Swati PUROHIT, Seema TRIVEDI, Günwant SHEKHAWAT

Analysis of similarities between viroid, prokaryote and eukaryote genomes to revisit theories of origin of viroids

Viroidler, bitkinin kendi kendini kopyalama mekanizmasını kullanarak çoğalan tek sarmallı dairesel RNA moleküllerinden.oluşan en küçük patojenlerdir. Bu çalışma "viroidlerin ilk ortaya çıkış teorisini" tekrar gözden geçirmek amacıyla viroidlerin virüs genomları hariç diğer genomlarla arasındaki dizi benzerliğini araştırmaktadır. Çalışmadaki BLASTn taraması viroid genomu ve diğer genomlarla arasında kayda değer bir benzerlik bulmamıştır. Bu genomlar sırasıyla; prokaryot genomları (Acetobacter aceti, Bordetella bronchiseptica, Borrelia garinii, Brucella abortus'biovar 1, str. 9-9, Brucella melitensis 16M, Brucella melitensis, Brucella suis 1330, Corynebacterium efficiens, Dechloromonas aromatica, Desulfotalea psychrophila, Xanthomonas campestris, Gluconobacter oxydans, Methanosarcina mazei, Mycoplasma gallisepticum strain R, Pseudoalteromonas haloplanktis, Pseudomonas aeruginosa PAO1, Pseudomonas fluorescens, Sinorhizobium meliloti, Streptomyces avermitilis, Vibrio parahaemolyticus ve Vibrio parahaemolyticus); fungi genomu Magnaporthe grisea, bitki genomları (Oryza sativa (japonica cultivar-group), Arabidopsis thaliana, Aspergillus fumigatus, Medicago truncatula ve Sorghum bicolour) ve hayvan genomlarıdır [Protozoa (Trypanosoma cruzi ve Entamoeba histolytica HM-İ), omurgasızlar(Caenorhabditis briggsae, Caenorhabditis elegans, Drosophila melanogaster, Anopheles gambiae, Strongylocentrotus purpuratus dve deniz kestanesi), Urochordata (jCiona intestinalis), memeliler dışındaki omurgalılar (Xenopus tropicalis ve Zebra balığı) ve memeliler (Bos Taurus, Mus musculus, Rattus norvegicus,¥a.re, Maçaca mulatto, Pan troglodytes ve Homo sapiens)]. Omurgalılardan sürüngen ve kuşlar ile hiçbir benzerlik görülmemiştir. Ayrıca, bu çalışma CG bolluğu (50%'den büyük olan) ve genom boyutu arasında bir ilişki bulmamıştır.

Viroidlerin orijini teorilerinin yeniden değerlendirilmesi için viroid, prokaryot ve ökaryot genomları arasındaki benzerliklerin analizi

Viroids are smallest pathogens that are single stranded circular RNA molecules capable of replication with help of plant replication machinery. Present study seeks sequence similarity of viroids with genomes excluding virus genomes with the aim to revisit theories of origin of viroids. BLASTn search in present study does not find significant similarity with other genomes Prokaryotes {Acetobacter aceti, Bordetella bronchiseptica, Borrelia garinii, Brucella abortus biovar 1, str. 9-9, Brucella melitensis 16M, Brucella melitensis, Brucella suis 1330, Corynebacterium efficiens, Dechloromonas aromatica, Desulfotalea psychrophila, Xanthomonas campestris, Gluconobacter oxydans, Methanosarcina mazei, Mycoplasma gallisepticum strain R, Pseudoalteromonas haloplanktis, Pseudomonas aeruginosa PAO1, Pseudomonas fluorescens, Sinorhizobium melihti, Streptomyces avermitilis, Vibrio parahaemolyticus and Vibrio parahaemolyticus), fungi (Magnaporthe grisea), plants (Oryza sativa (japonica cultivar-group), Arabidopsis ihaliana, Aspergillus fumigatus, Medicago truncatula and Sorghum bicolour) and animals [Protozoa (Trypanosoma cruzi and Entamoeba histolytica HM-1), Invertebrates (Caenorhabditis briggsae, Caenorhabditis elegans, Drosophila melanogaster, Anopheles gambiae, Strongylocentrotus purpuratus and Sea urchin), Urochordata (Ciona intestinalis), Vertebrates other than mammals (Xenopus tropicalis and Zebrafish) and Mammals (Bos Taurus, Mus musculus, Rattus norvegicus, Mouse, Maçaca mulatto, Pan troglodytes and Homo sapiens)] genomes. Among vertebrates, no similarity is seen with any reptile and aves genomes. Further, present study finds no correlation between CG richness (which is greater than 50%) and genome size.

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