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Comparative Study
. 2011 Oct;41(10):770-7.
doi: 10.1016/j.ibmb.2011.05.006. Epub 2011 May 27.

Complete sequences of mitochondria genomes of Aedes aegypti and Culex quinquefasciatus and comparative analysis of mitochondrial DNA fragments inserted in the nuclear genomes

Susanta K Behura  1 , Neil F Lobo, Brian Haas, Becky deBruyn, Diane D Lovin, Martin F Shumway, Daniela Puiu, Jeanne Romero-Severson, Vishvanath Nene, David W Severson
Affiliations
Comparative Study

Complete sequences of mitochondria genomes of Aedes aegypti and Culex quinquefasciatus and comparative analysis of mitochondrial DNA fragments inserted in the nuclear genomes

Susanta K Behura et al. Insect Biochem Mol Biol. 2011 Oct.

Abstract

We present complete sequences of the mitochondrial genomes for two important mosquitoes, Aedes aegypti and Culex quinquefasciatus, that are major vectors of dengue virus and lymphatic filariasis, respectively. The A. aegypti mitochondrial genome is 16,655 bp in length and that of C. quinquefasciatus is 15,587 bp, yet both contain 13 protein coding genes, 22 transfer RNA (tRNA) genes, one 12S ribosomal RNA (rRNA) gene, one 16S rRNA gene and a control region (CR) in the same order. The difference in the genome size is due to the difference in the length of the control region. We also analyzed insertions of nuclear copies of mtDNA-like sequences (NUMTs) in a comparative manner between the two mosquitoes. The NUMT sequences occupy ~0.008% of the A. aegypti genome and ~0.001% of the C. quinquefasciatus genome. Several NUMTs were found localized in the introns of predicted protein coding genes in both genomes (32 genes in A. aegypti but only four in C. quinquefasciatus). None of these NUMT-containing genes had an ortholog between the two species or had paralogous copies within a genome that was also NUMT-containing. It was further observed that the NUMT-containing genes were relatively longer but had lower GC content compared to the NUMT-less paralogous copies. Moreover, stretches of homologies are present among the genic and non-genic NUMTs that may play important roles in genomic rearrangement of NUMTs in these genomes. Our study provides new insights on understanding the roles of nuclear mtDNA sequences in genome complexities of these mosquitoes.

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Figures

Figure 1
Figure 1
The circular map of Aedes aegypti and Culex quinquefasciatus mtDNA. The predicted genes are labeled and color-coded; protein coding genes: blue, tRNA genes: red, rRNA genes: purple and control region (CR): grey. The gene names are labeled outside the circle.
Figure 2
Figure 2
Amount of NUMTs (in bp per 100 kb of genomic DNA) in the genome of the three mosquitoes and D. melanogaster and its comparison to species phylogeny and genome size. The estimated times of divergence are shown on the common ancestral nodes in millions of years. The tree is not shown to scale; it only shows the phylogenetic relationships. The species names are shown corresponding to each branch. The amount of NUMTs (in bp per 100 kb of genomic DNA) as well as the estimated genome size (in Mb) are shown on the right to each species.
Figure 3
Figure 3
Duplication of NUMT pairs in the genome of Aedes aegypti. Four NUMT pairs are shown (A-D). In each, the mtDNA sequences are shown on the top and the corresponding nuclear sequences are shown below (with the supercontig ID). The distance between their homolog sequences in the mtDNA is shown in each case. The arrows indicate their insertion in different supercontigs and their orientations based on the relative positions of one of the termini sequences (AAA) that is highlighted in black (also see Table 2).
Figure 4
Figure 4
Sequence deletion and end-joining of NUMT sequences. A) A 9-bp sequence (shown by a curve) was deleted as the left- and right- sequences were joined at the direct termini motif ‘CTCA’. B) A portion (641 bp, shown by curve) was deleted as the left- and right- sequences were joined at the direct termini motif ‘ATTT’.
Figure 5
Figure 5
Example of multiple events associated with NUMT rearrangements. The top panel shows three regions within positions 1946-2141 of the mtDNA of A. aegypti. Sequence-1 and -2 are overlapping (1 bp overlap), while sequence-3 is 9 bp from sequence-2. The bottom panel shows the structure of the NUMTs corresponding to these three sequences. They are located in a cluster in supercontig1.495. NUMT-2 and -3 are overlapping (by 3 bp) in the supercontig (position: 486627-486763). NUMT 1 is located 728 bp from NUMT 2 (position: 485851-486692).
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