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The Asian Rice Gall Midge (Orseolia oryzae) Mitogenome Has Evolved Novel Gene Boundaries and Tandem Repeats That Distinguish Its Biotypes.

Atray I, Bentur JS, Nair S - PLoS ONE (2015)

Bottom Line: All protein coding genes used conventional start codons and terminated with a complete stop codon.Rearrangements of the tRNAs and protein coding genes are explained on the basis of tandem duplication and random loss model and why intramitochondrial recombination is a better model for explaining rearrangements in the O. oryzae mitochondrial genome is discussed.Furthermore, we evaluated the number of iterations of the tandem repeat elements found in the mitogenome.

View Article: PubMed Central - PubMed

Affiliation: Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.

ABSTRACT
The complete mitochondrial genome of the Asian rice gall midge, Orseolia oryzae (Diptera; Cecidomyiidae) was sequenced, annotated and analysed in the present study. The circular genome is 15,286 bp with 13 protein-coding genes, 22 tRNAs and 2 ribosomal RNA genes, and a 578 bp non-coding control region. All protein coding genes used conventional start codons and terminated with a complete stop codon. The genome presented many unusual features: (1) rearrangement in the order of tRNAs as well as protein coding genes; (2) truncation and unusual secondary structures of tRNAs; (3) presence of two different repeat elements in separate non-coding regions; (4) presence of one pseudo-tRNA gene; (5) inversion of the rRNA genes; (6) higher percentage of non-coding regions when compared with other insect mitogenomes. Rearrangements of the tRNAs and protein coding genes are explained on the basis of tandem duplication and random loss model and why intramitochondrial recombination is a better model for explaining rearrangements in the O. oryzae mitochondrial genome is discussed. Furthermore, we evaluated the number of iterations of the tandem repeat elements found in the mitogenome. This led to the identification of genetic markers capable of differentiating rice gall midge biotypes and the two Orseolia species investigated.

No MeSH data available.


Related in: MedlinePlus

Gene rearrangements in O. oryzae mitogenome.The order of genes in the Orseolia oryzae mitochondrial genome relative to the ancestral order and two other gall midges, Mayetiola destructor [GQ387648] and Rhopalomyia pomum [GQ387649].
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pone.0134625.g005: Gene rearrangements in O. oryzae mitogenome.The order of genes in the Orseolia oryzae mitochondrial genome relative to the ancestral order and two other gall midges, Mayetiola destructor [GQ387648] and Rhopalomyia pomum [GQ387649].

Mentions: In the O. oryzae mitogenome, all the three major classes of gene rearrangements were observed i.e. translocation, local inversion (inverted in the local position) and shuffling and remote inversion (translocated and inverted) (Fig 5). Rearrangements involved a total of 5 PCGs and 15 tRNAs which were either translocated and/or inverted. Relative to the conserved gene order, only 14 ancestral gene boundaries were conserved in the genome. Furthermore, it was observed that maximum rearrangements were restricted to one portion of the genome i.e. the part of the genome upstream of ND5. Downstream of ND5 only one rearrangement was observed: the translocation of trnT and trnP but without inversion. Among all the rearrangements, two gene blocks could be identified that were translocated and inverted en masse with reference to the ancestral gene order. One such rearrangement involved both PCGs and tRNAs; ATP8-ATP6-COIII-trnG-ND3 to ND3-trnG-COIII-ATP6-ATP8 and the other comprising only tRNAs; trnR-trnN-trnS1-trnE-trnF to trnF-trnS1-trnE-trnN-trnR (Fig 5).


The Asian Rice Gall Midge (Orseolia oryzae) Mitogenome Has Evolved Novel Gene Boundaries and Tandem Repeats That Distinguish Its Biotypes.

Atray I, Bentur JS, Nair S - PLoS ONE (2015)

Gene rearrangements in O. oryzae mitogenome.The order of genes in the Orseolia oryzae mitochondrial genome relative to the ancestral order and two other gall midges, Mayetiola destructor [GQ387648] and Rhopalomyia pomum [GQ387649].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4520695&req=5

pone.0134625.g005: Gene rearrangements in O. oryzae mitogenome.The order of genes in the Orseolia oryzae mitochondrial genome relative to the ancestral order and two other gall midges, Mayetiola destructor [GQ387648] and Rhopalomyia pomum [GQ387649].
Mentions: In the O. oryzae mitogenome, all the three major classes of gene rearrangements were observed i.e. translocation, local inversion (inverted in the local position) and shuffling and remote inversion (translocated and inverted) (Fig 5). Rearrangements involved a total of 5 PCGs and 15 tRNAs which were either translocated and/or inverted. Relative to the conserved gene order, only 14 ancestral gene boundaries were conserved in the genome. Furthermore, it was observed that maximum rearrangements were restricted to one portion of the genome i.e. the part of the genome upstream of ND5. Downstream of ND5 only one rearrangement was observed: the translocation of trnT and trnP but without inversion. Among all the rearrangements, two gene blocks could be identified that were translocated and inverted en masse with reference to the ancestral gene order. One such rearrangement involved both PCGs and tRNAs; ATP8-ATP6-COIII-trnG-ND3 to ND3-trnG-COIII-ATP6-ATP8 and the other comprising only tRNAs; trnR-trnN-trnS1-trnE-trnF to trnF-trnS1-trnE-trnN-trnR (Fig 5).

Bottom Line: All protein coding genes used conventional start codons and terminated with a complete stop codon.Rearrangements of the tRNAs and protein coding genes are explained on the basis of tandem duplication and random loss model and why intramitochondrial recombination is a better model for explaining rearrangements in the O. oryzae mitochondrial genome is discussed.Furthermore, we evaluated the number of iterations of the tandem repeat elements found in the mitogenome.

View Article: PubMed Central - PubMed

Affiliation: Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.

ABSTRACT
The complete mitochondrial genome of the Asian rice gall midge, Orseolia oryzae (Diptera; Cecidomyiidae) was sequenced, annotated and analysed in the present study. The circular genome is 15,286 bp with 13 protein-coding genes, 22 tRNAs and 2 ribosomal RNA genes, and a 578 bp non-coding control region. All protein coding genes used conventional start codons and terminated with a complete stop codon. The genome presented many unusual features: (1) rearrangement in the order of tRNAs as well as protein coding genes; (2) truncation and unusual secondary structures of tRNAs; (3) presence of two different repeat elements in separate non-coding regions; (4) presence of one pseudo-tRNA gene; (5) inversion of the rRNA genes; (6) higher percentage of non-coding regions when compared with other insect mitogenomes. Rearrangements of the tRNAs and protein coding genes are explained on the basis of tandem duplication and random loss model and why intramitochondrial recombination is a better model for explaining rearrangements in the O. oryzae mitochondrial genome is discussed. Furthermore, we evaluated the number of iterations of the tandem repeat elements found in the mitogenome. This led to the identification of genetic markers capable of differentiating rice gall midge biotypes and the two Orseolia species investigated.

No MeSH data available.


Related in: MedlinePlus