Abstract
BackgroundCopepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus 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.ResultsThe mitochondrial genome of C. sinicus 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 C. sinicus include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes atp6 and atp8 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 C. sinicus mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci.ConclusionThe occurrence of the circular subgenomic fragment 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 C. sinicus 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 C. sinicus mitogenomes provide a solid foundation for population genetic studies.
Highlights
Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems
The circular subgenomic fragment obtained invoked caution when analyzing the mitogenome of copepods using long polymerase chain reaction (PCR) technology, and may offer additional evidence for mitochondrial recombination
The contents and lengths of individual genes are similar to other arthropods, the mitogenome of C. sinicus, one of the largest mitochondrial DNA (mtDNA) in crustaceans, is enlarged by the prevalence and extended length of noncoding regions
Summary
Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. Copepods play an important role in the aquatic ecosystem and are highly diverse. They comprise a multitude of taxa including 200 families, 1,650 genera and 11,500 species [1], this estimation may represent only 15% of the actual number [2]. Phylogenetic studies are required to develop a complete biodiversity inventory of the group, which will enable the question of how copepods have acquired such diversity over time to be investigated. Since the incorporation of copepods as a monophyletic group in 1859, phylogenetic studies have focused on the natural relationships between the incorporated orders, Calanoida, Cyclopoida, Gellyelloida, Harpacticoida, Misophrioida, Monstrilloida, Mormonilloida, Platycopioida, Poecilostomatoida and Siphonostomatoida [3]. The recent ambiguous status of copepod phylogenetic research is due at least in part to the limited diagnostic morphological characteristics, difficulty in accessing morphological homology and a poor fossil record
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