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Fragmented mitochondrial genomes in two suborders of parasitic lice of eutherian mammals (Anoplura and Rhynchophthirina, Insecta).

Shao R, Barker SC, Li H, Song S, Poudel S, Su Y - Sci Rep (2015)

Bottom Line: The typical animal mitochondrial (mt) genome organization, which consists of a single chromosome with 37 genes, was found in chewing lice in the suborders Amblycera and Ischnocera.Each minichromosome is 3.5-4.2 kb in size and has 2-6 genes.Our results indicate that mt genome fragmentation is shared by the suborders Anoplura and Rhynchophthirina.

View Article: PubMed Central - PubMed

Affiliation: GeneCology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland 4556, Australia.

ABSTRACT
Parasitic lice (order Phthiraptera) infest birds and mammals. The typical animal mitochondrial (mt) genome organization, which consists of a single chromosome with 37 genes, was found in chewing lice in the suborders Amblycera and Ischnocera. The sucking lice (suborder Anoplura) known, however, have fragmented mt genomes with 9-20 minichromosomes. We sequenced the mt genome of the elephant louse, Haematomyzus elephantis - the first species of chewing lice investigated from the suborder Rhynchophthirina. We identified 33 mt genes in the elephant louse, which were on 10 minichromosomes. Each minichromosome is 3.5-4.2 kb in size and has 2-6 genes. Phylogenetic analyses of mt genome sequences confirm that the elephant louse is more closely related to sucking lice than to the chewing lice in the Amblycera and Ischnocera. Our results indicate that mt genome fragmentation is shared by the suborders Anoplura and Rhynchophthirina. Nine of the 10 mt minichromosomes of the elephant louse differ from those of the sucking lice (Anoplura) known in gene content and gene arrangement, indicating that distinct mt karyotypes have evolved in Anoplura and Rhynchophthirina since they diverged ~92 million years ago.

No MeSH data available.


