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

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.

Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies

“…Recent study using concatenated twelve mitochondrial genes showed that Harpacticoida ( Tigriopus californicus ) was more closely related to Siphonostomatoida ( Lepeophtheirus salmonis and Caligus rogercresseyi ) than Calanoida ( Calanus sinicus ) (Fig. 2d) [23]. This mitochondrial phylogenetic hypothesis was generally congruent with the majority of the morphological phylogenies [5, 12, 13] except for the phylogenetic position of Poecilostomatoida (Fig.…”

Postglacial expansion of the Arctic keystone copepod Calanus glacialis

“…The PCR product, covering 1465 base pairs (bp) of the mitochondrial ND5 gene encoding the fifth subunit of the respiratory chain complex I (NADH dehydrogenase subunit 5), was obtained. This fragment was chosen based on the length of mitochondrial genes, their intermediate intra-and interspecies polymorphism in comparison to conserved CYTB, cytochrome oxidase subunit I (COI) and highly variable NADH dehydrogenase subunits 3 and 4 (ND3 and ND4) genes in the copepod subclass (Minxiao et al 2011).…”

Population Genomics of Marine Zooplankton

“…2; Jung et al 2006;Minxiao et al 2011). The most exceptional cases of mitochondrial variability documented to date are in the chaetognaths, Spadella cephaloptera and Sagitta elegans, for which natural populations exhibit unprecedented levels of intra-specific divergence (Marlétaz et al 2017).…”

“…Within the chaetognaths, mitogenomes are also very reduced compared to other metazoans, missing several common genes (Helfenbein et al 2004;Papillon et al 2004). On the other hand, the longest mitogenomes documented belong to the Copepods, up to 20 kb (Minxiao et al 2011). Several mitogenomes were found to contain multiple copies of some sequences (Ogoh and Ohmiya 2004;Burton et al 2007), or short tandem repeats, similar to microsatellites (Shen et al 2011). 19.2.3.4.…”