| Daphnia carinata belongs to Daphniidae, Clasocera, Branchiapoda, Crustacea,Arthropoda, which plays important role in fresh-water ecosystem. The standard oftheir species identification has been contradictory, however, taking advantage ofmolecular biology methods might effectively revalue the taxonomy of differentDaphnia animals, and reveal the true variations in the similar morphological group.This thesis aims to determine the sequence of its mitochondrial genome and analyzethe genetic composition and structural characteristics, to provide a basis for theevolution analysis of Daphnia animals.In this research, we used Long-PCR and normal PCR methods to amplify thecomplete mitochondrial genome of Daphnia carinata, then determined and analyzedthe PCR products. The full-length of mtDNA is14747bp, in which the content of A,T, G, C is33.8%,36.5%,14.4%,15.3%, and the value of GC-Skew, AT-Skew werecalculated as-0.009and-0.027respectively. By the analysis of sequence homologyand structural characterization, we identified36genes, containing13protein codinggenes,21tRNA and2rRNA genes, but the gene of tRNAIle, tRNAMetand controlregion can’t be sequenced.In13protein-coding genes, the start codons include ATA(ND5), ATG(COII,ATP6, COIII, ND4, CYTB, ND1, ND2), ATT(ND3, ND4L, ND6), GTG(ATP8), and aspecial start codon ACTA(COI), the stop codons include TAA(ATP6, ND4L, ND6,ND1), TAG(ATP8, COIII, ND3, CYTB), and four incomplete stop codons(COI, COII,ND5, ND4). The secondary structures of21predicted tRNA are typical cloverleaf,except the one of tRNASer(GCU), which miss the dihydrouridine arm. Totally, there are two U-C mismatches and one mismatch of U-U and A-A in all of the structurepredictions.Among these36genes,9protein-coding genes(ND2, COI, COII, ATP8, ATP6,COIII, ND3, ND6, CYTB) and9tRNA genes(tRNAMet, tRNATrp, tRNALeu2, tRNALys,tRNAAsp, tRNAAla, TrnaGly, tRNAAla, tRNAArg, tRNAAsn, tRNASer1, tRNAGlu, tRNAThr,tRNASer2)are located in the H strand, and the rest of genes are located in L strand.Based on the DNA and the amino acid sequences, the identity matrix, theevolutionary divergence and the codon usage were analyzed and the molecularphylogentic trees were reconstructed using Mega5.05and RaxML-7.2.8software.The results showed that there was a closer relationship between Daphnia carinata andDaphnia magna, which is consistent with the traditional taxonomy based on themorphological characteristics. However, the long-period geographic isolation mayincrease the genetics distance between two distant populations of Daphnia pulex fromNorth American and China. |