Related in: MedlinePlus

(A) Mitochondrial minichromosomes of the elephant louse, Haematomyzus elephantis. Arrows indicate protein-coding and rRNA genes: cox1-3 for cytochrome c oxidase subunits 1–3, cob for cytochrome b, nad1-5 and nad4L for NADH dehydrogenase subunits 1–5 and 4L, rrnS and rrnL for small and large ribosome RNA subunits. Triangles indicate tRNA genes (labeled with single-letter abbreviations of their corresponding amino acids). Numbers near each gene indicate gene length in bp. Non-coding regions are in black. Drawing of elephant louse was by Hu Li. (B) Verification of mitochondrial minichromosomes of H. elephantis by PCR. Lanes 1–11: amplicons from minichromosomes T-nad1-Q, S2(tga)-R-nad4L-M-G-nad3, K-nad4-C, H-nad5, I-cox1-E, Y-cox2-E, atp8-atp6-P-cox3, cob-A-W-F-nad6, L1(tag)-rrnL-V, L2(taa)-rrnS, and H-nad5 (genes from which PCR primers were designed are in bold). Lanes 12-13: DNA Molecular Weight Marker VII (Roche) and Low DNA Mass Ladder (Life Technologies). (C) PCR amplicons with elephant-louse-specific primers (see also Table S5). (C1) Lane 1: primer pair EL16SF-EL16SR, which amplified trnL1(tag)-rrnL-trnV minichromosome in near full length. Lanes 2, 5 and 6: negative controls for EL16SF-LX16SR that had no forward primer, no reverse primer and no DNA template respectively. Lanes 3 and 4: Low Mass Ladder (LML) and DNA Molecular Weigh Marker X (DMWMX). Lane 7: primer pair ELC1F-ELC1R, which amplified trnI-cox1-trnE minichromosome in near full length. Lanes 8, 9 and 10: negative controls for ELC1F-ELC1R that had no forward primer, no reverse primer and no DNA template respectively. (C2) Lane 1: primer pair ELC2F-ELC2R1, which amplified trnY-cox2-trnE minichromosome in near full length. Lanes 2, 3 and 4: negative controls for ELC2F-ELC2R1 that had no forward primer, no reverse primer and no DNA template respectively. Lanes 6 and 7: DMWMX and LML. Lane 8: primer pair EL12SF1-EL12SR, which amplified trnL2(taa)-rrnS minichromosome in near full length. Lanes 9, 10 and 11: negative controls for EL12SF1-EL12SR that had no forward primer, no reverse primer and no DNA template respectively. (C3) Lanes 1 and 2: amplicons produced by the primer pair USFB1567-ELR from the full-length coding regions of all mitochondrial minichromosomes. Lane 3: LML.
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f1: (A) Mitochondrial minichromosomes of the elephant louse, Haematomyzus elephantis. Arrows indicate protein-coding and rRNA genes: cox1-3 for cytochrome c oxidase subunits 1–3, cob for cytochrome b, nad1-5 and nad4L for NADH dehydrogenase subunits 1–5 and 4L, rrnS and rrnL for small and large ribosome RNA subunits. Triangles indicate tRNA genes (labeled with single-letter abbreviations of their corresponding amino acids). Numbers near each gene indicate gene length in bp. Non-coding regions are in black. Drawing of elephant louse was by Hu Li. (B) Verification of mitochondrial minichromosomes of H. elephantis by PCR. Lanes 1–11: amplicons from minichromosomes T-nad1-Q, S2(tga)-R-nad4L-M-G-nad3, K-nad4-C, H-nad5, I-cox1-E, Y-cox2-E, atp8-atp6-P-cox3, cob-A-W-F-nad6, L1(tag)-rrnL-V, L2(taa)-rrnS, and H-nad5 (genes from which PCR primers were designed are in bold). Lanes 12-13: DNA Molecular Weight Marker VII (Roche) and Low DNA Mass Ladder (Life Technologies). (C) PCR amplicons with elephant-louse-specific primers (see also Table S5). (C1) Lane 1: primer pair EL16SF-EL16SR, which amplified trnL1(tag)-rrnL-trnV minichromosome in near full length. Lanes 2, 5 and 6: negative controls for EL16SF-LX16SR that had no forward primer, no reverse primer and no DNA template respectively. Lanes 3 and 4: Low Mass Ladder (LML) and DNA Molecular Weigh Marker X (DMWMX). Lane 7: primer pair ELC1F-ELC1R, which amplified trnI-cox1-trnE minichromosome in near full length. Lanes 8, 9 and 10: negative controls for ELC1F-ELC1R that had no forward primer, no reverse primer and no DNA template respectively. (C2) Lane 1: primer pair ELC2F-ELC2R1, which amplified trnY-cox2-trnE minichromosome in near full length. Lanes 2, 3 and 4: negative controls for ELC2F-ELC2R1 that had no forward primer, no reverse primer and no DNA template respectively. Lanes 6 and 7: DMWMX and LML. Lane 8: primer pair EL12SF1-EL12SR, which amplified trnL2(taa)-rrnS minichromosome in near full length. Lanes 9, 10 and 11: negative controls for EL12SF1-EL12SR that had no forward primer, no reverse primer and no DNA template respectively. (C3) Lanes 1 and 2: amplicons produced by the primer pair USFB1567-ELR from the full-length coding regions of all mitochondrial minichromosomes. Lane 3: LML.

Mentions: We obtained 14,760 and 1,137,360 sequence-reads from the amplicons of the mt genome of the elephant louse, H. elephantis, by Roche 454 sequencing and Illumina Hiseq sequencing, respectively (Table 1, Table 2). Roche sequence-reads are 100–611 bp in size (mean 344 bp, standard deviation 108); Illumina sequence-reads are all 90 bp in size. We assembled these sequence-reads into contigs and identified 33 of the 37 mt genes typical of bilateral animals. These genes are on 10 minichromosomes; each minichromosome is 3.5–4.2 kb in size and consists of a coding region and a non-coding region (NCR) in a circular organization (Fig. 1A,B). The coding regions have 2–6 genes each and vary in size from 857 bp to 1,879 bp (Table 1; Fig. 1A). All of the mt genes of the elephant louse have the same orientation of transcription relative to the NCRs, except for trnT, nad1 and trnQ, which form a cluster and have an opposite orientation of transcription to that of other genes (Fig. 1A; see Fig. 1 legend for the full name of each mt gene). With the exception of trnE, all of the mt genes we identified in the elephant louse were found in only one type of minichromosome. trnE gene was found in two types of minichromosomes in the elephant louse: one in the trnI-cox1-trnE minichromosome and the other in the trnY-cox2-trnE minichromosome (Note: minichromosomes are named after the genes they contain hereafter). Further, the two copies of trnE gene have identical sequences to each other. We did not find trnD, trnN, trnS1(tct) and nad2 genes in the sequence-reads of the elephant louse generated by Roche sequencing, nor Illumina sequencing. A possible explanation is that the primer pair USFB1567–ELR, which we used to amplify the coding regions of the mt minichromosomes of the elephant louse, are not conserved in the minichromosome(s) that contain trnD, trnN, trnS1(tct) and nad2 genes; these minichromosome(s) were thus not amplified by the PCR with USFB1567–ELR.


