drought stress conditions. BMC Plant Biology 12: 74. Link

 

2011

Kondrák M, Marincs F, Kalapos B, Juhász Zs and Bánfalvi Zs (2011) Transcriptome analysis of potato leaves expressing the trehalose-6-phosphate synthase 1 gene of yeast. PLoS ONE 6: e23466 Link

Nagy A, Kenesi E, Rentsendorj O, Molnar A, Szenasi T, Sinko I, Zvara A, Oommen ST, Barta E, Puskas LG, Lefebvre V, Kiss I (2011) Evolutionarily conserved, growth plate zone-specific regulation of the matrilin-1 promoter: L-Sox5/Sox6 and Nfi factors bound near TATA finely tune activation by Sox9. MOLECULAR AND CELLULAR BIOLOGY 31:(4) pp. 686-699.

 

2010

del Val C, Pelz O, Glatting KH, Barta E, Hotz-Wagenblatt A (2010) PromoterSweep: a tool for identification of transcription factor binding sites. THEORETICAL CHEMISTRY ACCOUNTS 125:(3-6) pp. 583-591.

Stéger V, Molnár A, Borsy A, Gyurján I, Szabolcsi Z, Dancs G, Molnár J, Papp P, Nagy J, Puskás L, Barta E, Zomborszky Z, Horn P, Podani J, Semsey S, Lakatos P, Orosz L (2010) Antler development and coupled osteoporosis in the skeleton of red deer Cervus elaphus: expression dynamics for regulatory and effector genes. MOLECULAR GENETICS AND GENOMICS 284:(4) pp. 273-287.

Szittya G, Moxon S, Pantaleo V, Tóth G, Rusholme Pilcher RL, Moulton V, Burgyán J and Dalmay T (2010) Structural and functional analysis of viral siRNAs. PLoS Pathog 6:e1000838.

 

2009

Borsy A, Podani J, Stéger V, Balla B, Horváth A, Kósa JP, Gyurján I Jr, Molnár A, Szabolcsi Z, Szabó L, Jakó E, Zomborszky Z, Nagy J, Semsey S, Vellai T, Lakatos P, Orosz L (2009) Identifying novel genes involved in both deer physiological and human pathological osteoporosis. MOLECULAR GENETICS AND GENOMICS 281: pp 301-313.      

Sebestyen E, Nagy T, Suhai S, Barta E (2009) DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes. BMC BIOINFORMATICS 10:(6) p S6.

Süveges D, Gáspári Z, Tóth G,Nyitray L (2009) Charged single α-helix: A versatile protein structural motif Proteins. 74: 905-916.

 

2008

Garnett JA, Marincs F, Baumberg S, Stockley PG, Phillips SEV (2008) Structure and function of the arginine repressor‑operator complex from Bacillus subtilis. J Mol Biol 379: 284-298. Link

Kassai-Jáger E, Ortutay C, Tóth G, Vellai T, Gáspári Z (2008) Distribution and evolution of short tandem repeats in closely related bacterial genomes. Gene 410: 18-25.

Kerenyi Z, Merai Z, Hiripi L, Benkovics A, Gyula P, Lacomme C, Barta E, Nagy F, Silhavy D (2008) Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay. EMBO JOURNAL 27:(11) pp 1585-1595.

Villányi Z, Gyurján I, Stéger V, Orosz L (2008) Plaque based competitive hybridization. J Biomol Screen 13: 80-84.  

 

2007

Barta E (2007)Comparative Genomics-Based Orthologous Promoter Analysis using the DoOP database and the DoOPSearch web tool. Comparative Genomics Vol I Totowa: pp 319-328.(Methods in Molecular Biology; 395-396) (ISBN:9781934115374 (v 2)

Gáspári Z, Ortutay C, Tóth G (2007) Divergent microsatellite evolution in the human and chimpanzee lineages. FEBS Lett 581: 2523-2526.

Gyurján I, Molnár A, Borsy A, Stéger V, Hackler L, Zomborszky Z, Papp P, Duda E, Deák F, Lakatos P, Puskás L, Orosz L(2007) Gene expression dynamics in deer antler: mesenchymal differentiation toward chondrogenesis. MOLECULAR GENETICS AND GENOMICS 277:(3) pp 221-235.

Kiss J, Nagy Z, Tóth G, Kiss GB, Jakab J, Chandler M, Olasz F (2007) Transposition and target specificity of the typical IS30 family element IS1655 from Neisseria meningitidis. Mol Microbiol 63: 1731-1747.

Molnar A, Gyurjan I, Korpos E, Borsy A, Steger V, Buzas Z, Kiss I, Zomborszky Z, Papp P, Deak F, Orosz L (2007) Identification of Differentially Expressed Genes in The Developing Antler of Red Deer Cervus Elaphus. MOLECULAR GENETICS AND GENOMICS 277:(3) pp 237-248.

Szatmari I, Torocsik D, Agostini M, Nagy T, Gurnell M, Barta E, Chatterjee K, Nagy L (2007) PPARgamma regulates the function of human dendritic cells primarily by altering lipid metabolism. BLOOD 110:(9) pp 3271-3280.

Szomor KN, Dencs Á, Tóth G, Kovács GM, Saleh Ali Y, Berencsi G, Takács M (2007) Variability of the PreS1/PreS2/S regions of hepatitis B virus in Hungary. Arch Virol 152: 697-704.

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