The single mitochondrial chromosome typical of animals has evolved into 18 minichromosomes in the human body louse, Pediculus humanus

Abstract

The mitochondrial (mt) genomes of animals typically consist of a single circular chromosome that is approximately 16-kb long and has 37 genes. Our analyses of the sequence reads from the Human Body Louse Genome Project and the patterns of gel electrophoresis and Southern hybridization revealed a novel type of mt genome in the sucking louse, Pediculus humanus. Instead of having all mt genes on a single chromosome, the 37 mt genes of this louse are on 18 minicircular chromosomes. Each minicircular chromosome is 3-4 kb long and has one to three genes. Minicircular mt chromosomes are also present in the four other species of sucking lice that we investigated, but not in chewing lice nor in the Psocoptera, to which sucking lice are most closely related. We also report unequivocal evidence for recombination between minicircular mt chromosomes in P. humanus and for sequence variation in mt genes generated by recombination. The advantages of a fragmented mt genome, if any, are currently unknown. Fragmentation of mt genome, however, has coevolved with blood feeding in the sucking lice. It will be of interest to explore whether or not life history features are associated with the evolution of fragmented chromosomes.

Figure 1.

(A) The typical mitochondrial (mt) genome of animals, represented here by a fruitfly, Drosophila yakuba; (B) the mt genome of the human body louse, Pediculus humanus. The mt genome of Drosophila yakuba consists of a single circular chromosome that is 16,019-bp long and has 37 genes (GenBank accession no. NC_001322). The mt genome of P. humanus, however, consists of 18 minicircular chromosomes; each minicircular chromosome is 3000–4000-bp long and has one to three genes. Genes are represented as boxes and are drawn to scale. The length of each gene of P. humanus is indicated near the box that represents the gene. Arrows indicate the direction of transcription. Protein-coding genes are abbreviated as atp6 and atp8 (for ATP synthase subunits 6 and 8), cox1-3 (for cytochrome c oxidase subunits 1 to 3), cob (for cytochrome b), and nad1-6 and 4L (for NADH dehydrogenase subunits 1–6 and 4L). rrnL and rrnS are for large and small rRNA subunits. tRNA genes are shown with the single-letter abbreviations of their corresponding amino acids. The noncoding regions are in black. The 18 minichromosomes of P. humanus are in alphabetical order according to the names of their protein-coding and rRNA genes; those with only tRNA genes are in the last row.

Figure 2.

Agarose gel electrophoresis (left) and Southern hybridization (right) of the mitochondrial (mt) DNA of a fruitfly, D. melanogaster; a mouse, Mus musculus; and the human body louse, P. humanus. (Lanes 1,9) Two microliters low mass ladder DNA marker (Invitrogen); (lane 2) EcoRI-digested mtDNA extracted from182 mg of fruitflies; (lanes 3,5,6) 2 μL DNA molecular weight marker X (Roche); (lane 4) BamHI-digested mtDNA extracted from 36 mg of mouse liver tissues; (lane 7) undigested mtDNA extracted from 212 mg of human body lice; (lane 8) ApaI-digested mtDNA extracted from 212 mg of human body lice. The fruitfly and the mouse were experimental controls. As expected, the 19,517-bp mt chromosome of the fruitfly was cut into four fragments by EcoRI: ∼12,000, ∼5500, ∼1700, and ∼900 bp (lane 2); and the 16,300-bp mt chromosome of the mouse was cut into three fragments by BamHI: ∼8600, ∼7000, and ∼700 bp (lane 4). The undigested mtDNA of P. humanus migrated as a smear with a predominant size of 6000–9000 bp (lane 7), whereas the ApaI-digested mtDNA of P. humanus appeared as a block that ranges from 3000 to 4000 bp (lane 8).

Figure 3.

Alignment of the nucleotide sequences of the noncoding regions from plasmid clones with the cox1 (three clones), nad4 (two clones), and nad5 (four clones) minicircular mitochondrial chromosomes. Dashes indicate gaps. The three highly conserved blocks of sequences at the start, middle, and end of the noncoding region are boxed. The sequence that can form a stem-loop is marked with asterisks (see also Fig. 5). The coding region (data not shown) of each clone is located between the end and start of these noncoding regions.

Figure 4.

An unrooted neighbor-joining (NJ) tree inferred from the nucleotide sequences of the noncoding regions of cox1, nad4, and nad5 minicircular mitochondrial chromosomes (see also Fig. 3). Gaps in sequence alignment were excluded. Bootstrap support in percentage (1000 replicates) is shown near each branch. Noncoding regions (e.g., cox1.1) are named after the minicircular chromosome and the plasmid clone number.

Figure 5.

A putative stem-loop in the 302-bp highly conserved segment of the noncoding regions of the minicircular mitochondrial chromosomes of the human body louse, P. humanus.

Figure 6.

Evolution of minicircular mitochondrial (mt) chromosomes in the sucking lice of primates. The phylogeny of the sucking lice of primates and the estimate of the date of their most recent common ancestor (22.5 Mya) are after Barker et al. (2003) and Reed et al. (2004). The preferred habitats of lice on humans (i.e., body, head, and pubis) are in parentheses. The 18 minicircular mt chromosomes of the human body louse were sequenced entirely; the minicircular mt chromosomes of other lice were partially sequenced or identified by PCR tests (underlined). Hyphens link neighboring genes on the same minicircular chromosome.