A protocol for isolating insect mitochondrial genomes: a case study of NUMT in Melipona flavolineata (Hymenoptera: Apidae)

Abstract The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.

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From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity

Computational Biology and Chemistry ◽

10.1016/j.compbiolchem.2016.02.016 ◽

2016 ◽

Vol 61 ◽

pp. 258-269 ◽

Cited By ~ 4

Author(s):

Elizabeth Misas ◽

José Fernando Muñoz ◽

Juan Esteban Gallo ◽

Juan Guillermo McEwen ◽

Oliver Keatinge Clay

Keyword(s):

Mitochondrial Genomes ◽

Genome Complexity

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Linear Mitochondrial genome in Anthozoa (Cnidaria): A case study in Ceriantharia

10.7287/peerj.preprints.27042 ◽

2018 ◽

Author(s):

Sergio N Stampar ◽

Michael B Broe ◽

Jason Macrander ◽

Adam M Reitzel ◽

Marymegan Daly

Keyword(s):

Mitochondrial Genome ◽

Gene Order ◽

Mitochondrial Gene ◽

Phylogenetic Position ◽

Mitochondrial Genomes ◽

Gene Sequences ◽

Phylogenetic Placement ◽

Organellar Genome ◽

Linear Mitochondrial Genome

Sequences and structural attributes of mitochondrial genomes have played a key role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia ("tube anemones") remains one of the most enigmatic groups in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both ceriantharian species studied, the mitochondrial gene sequences could not be assembled into a circular genome. Instead, our analyses suggest both species have fragmented mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The number of fragments and the variation in gene order between species is much greater in Ceriantharia than among Medusozoa. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other anthozoan groups.

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Can Long-Range PCR Be Used to Amplify Genetically Divergent Mitochondrial Genomes for Comparative Phylogenetics? A Case Study within Spiders (Arthropoda: Araneae)

PLoS ONE ◽

10.1371/journal.pone.0062404 ◽

2013 ◽

Vol 8 (5) ◽

pp. e62404 ◽

Cited By ~ 10

Author(s):

Andrew G. Briscoe ◽

Sara Goodacre ◽

Susan E. Masta ◽

Martin I. Taylor ◽

Miquel A. Arnedo ◽

...

Keyword(s):

Long Range ◽

Mitochondrial Genomes ◽

Comparative Phylogenetics ◽

Long Range Pcr

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An optimised protocol for barcoding museum collections of decapod crustaceans: a case-study for a 10 - 40-years-old collection

Invertebrate Systematics ◽

10.1071/is12027 ◽

2012 ◽

Vol 26 (6) ◽

pp. 592 ◽

Cited By ~ 9

Author(s):

Dario Zuccon ◽

Julien Brisset ◽

Laure Corbari ◽

Nicolas Puillandre ◽

José Utge ◽

...

Keyword(s):

Mitochondrial Genomes ◽

Museum Collections ◽

Base Pairs ◽

Amplification Success ◽

Coi Barcoding ◽

Amplification Success Rate ◽

Coi Sequences ◽

Amplification Strategy

The sequencing of the crustacean collection of the MNHN, Paris, constitutes a promising yet very challenging barcoding project. For the collection’s crustacean specimens preserved in ethanol, some of which were collected up to 40 years ago, the conventional COI barcoding procedure of amplification with Folmer primers failed for more than half of the specimens (58%, n = 1920). We hypothesised that this failure may have been due to incompatible mismatches between the crustaceans targeted and the Folmer primer sequences and/or the amount of degradation of the DNA extracted from museum specimens. The comparison of the Folmer primers against the COI sequences from GenBank complete decapod mitochondrial genomes revealed that the annealing regions were, in fact, rather conserved, suggesting that the amplification failures were due more likely to the low quality of the DNA isolated. Using an alignment of all available decapod sequences we designed two internal primers in the middle of the barcoding COI region and also selected two additional external primers to be used as alternative to the standard Folmer primers. Using a two-overlapping-fragments amplification strategy and different primer combinations, our new protocol significantly increased the amplification success rate of the collection material from 42% with the Folmer primers to 84%, recovering an additional 364 complete barcodes and 443 minibarcodes (i.e. fragments of less than 400 base pairs), and expanding the species coverage from 254 to 397 barcoded crustaceans.

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Revisiting Ceriantharian (Anthozoa) Mitochondrial Genomes: Casting Doubts about Their Structure and Size

Genome Biology and Evolution ◽

10.1093/gbe/evaa130 ◽

2020 ◽

Vol 12 (8) ◽

pp. 1440-1443

Author(s):

David Roy Smith

Keyword(s):

Mitochondrial Genome ◽

News Media ◽

Chromosome Numbers ◽

Mitochondrial Genomes ◽

Mitochondrial Dnas ◽

Linear Mitochondrial Genome ◽

Significant Attention

Abstract Recently, Stampar et al. (2019. Linear mitochondrial genome in Anthozoa (Cnidaria): a case study in. Sci Rep. 9(1):6094.) uncovered highly atypical mitochondrial genome structures in the cnidarian species Pachycerianthus magnus and Isarachnanthus nocturnus (Anthozoa, Ceriantharia). These two mitochondrial DNAs assembled as linear fragmented genomes, comprising eight and five chromosomes, respectively—architectures unlike any other anthozoan mitogenome described to date. What’s more, they have cumulative lengths of 77.8 (P. magnus) and 80.9 kb (I. nocturnus), making them the largest animal mitochondrial DNAs on record, a finding which garnered significant attention by various news media. Here, I take a closer look at the work of Stampar et al. and question their key results. I provide evidence that the currently available mitogenome sequences for I. nocturnus and P. magnus, including their structures, sizes, and chromosome numbers, should be treated with caution. More work must be done on these genomes before one can say with any certainty that they are linear, fragmented, or the largest animal mitogenomes observed to date.

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Linear Mitochondrial genome in Anthozoa (Cnidaria): A case study in Ceriantharia

10.7287/peerj.preprints.27042v1 ◽

2018 ◽

Author(s):

Sergio N Stampar ◽

Michael B Broe ◽

Jason Macrander ◽

Adam M Reitzel ◽

Marymegan Daly

Keyword(s):

Mitochondrial Genome ◽

Gene Order ◽

Mitochondrial Gene ◽

Phylogenetic Position ◽

Mitochondrial Genomes ◽

Gene Sequences ◽

Phylogenetic Placement ◽

Organellar Genome ◽

Linear Mitochondrial Genome

Sequences and structural attributes of mitochondrial genomes have played a key role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia ("tube anemones") remains one of the most enigmatic groups in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both ceriantharian species studied, the mitochondrial gene sequences could not be assembled into a circular genome. Instead, our analyses suggest both species have fragmented mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The number of fragments and the variation in gene order between species is much greater in Ceriantharia than among Medusozoa. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other anthozoan groups.

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