The mitochondrial genome of Octostruma stenognatha and its phylogenetic implications

Ströher, Patrícia R.; Zarza, Eugenia; Tsai, Whitney L. E.; McCormack, John E.; Feitosa, Rodrigo M.; Pie, Márcio R.

doi:10.1007/s00040-016-0525-8

Cited by 21 publications

(13 citation statements)

References 50 publications

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“…We assembled mitochondrial genome fragments from whole genome shotgun sequencing, but our approach could also be used with reads generated from target capture methods (e.g., ultra-conserved elements (UCEs)). These genome reduction methods target nuclear regions, but mitochondrial reads are also captured at relatively high depth as ''by-catch'' in the process (Amaral et al, 2015;Ströher et al, 2017). Utilizing the ever-growing diversity of genomic data, most of which is publicly available through databases such as GenBank, allows for further exploration of mitochondrial genome architecture and arrangements on a broad taxonomic scale.…”

Section: Assembling Fragmented Mitochondrial Genomes With a Fully Biomentioning

confidence: 99%

Mitochondrial genomes ofColumbicolafeather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice

Sweet

Johnson

Cameron

2020

PeerJ

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Most animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes (“minicircles”) are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between nine and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation. Nevertheless, other work indicates a lesser degree of fragmentation (2–3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genus Columbicola (Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling the Columbicola mitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome of Pediculus humanus from shotgun sequencing reads, a species known to have minicircles. Columbicola spp. genomes are highly fragmented into 15–17 minicircles between ∼1,100 and ∼3,100 bp in length, with 1–4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species of Columbicola represent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice.

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Section: Assembling Fragmented Mitochondrial Genomes With a Fully Biomentioning

confidence: 99%

Mitochondrial genomes ofColumbicolafeather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice

Sweet

Johnson

Cameron

2020

PeerJ

View full text Add to dashboard Cite

show abstract

“…We assembled mitochondrial fragments from whole genome shotgun sequencing, but our approach could also be used with reads generated from target capture methods (e.g., ultra-conserved elements (UCEs)). These genome reduction methods target nuclear regions, but mitochondrial reads are also captured at relatively high depth as "by-catch" in the process (Amaral et al 2015, Ströher et al 2017. Utilizing the ever-growing diversity of genomic data, most of which is publicly available through databases such as GenBank, allows for further exploration of mitochondrial genome architecture and arrangements on a broad taxonomic scale.…”

Section: Assembling Fragmented Mitochondrial Genomes With a Fully Biomentioning

confidence: 99%

Mitochondrial genomes ofColumbicolafeather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice

Sweet

Johnson

Cameron

2019

Preprint

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Most animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes ("minicircles") are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between 9 and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation.Nevertheless, other work indicates a lesser degree of fragmentation (2-3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genus Columbicola (Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling the Columbicola mitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome of Pediculus humanus from shotgun sequencing reads, a species known to have minicircles. All three methods indicated Columbicola spp. genomes are highly fragmented into 15-17 minicircles between 1,119 and 3,173 bp in length, with 1-4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species of Columbicola represent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice.

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“…UCE sequencing data have been previously used to study ant phylogeny (Blaimer et al, 2015; Ward & Branstetter, 2017; Branstetter et al., 2017), but attempts to recover mitochondrial sequences from the off-target data generated are limited (Ströher et al, 2017). Thus, these pieces of information have not been used to further understand evolutionary relationships for the clade.…”

Section: Introductionmentioning

confidence: 99%

Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data

Vieira

Prosdocimi

2019

PeerJ

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The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogenomes in research and presence of mitochondrial data in different public dataset types makes the “no budget mitogenomics” approach ideal for comprehensive molecular studies, especially for subsampled taxa.

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The mitochondrial genome of Octostruma stenognatha and its phylogenetic implications

Cited by 21 publications

References 50 publications

Mitochondrial genomes ofColumbicolafeather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice

Mitochondrial genomes ofColumbicolafeather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice

Mitochondrial genomes ofColumbicolafeather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice

Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data

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