Limits...
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 relative synonymous codon usage (RSCU) values of the J-strand, N-strand and the complete mitochondrial genome of Orseolia oryzae.The RSCU values are shown on the Y-axis and the codon families are provided on the X-axis.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4520695&req=5

pone.0134625.g002: The relative synonymous codon usage (RSCU) values of the J-strand, N-strand and the complete mitochondrial genome of Orseolia oryzae.The RSCU values are shown on the Y-axis and the codon families are provided on the X-axis.

Mentions: The codon usage in the O. oryzae mitogenome was analysed using the standard invertebrate mitochondrial genetic code and the results are presented in Fig 2. A total of 3573 codons were detected out of which 2209 (61.8%) were found on the J-strand and 1364 (38.2%) on the N-strand. Overall, Phe (TTT,14.6%), Ile (ATT,11.1%), Leu (TTA,8.5%) and Tyr (TAT,6.9%) were the four most commonly represented codons wholly composed of A and/or T, which contributed towards the high A+T content of the entire mitogenome. Together these codons comprised 41.3% of the total codons in the mitogenome. The four-fold degenerate codons showed a bias towards A or T at the third codon position with a preference for A except for isoleucine, valine and alanine. A similar pattern was observed for two-fold degenerate codons at the third codon position, with higher preference for an A/T than G/C indicating an influence of a biased codon usage.


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 relative synonymous codon usage (RSCU) values of the J-strand, N-strand and the complete mitochondrial genome of Orseolia oryzae.The RSCU values are shown on the Y-axis and the codon families are provided on the X-axis.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134625.g002: The relative synonymous codon usage (RSCU) values of the J-strand, N-strand and the complete mitochondrial genome of Orseolia oryzae.The RSCU values are shown on the Y-axis and the codon families are provided on the X-axis.
Mentions: The codon usage in the O. oryzae mitogenome was analysed using the standard invertebrate mitochondrial genetic code and the results are presented in Fig 2. A total of 3573 codons were detected out of which 2209 (61.8%) were found on the J-strand and 1364 (38.2%) on the N-strand. Overall, Phe (TTT,14.6%), Ile (ATT,11.1%), Leu (TTA,8.5%) and Tyr (TAT,6.9%) were the four most commonly represented codons wholly composed of A and/or T, which contributed towards the high A+T content of the entire mitogenome. Together these codons comprised 41.3% of the total codons in the mitogenome. The four-fold degenerate codons showed a bias towards A or T at the third codon position with a preference for A except for isoleucine, valine and alanine. A similar pattern was observed for two-fold degenerate codons at the third codon position, with higher preference for an A/T than G/C indicating an influence of a biased codon usage.

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