Fragmented mitochondrial genomes in two suborders of parasitic lice of eutherian mammals (Anoplura and Rhynchophthirina, Insecta).

Shao R, Barker SC, Li H, Song S, Poudel S, Su Y - Sci Rep (2015)

(A) Mitochondrial minichromosomes of the elephant louse, Haematomyzus elephantis. Arrows indicate protein-coding and rRNA genes: cox1-3 for cytochrome c oxidase subunits 1–3, cob for cytochrome b, nad1-5 and nad4L for NADH dehydrogenase subunits 1–5 and 4L, rrnS and rrnL for small and large ribosome RNA subunits. Triangles indicate tRNA genes (labeled with single-letter abbreviations of their corresponding amino acids). Numbers near each gene indicate gene length in bp. Non-coding regions are in black. Drawing of elephant louse was by Hu Li. (B) Verification of mitochondrial minichromosomes of H. elephantis by PCR. Lanes 1–11: amplicons from minichromosomes T-nad1-Q, S2(tga)-R-nad4L-M-G-nad3, K-nad4-C, H-nad5, I-cox1-E, Y-cox2-E, atp8-atp6-P-cox3, cob-A-W-F-nad6, L1(tag)-rrnL-V, L2(taa)-rrnS, and H-nad5 (genes from which PCR primers were designed are in bold). Lanes 12-13: DNA Molecular Weight Marker VII (Roche) and Low DNA Mass Ladder (Life Technologies). (C) PCR amplicons with elephant-louse-specific primers (see also Table S5). (C1) Lane 1: primer pair EL16SF-EL16SR, which amplified trnL1(tag)-rrnL-trnV minichromosome in near full length. Lanes 2, 5 and 6: negative controls for EL16SF-LX16SR that had no forward primer, no reverse primer and no DNA template respectively. Lanes 3 and 4: Low Mass Ladder (LML) and DNA Molecular Weigh Marker X (DMWMX). Lane 7: primer pair ELC1F-ELC1R, which amplified trnI-cox1-trnE minichromosome in near full length. Lanes 8, 9 and 10: negative controls for ELC1F-ELC1R that had no forward primer, no reverse primer and no DNA template respectively. (C2) Lane 1: primer pair ELC2F-ELC2R1, which amplified trnY-cox2-trnE minichromosome in near full length. Lanes 2, 3 and 4: negative controls for ELC2F-ELC2R1 that had no forward primer, no reverse primer and no DNA template respectively. Lanes 6 and 7: DMWMX and LML. Lane 8: primer pair EL12SF1-EL12SR, which amplified trnL2(taa)-rrnS minichromosome in near full length. Lanes 9, 10 and 11: negative controls for EL12SF1-EL12SR that had no forward primer, no reverse primer and no DNA template respectively. (C3) Lanes 1 and 2: amplicons produced by the primer pair USFB1567-ELR from the full-length coding regions of all mitochondrial minichromosomes. Lane 3: LML.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4663631&req=5

