The Analysis Of The Complete Mitochondrial Genome Of Chinese Common Daphnia(Daphniidae:Daphnia)

Cladocerans(“water fleas”) are primarily-freshwater small-sized branchiopod crustaceans, an important monophyletic group of the microcrustacean zooplankton. They inhabit most types of fresh or saline water habitats, and continental saline waters. So far there were fewer than ten species existent in China. Daphnia magna, Daphnia similoides and Daphnia pulex have become well-known model species for studying morphology, population ecology, evolutionary biology, environmental toxicology and ecology. Although other related researthes have been done, there are still some difficulties with species identification. To obtain the complete mitochondrial genome sequences of Daphnia magna and Daphnia pulex, conventional PCR and long-PCR methods were used in this study, and the genetic compositions and structural characteristics were analyzed. The conclusions drawn from this study were shown as follows:(1) The complete mitochondrial genome sequences of Chinese Daphnia magna and Daphnia pulex are 14,948 bp and 15,306 bp in size, respectively. They typically encoded 37 genes, namely: 13 protein-coding genes(PCGs), 2 r RNA genes(16S r RNA and 12 S r RNA), 22 t RNA genes and an A+T-rich region. These genes orders and orientation are identical to that of most arthropod.(2) The nucleotide compositions of every region in mitochondrial genome of Chinese Daphnia magna and Daphnia pulex were no less than 65.00% or 60.00%, respectively. So A+T bias pattern holds for all functional segments of the two Chinese Daphnia.(3) Except for the A+T-rich region, many intergenic spacers and overlap regions with different sizes were found in the two Chinese Daphnia mitochondrial DNA. These intergenic spacers and overlap regions in the whole mt DNA indicated a compact arrangement of the mt genome.(4) In these 13 protein-coding genes, about the usages of start and stop codon, there were some similarities and differences between Chinese Daphnia magna and Daphnia pulex. The similarities showed that classical initiation codon ATG(ND2, COⅡ, ATPase6, COⅢ, Cytb and ND1) and GTG(ATPase8); the differences of Chinese Daphnia magna and Daphnia pulex within start codon showed that COⅠ(CTA and ATA, respectively), ND3(ATG and ATC, respectively), ND5(ATG and GTG, respectively), ND4L(ATG and GCT, respectively) and ND6(ATT and ATC, respectively). These ND2, ATPase8, ATPase6, COⅢ, ND3, ND4 L, ND6, Cytb and ND1 genes used the typical termination codon TAN. However, all the COⅠ, COⅡ, ND5 and ND4 genes stopped with incomplete termination codon T.(5) All of the 22 typical t RNAs were found in the two Chinese Daphnia magna and Daphnia pulex mitochondrial genome. All t RNA genes had a clover-leaf structure except for trn S1, in which its DHU arm simply formed a loop. There were 27 base pair mismatches present in 17 t RNAs secondary structures of Chinese Daphnia magna mt DNA, including 19 wobble G·U pairs, 7 U·G pairs and one C·U pair mismatch. There were 32 base pair mismatches found in 16 t RNAs secondary structures of Chinese Daphnia pulex mt DNA, containing 15 wobble G·U pairs, 13 U·G pairs, two U·U pairs, one A·A pair and one U·C pair mismatch.It provided evidence for the study of Morphology, Population ecology, Genetics and Evolutionary history of these Daphnia species in this paper.