Mitochondrial DNA segments in Catlle nuclear genome

U mnogim vrstama životinja (i ljudi) otkrivene su stotine sekvenci koje potječu od insercija mtDNA u nuklearni genom. Danas se te sekvence zovu numt-ovi (nuklearne mitohondrijske DNA) ili mitohondrijski pseudogeni. Međutim, distribucija numt-ova kod goveda se tek odnedavno počela istraživati. Cilj rada bio je identificirati i istražiti učestalost pojave segmenata mitohondrijske DNA u genomu jezgre goveda. Za istraživanje su korištene 33 sekvence iz projekta MitoTAUROmics te referentni kromosomi i mtDNA Bos taurusa i Bos indicusa koji su dostupni u javnim bazama podataka. Usporedbe su se radile uz pomoć BLAST+ softvera, a poravnanje sekvenci se radilo pomoću MEGA 7.0.26. softvera. Pronađeno je ukupno 156 potencijalnih numt-ova, od kojih je 86 potvrđeno. Iako su više kromosoma Bos indicusa imali podudaranja sa traženim sekvencama, sama duljina segmenata je bila veća kod Bos taurusa. Najduži numt ima 6393 pb, dok najkraći 27 pb. Podudarnost između numt-ova i mtDNA varira od 70% do 100%. Ukupna duljina fragmenata kod Bos taurusa je bila 57189 pb, što je 3,5 puta dulje od ukupne duljine mitogenoma. Duljina fragmenata Bos indicusa je 30609 pb, što je 1,9 puta dulje od ukupne duljine mitogenoma. U mtDNA Bos taurusa identificirano je 5 potpunih gena koji kodiraju proteine, a to su 12s rRNA, COX1, COX2, COX3, ATP6 koji su pronađeni u 9 numt-ova. Kod Bos indicusa identificirano je 6 potpunih gena: ND3, ND6, ATP6, ATP8, COX3, ND4L u 5 numt-ova. Većina ostalih numt-ova kodira mt-tRNA gene. Iako su otkriveni geni koji kodiraju proteine, potrebna su daljnja istraživanja radi provjere funkcionalnosti numt-ova koji kodiraju mt-tRNA molekule.In many animal species (and humans), hundreds of sequences, which originated from the insertion of mtDNA into the nuclear genome, have been discovered. Today, these sequences are called numts (nuclear mitochondrial DNAs) or mitochondrial pseudogenes. However, the distribution of cattle numts has only recently begun to be investigated. The aim of the study was to identify and investigate the incidence of mitochondrial DNA segments in the cattle nuclear genome. For this study 33 mitochondrial sequences, which were available from the MitoTAUROmics project and reference chromosomes and mtDNA of Bos taurus and Bos indicus that are available in public databases, were used. Comparisons were made with BLAST+ software, and alignment of sequences was performed using MEGA 7.0.26. software. A total of 156 potential numts were found, of which 86 were confirmed. Although more chromosomes of Bos indicus had matched sequences, the segment length itself was larger in Bos taurus. The longest numt was 6393 bp long, while the shortest was 27 bp. The correspondence between numt and mtDNA varies from 70% to 100%. The total length of fragments in Bos taurus was 57189 bp, which is 3.5 times longer than the total length of the mitogenome. The length of the Bos indicus’s segments fragment is 30609 pb, which is 1.9 times longer than the total length of the mitogenome. In the mtDNA of Bos taurus, 5 full genes coding for proteins were identified, namely 12s rRNA, COX1, COX2, COX3, ATP6, and they were found in 9 numts. In total, 6 full genes: ND3, ND6, ATP6, ATP8, COX3, ND4L in 5 numts were identified with mtDNA of Bos indicus. Most other numts encode the mt-tRNA genes. Although protein-encoding genes have been discovered, further investigations are required to verify the functionality of numts encoding mt-tRNA molecules