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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 structure of Orseolia oryzae mitochondrial genome.The light grey areas indicate the PCGs, rRNAs and the control region and the dark grey areas indicate the different tRNAs. The exploding slices of the doughnut indicate the location of two repeat regions, RR-I and RR-II.
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pone.0134625.g001: The structure of Orseolia oryzae mitochondrial genome.The light grey areas indicate the PCGs, rRNAs and the control region and the dark grey areas indicate the different tRNAs. The exploding slices of the doughnut indicate the location of two repeat regions, RR-I and RR-II.

Mentions: The complete mitochondrial genome of O. oryzae is a circular, double stranded DNA molecule of 15,286 bp (Fig 1). The mitogenome was assembled using 18 overlapping cloned PCR fragments. These fragments were 400 bp to 2.0 Kb long enabling large overlaps at the two ends of these fragments. This further ensured that the assembly did not contain nuclear sequences of mitochondrial origin (numts). Two clones of each fragment were sequenced and contigs were generated. The mitogenome has the typical number of 37 genes, 13 PCGs, 2 rRNAs and 22 tRNAs (Table 1), as reported for other insects. In addition, a 578 bp control region (CR) was present between 12S rRNA and trnQ. A distinctive feature identified in the mitogenome of O. oryzae was the presence of two repeat regions, RR-I and RR-II located between trnW and trnA and between trnI and COI, respectively. Such repeats have been previously unreported from any other arthropod mitogenomes. In addition to the control region and the repeat regions, 665 nucleotides of non-coding DNA was present dispersed in the genome. Among the different intergenic spacer regions found between various genes, the longest was 155 bp between trnI and COI and the smallest 1 bp between COIII and ATP6. The order of the genes was found to be different from the conserved arthropod gene organization. Twenty genes were either translocated and/or inverted, out of which 15 were tRNAs and 5 were PCGs. In all, 15 gene boundaries shared overlapping sequences that ranged from 2 (between trnT and ND6) to 31 nucleotides (between ND6 and trnH).


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 structure of Orseolia oryzae mitochondrial genome.The light grey areas indicate the PCGs, rRNAs and the control region and the dark grey areas indicate the different tRNAs. The exploding slices of the doughnut indicate the location of two repeat regions, RR-I and RR-II.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134625.g001: The structure of Orseolia oryzae mitochondrial genome.The light grey areas indicate the PCGs, rRNAs and the control region and the dark grey areas indicate the different tRNAs. The exploding slices of the doughnut indicate the location of two repeat regions, RR-I and RR-II.
Mentions: The complete mitochondrial genome of O. oryzae is a circular, double stranded DNA molecule of 15,286 bp (Fig 1). The mitogenome was assembled using 18 overlapping cloned PCR fragments. These fragments were 400 bp to 2.0 Kb long enabling large overlaps at the two ends of these fragments. This further ensured that the assembly did not contain nuclear sequences of mitochondrial origin (numts). Two clones of each fragment were sequenced and contigs were generated. The mitogenome has the typical number of 37 genes, 13 PCGs, 2 rRNAs and 22 tRNAs (Table 1), as reported for other insects. In addition, a 578 bp control region (CR) was present between 12S rRNA and trnQ. A distinctive feature identified in the mitogenome of O. oryzae was the presence of two repeat regions, RR-I and RR-II located between trnW and trnA and between trnI and COI, respectively. Such repeats have been previously unreported from any other arthropod mitogenomes. In addition to the control region and the repeat regions, 665 nucleotides of non-coding DNA was present dispersed in the genome. Among the different intergenic spacer regions found between various genes, the longest was 155 bp between trnI and COI and the smallest 1 bp between COIII and ATP6. The order of the genes was found to be different from the conserved arthropod gene organization. Twenty genes were either translocated and/or inverted, out of which 15 were tRNAs and 5 were PCGs. In all, 15 gene boundaries shared overlapping sequences that ranged from 2 (between trnT and ND6) to 31 nucleotides (between ND6 and trnH).

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