Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies

<p>Abstract</p> <p>Background</p> <p>Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. <it>Calanus sinicus </it>dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies.</p> <p>Results</p> <p>The mitochondrial genome of <it>C. sinicus </it>is distinct from other arthropods owing to the concurrence of multiple non-coding regions and a reshuffled gene arrangement. Further particularities in the mitogenome of <it>C. sinicus </it>include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes <it>atp6 </it>and <it>atp8 </it>relative to other copepods. The monophyletic Copepoda should be placed within the Vericrustacea. The close affinity between Cyclopoida and Poecilostomatoida suggests reassigning the latter as subordinate to the former. Monophyly of Maxillopoda is rejected. Within the alignment of 11 <it>C. sinicus </it>mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci.</p> <p>Conclusion</p> <p>The occurrence of the <it>circular subgenomic fragment </it>during laboratory assays suggests that special caution should be taken when sequencing mitogenomes using long PCR. Such a phenomenon may provide additional evidence of mitochondrial DNA recombination, which appears to have been a prerequisite for shaping the present mitochondrial profile of <it>C. sinicus </it>during its evolution. The lack of synapomorphic gene arrangements among copepods has cast doubt on the utility of gene order as a useful molecular marker for deep phylogenetic analysis. However, mitochondrial genomic sequences have been valuable markers for resolving phylogenetic issues concerning copepods. The variable site maps of <it>C. sinicus </it>mitogenomes provide a solid foundation for population genetic studies.</p

The Excess of Small Inverted Repeats in Prokaryotes

Recent analyses have shown that there is a large excess of perfect inverted repeats in many prokaryotic genomes but not in eukaryotic ones. This difference could be due to a genuine difference between prokaryotes and eukaryotes or to differences in the methods and types of data analyzed ¿ full genome versus protein coding sequences. We used simulations to show that the method used previously tends to underestimate the expected number of inverted repeats. However, this bias is not large and cannot explain the excess of inverted repeats observed in real data. In contrast, our method is unbiased. When both methods are applied to bacterial protein coding sequences they both detect an excess of inverted repeats, which is much lower than previously reported in whole prokaryotic genomes. This suggests that the reported large excess of inverted repeats is due to repeats found in intergenic regions. These repeats could be due to transcription factor binding sites, or other types of repetitive DNA, on opposite strands of the DNA sequence. In contrast, the smaller, but significant, excess of inverted repeats that we report in protein coding sequences may be due to sequence-directed mutagenesis (SDM). SDM is a process where one copy of a small, imperfect, inverted repeat corrects the other copy via strand misalignment, resulting in a perfect repeat and a series of mutations. We show by simulation that even very low levels of SDM, relative to the rate of point mutation, can generate a substantial excess of inverted repeats

Species status and population structure of mussels (Mollusca: Bivalvia: Mytilus spp.) in the Wadden Sea of Lower Saxony (Germany)

Three species of mussel (genus Mytilus) occur in Europe: M. edulis (Linnaeus 1758), M. galloprovincialis (Lamarck 1819) and M. trossulus (Gould, Boston Society of Natural History 3:343-348, 1850). Although these species are indigenous to the North Sea, the Mediterranean and the Baltic Sea, respectively, they form an extended patchy species complex along the coasts of Europe ("the Mytilus edulis complex") and are able to hybridize where their distributions overlap. Recent studies examining the taxonomic status and genetic composition of Mytilus populations in the Netherlands and the British Isles have revealed introgressive hybridization processes within this species complex, with hints of an invasion of nonindigenous M. galloprovincialis into the North Sea. Furthermore, an extensive international mussel fishery industry in Europe (i.e., Great Britain, the Netherlands, Denmark, and Germany) is also in discussion for a possibly anthropogenically induced bioinvasion of nonindigenous Mytilus traits into the Wadden Sea area. Although it is assumed that the Wadden Sea of Germany comprises M. edulis only, this has never been confirmed in a molecular genetic study. To assess the situation for the Wadden Sea of Lower Saxony, we conducted the first molecular study of the Mytilus genus in the region. Taxonomic identification of 504 mussels from 13 intertidal mussel banks using the nDNA marker Me15/16 revealed a population composition of 99% M. edulis and 1% M. edulis X M. galloprovincialis hybrids. Hence, the Wadden Sea population is unaffected by range expansion of nonindigenous Mytilus traits. The genetic structure of the M. edulis populations was investigated using the phylogenetic and population genetics analyses of the mitochondrial DNA cytochrome-c-oxidase subunit I (COI) and the first variable domain of the control region (VD1), which were sequenced for >120 female individuals. These results showed a heterogeneous, panmictic population due to unrestricted gene flow. This can be attributed to extensive larval dispersal linked to the tidal circulation system in the back barrier basins of the Wadden Sea

Novel mitochondrial gene content and gene arrangement indicate illegitimate inter-mtDNA recombination in the chigger mite, Leptotrombidium pallidum

To better understand the evolution of mitochondrial (mt) genomes in the Acari (mites and ticks), we sequenced the mt genome of the chigger mite, Leptotrombidium pallidum (Arthropoda: Acari: Acariformes). This genome is highly rearranged relative to that of the hypothetical ancestor of the arthropods and the other species of Acari studied. The mt genome of L. pallidum has two genes for large subunit rRNA, a pseudogene for small subunit rRNA, and four nearly identical large noncoding regions. Nineteen of the 22 tRNAs encoded by this genome apparently lack either a T-arm or a D-arm. Further, the mt genome of L. pallidum has two distantly separated sections with identical sequences but opposite orientations of transcription. This arrangement cannot be accounted for by homologous recombination or by previously known mechanisms of mt gene rearrangement. The most plausible explanation for the origin of this arrangement is illegitimate inter-mtDNA recombination, which has not been reported previously in animals. In light of the evidence from previous experiments on recombination in nuclear and mt genomes of animals, we propose a model of illegitimate inter-mtDNA recombination to account for the novel gene content and gene arrangement in the mt genome of L. pallidum

Complete Anopheles funestus mitogenomes reveal an ancient history of mitochondrial lineages and their distribution in southern and central Africa

Anopheles funestus s.s. is a primary vector of malaria in sub-Saharan Africa. Despite its important role in human Plasmodium transmission, evolutionary history, genetic diversity, and population structure of An. funestus in southern and central Africa remains understudied. We deep sequenced, assembled, and annotated the complete mitochondrial genome of An. funestus s.s. for the first time, providing a foundation for further genetic research of this important malaria vector species. We further analyzed the complete mitochondrial genomes of 43 An. funestus s.s. from three sites in Zambia, Democratic Republic of the Congo, and Tanzania. From these 43 mitogenomes we identified 41 unique haplotypes that comprised 567 polymorphic sites. Bayesian phylogenetic reconstruction confirmed the co-existence of two highly divergent An. funestus maternal lineages, herein defined as lineages I and II, in Zambia and Tanzania. The estimated coalescence time of these two mitochondrial lineages is ~500,000 years ago (95% HPD 426,000-594,000 years ago) with subsequent independent diversification. Haplotype network and phylogenetic analysis revealed two major clusters within lineage I, and genetic relatedness of samples with deep branching in lineage II. At this time, data suggest that the lineages are partially sympatric. This study illustrates that accurate retrieval of full mitogenomes of Anopheles vectors enables fine-resolution studies of intraspecies genetic relationships, population differentiation, and demographic history. Further investigations on whether An. funestus mitochondrial lineages represent biologically meaningful populations and their potential implications for malaria vector control are warranted