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

PLoS One. 2015 Jul 30;10(7):e0134625. doi: 10.1371/journal.pone.0134625. eCollection 2015.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Codon, Initiator / genetics
  • Codon, Terminator / genetics
  • Diptera / genetics*
  • Genes, Insect / genetics*
  • Genome, Insect / genetics*
  • Mitochondria / genetics*
  • Molecular Sequence Data
  • Phylogeny
  • Polymerase Chain Reaction
  • RNA, Ribosomal / genetics
  • RNA, Transfer / genetics
  • RNA, Untranslated / genetics
  • Tandem Repeat Sequences / drug effects*

Substances

  • Codon, Initiator
  • Codon, Terminator
  • RNA, Ribosomal
  • RNA, Untranslated
  • RNA, Transfer

Associated data

  • GENBANK/KM888183
  • GENBANK/KM894411
  • GENBANK/KM894412
  • GENBANK/KM894413
  • GENBANK/KP109815
  • GENBANK/KP109816
  • GENBANK/KP109817
  • GENBANK/KP109818
  • GENBANK/KP109819
  • GENBANK/KP109820
  • GENBANK/KP261027
  • GENBANK/KP261028

Grants and funding

Research on rice gall midge and gall midge-rice interaction in SN’s laboratory is partially supported by core grants from ICGEB and extramural funding from the Department of Biotechnology (DBT) and the Indian Council of Agricultural Research (ICAR), Government of India. JSB wishes to acknowledge extramural funding from DBT and ICAR. IA thanks the University Grants Commission (UGC), Government of India, for a Senior Research Fellowship.