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.
Highlights
The Asian rice gall midge, Orseolia oryzae (Diptera: Cecidomyiidae) is an important pest of rice that is responsible for an average yield loss of US $ 80 million annually in India alone [1]
We present the complete sequence of the mitochondrial genome of the Asian rice gall midge, O. oryzae highlighting its unique features such as highly rearranged gene order, involving both protein-coding genes (PCGs) and tRNAs; tandem repeats at two separate non-coding regions which have the potential to differentiate gall midge biotypes and species of the genus and truncation in the predicted secondary structures of the tRNAs
The mitogenome has the typical number of 37 genes, 13 PCGs, 2 rRNAs and 22 tRNAs (Table 1), as reported for other insects
Summary
The Asian rice gall midge, Orseolia oryzae (Diptera: Cecidomyiidae) is an important pest of rice that is responsible for an average yield loss of US $ 80 million annually in India alone [1]. Biological and chemical control methods have been employed to alleviate this loss. The most effective method of controlling the pest has been the development of resistant rice varieties whose extensive cultivation could be responsible for the emergence of new virulent biotypes and breakdown of host resistance genes [2,3]. To get a better understanding of the PLOS ONE | DOI:10.1371/journal.pone.0134625. The Asian Rice Gall Midge Mitogenome oryzivora and O. fluvialis are [GenBank:KP109819KP109820], respectively
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