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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

The control region of Orseolia oryzae mitochondrial genome.(a) The structural elements in the control region. The regions flanking the control region i.e. 12S and trnQ, trnM and ND2 are represented by the dark grey boxes (b) The secondary structure of the putative stem loop found in the control region.
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pone.0134625.g004: The control region of Orseolia oryzae mitochondrial genome.(a) The structural elements in the control region. The regions flanking the control region i.e. 12S and trnQ, trnM and ND2 are represented by the dark grey boxes (b) The secondary structure of the putative stem loop found in the control region.

Mentions: The control region for O. oryzae was found to be 578 bp long with an A+T content of 93.8%. Analysis of the region revealed five structural elements conserved in other arthropods as well ie: a poly-T, a [TA(a)]n-like-structure, a highly conserved stem loop structure, a pair of sequences immediately flanking the stem loop with a 5’ consensus of ‘TATA’ and 3’ consensus of ‘G(A)nT’ and finally a G+A rich region downstream of the secondary structure (Fig 4). A comparison of these structural elements was carried out with other members of Diptera (S5 Table). All the above five structural elements of the control region were found to be present in the conserved order in the O. oryzae mitogenome, as observed in other arthropod genomes, and on the same strand. Though the five conserved elements are present in all the dipteran insects analysed, the 3’ consensus motif, G(A)nT, was lacking in C. quinquefasciatus.


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)

The control region of Orseolia oryzae mitochondrial genome.(a) The structural elements in the control region. The regions flanking the control region i.e. 12S and trnQ, trnM and ND2 are represented by the dark grey boxes (b) The secondary structure of the putative stem loop found in the control region.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134625.g004: The control region of Orseolia oryzae mitochondrial genome.(a) The structural elements in the control region. The regions flanking the control region i.e. 12S and trnQ, trnM and ND2 are represented by the dark grey boxes (b) The secondary structure of the putative stem loop found in the control region.
Mentions: The control region for O. oryzae was found to be 578 bp long with an A+T content of 93.8%. Analysis of the region revealed five structural elements conserved in other arthropods as well ie: a poly-T, a [TA(a)]n-like-structure, a highly conserved stem loop structure, a pair of sequences immediately flanking the stem loop with a 5’ consensus of ‘TATA’ and 3’ consensus of ‘G(A)nT’ and finally a G+A rich region downstream of the secondary structure (Fig 4). A comparison of these structural elements was carried out with other members of Diptera (S5 Table). All the above five structural elements of the control region were found to be present in the conserved order in the O. oryzae mitogenome, as observed in other arthropod genomes, and on the same strand. Though the five conserved elements are present in all the dipteran insects analysed, the 3’ consensus motif, G(A)nT, was lacking in C. quinquefasciatus.

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