f1: (A) Mitochondrial minichromosomes of the elephant louse, Haematomyzus elephantis. Arrows indicate protein-coding and rRNA genes: cox1-3 for cytochrome c oxidase subunits 1–3, cob for cytochrome b, nad1-5 and nad4L for NADH dehydrogenase subunits 1–5 and 4L, rrnS and rrnL for small and large ribosome RNA subunits. Triangles indicate tRNA genes (labeled with single-letter abbreviations of their corresponding amino acids). Numbers near each gene indicate gene length in bp. Non-coding regions are in black. Drawing of elephant louse was by Hu Li. (B) Verification of mitochondrial minichromosomes of H. elephantis by PCR. Lanes 1–11: amplicons from minichromosomes T-nad1-Q, S2(tga)-R-nad4L-M-G-nad3, K-nad4-C, H-nad5, I-cox1-E, Y-cox2-E, atp8-atp6-P-cox3, cob-A-W-F-nad6, L1(tag)-rrnL-V, L2(taa)-rrnS, and H-nad5 (genes from which PCR primers were designed are in bold). Lanes 12-13: DNA Molecular Weight Marker VII (Roche) and Low DNA Mass Ladder (Life Technologies). (C) PCR amplicons with elephant-louse-specific primers (see also Table S5). (C1) Lane 1: primer pair EL16SF-EL16SR, which amplified trnL1(tag)-rrnL-trnV minichromosome in near full length. Lanes 2, 5 and 6: negative controls for EL16SF-LX16SR that had no forward primer, no reverse primer and no DNA template respectively. Lanes 3 and 4: Low Mass Ladder (LML) and DNA Molecular Weigh Marker X (DMWMX). Lane 7: primer pair ELC1F-ELC1R, which amplified trnI-cox1-trnE minichromosome in near full length. Lanes 8, 9 and 10: negative controls for ELC1F-ELC1R that had no forward primer, no reverse primer and no DNA template respectively. (C2) Lane 1: primer pair ELC2F-ELC2R1, which amplified trnY-cox2-trnE minichromosome in near full length. Lanes 2, 3 and 4: negative controls for ELC2F-ELC2R1 that had no forward primer, no reverse primer and no DNA template respectively. Lanes 6 and 7: DMWMX and LML. Lane 8: primer pair EL12SF1-EL12SR, which amplified trnL2(taa)-rrnS minichromosome in near full length. Lanes 9, 10 and 11: negative controls for EL12SF1-EL12SR that had no forward primer, no reverse primer and no DNA template respectively. (C3) Lanes 1 and 2: amplicons produced by the primer pair USFB1567-ELR from the full-length coding regions of all mitochondrial minichromosomes. Lane 3: LML.
Mentions: We obtained 14,760 and 1,137,360 sequence-reads from the amplicons of the mt genome of the elephant louse, H. elephantis, by Roche 454 sequencing and Illumina Hiseq sequencing, respectively (Table 1, Table 2). Roche sequence-reads are 100–611 bp in size (mean 344 bp, standard deviation 108); Illumina sequence-reads are all 90 bp in size. We assembled these sequence-reads into contigs and identified 33 of the 37 mt genes typical of bilateral animals. These genes are on 10 minichromosomes; each minichromosome is 3.5–4.2 kb in size and consists of a coding region and a non-coding region (NCR) in a circular organization (Fig. 1A,B). The coding regions have 2–6 genes each and vary in size from 857 bp to 1,879 bp (Table 1; Fig. 1A). All of the mt genes of the elephant louse have the same orientation of transcription relative to the NCRs, except for trnT, nad1 and trnQ, which form a cluster and have an opposite orientation of transcription to that of other genes (Fig. 1A; see Fig. 1 legend for the full name of each mt gene). With the exception of trnE, all of the mt genes we identified in the elephant louse were found in only one type of minichromosome. trnE gene was found in two types of minichromosomes in the elephant louse: one in the trnI-cox1-trnE minichromosome and the other in the trnY-cox2-trnE minichromosome (Note: minichromosomes are named after the genes they contain hereafter). Further, the two copies of trnE gene have identical sequences to each other. We did not find trnD, trnN, trnS1(tct) and nad2 genes in the sequence-reads of the elephant louse generated by Roche sequencing, nor Illumina sequencing. A possible explanation is that the primer pair USFB1567–ELR, which we used to amplify the coding regions of the mt minichromosomes of the elephant louse, are not conserved in the minichromosome(s) that contain trnD, trnN, trnS1(tct) and nad2 genes; these minichromosome(s) were thus not amplified by the PCR with USFB1567–ELR.

Bottom Line: The typical animal mitochondrial (mt) genome organization, which consists of a single chromosome with 37 genes, was found in chewing lice in the suborders Amblycera and Ischnocera.Each minichromosome is 3.5-4.2 kb in size and has 2-6 genes.Our results indicate that mt genome fragmentation is shared by the suborders Anoplura and Rhynchophthirina.

View Article: PubMed Central - PubMed

Affiliation: GeneCology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland 4556, Australia.

ABSTRACT
Parasitic lice (order Phthiraptera) infest birds and mammals. The typical animal mitochondrial (mt) genome organization, which consists of a single chromosome with 37 genes, was found in chewing lice in the suborders Amblycera and Ischnocera. The sucking lice (suborder Anoplura) known, however, have fragmented mt genomes with 9-20 minichromosomes. We sequenced the mt genome of the elephant louse, Haematomyzus elephantis - the first species of chewing lice investigated from the suborder Rhynchophthirina. We identified 33 mt genes in the elephant louse, which were on 10 minichromosomes. Each minichromosome is 3.5-4.2 kb in size and has 2-6 genes. Phylogenetic analyses of mt genome sequences confirm that the elephant louse is more closely related to sucking lice than to the chewing lice in the Amblycera and Ischnocera. Our results indicate that mt genome fragmentation is shared by the suborders Anoplura and Rhynchophthirina. Nine of the 10 mt minichromosomes of the elephant louse differ from those of the sucking lice (Anoplura) known in gene content and gene arrangement, indicating that distinct mt karyotypes have evolved in Anoplura and Rhynchophthirina since they diverged ~92 million years ago.

No MeSH data available.


Related in: MedlinePlus