A Study On The Full Mitochondrial Genome Of The Plateau Cockroach And Its Parasitic Third Generation Worm

In this study, the complete mitochondrial genomes of Triplophysa sp. and three Gyrodactylus spp. which are ectoparasitic on the fish including Gyrodactylus sp.1, Gyrodactylus sp.2 and Gyrodactylus sp.3 were determined and described by a combined with the available data form GenBank. A comparative analysis of 4 major datasets (PCGs, tRNA, rRNA and NCRs) about A+T content and AT skew of base composition, condon usage etc. among 6 Gyrodactylus were performed. Moreover, phylogenetic relationship of Gyrodactylidae has been reconstructed by using the methods of Maximum Likelihood (ML) and Bayesian Inference (BI), which based on thirty-four 18S rRNA sequence are available data form GenBank, and Haliotrema pratasensis as the outer group. Followings are the main results and conclusion:1. The size of Triplophysa sp., Gyrodactylus sp.1, Gyrodactylus sp.2 and Gyrodactylus sp.3 are 16,570 bp,14,734 bp,15,717 bp and 14,739 bp, respectively. The composition and arrangement of Triplophysa sp. mitogenome are consistent with bony fish, including 13 protein-coding genes,2 rRNA,22 tRNA and a D-loop. The composition and arrangement of all the newly sequenced Gyrodactylus spp. mitochondrial genomes except for major non-coding regions are identical with available Monogenea and contain 12 protein-coding,2 rRNA,22 tRNA and major non-coding regions.2. In Triplophysa sp., the ND6 and eight tRNAs (tRNAAla, tRNASer (UCN), tRNACys, tRNAGlu, tRNAAsn, tRNAGln, tRNATyr, tRNAPro) are coding by light strand and the rest of 28 genes were coded by heavy strand. However, all the genes of Gyrodactylus mitochondrial genomes are transcribed from the same strand.3. The A+T content in 4 major datasets of Triplophysa sp. are all obviously biased, especially in D-loop, which is up to 66.5%. The similar case occurs in all the newly sequenced Gyrodactylus spp., and the A+T content are higher than published mitogenome of Gyrodactylus.4. The frequences of synonymous codon usage and amino acids are as follows:In Triplophysa sp., the frequences of AUU, UUA, CUU, CUA, GCC are higher than others and UGU is lower than others. The frequences of amino acids are identical with the synonymous codon usage, Leu, Ala, Thr, Ile and Val are the most frequent; All synonymous codon are present in six Gyrodactylus. The most frequent synonymous codon usage is UAA in G. sp.1, G. sp.2 and G. sp.3, and AUA in G. derjavinoides, G. thymalli and G. salaris.5. The arrangement of all the Triplophysa sp. tRNAs are identical with most fish, no gene rearrangement. Except for tRNASet (AGN), lack of the DHU arm, other tRNAs have the typical clover leaf structure. In G. sp.1, G. sp.2 and G. sp.3, tRNASer (AGN), tRNASer(UCN), and tRNACys are also lack of the DHU arm. Mispair are observed in all the newly sequenced species, and G-U mispair is frequent.6. The control region of Triplophysa sp. contains one TAS1 regions associated with terminate, two central conservative blocks F/D and three conservative sequence blocks 1-3, which is similar to cyprinidae fish. The six Gyrodactylus compared in this study all contain two major non-coding regions (NCRs), and the similarity between NCRs is very high in each species. Seven conserved blocks (A-G) are observed in the six Gyrodactylus.7. The phylogeny of Gyrodactylidae was reconstructed based on 18S rRNA gene, using the methods of ML and BI, and the results reveal that topology of two trees is identical. The viviparous species and oviparous species were proven to be monophyletic group, respectively and Gyrodactylus was a paraphyletic group.8. Given the different applicability of the various markers, we suggest the approach offered by Moszczynska et al. for digeneans would be a suitable way forward in our target organisms as well. Given to the primers of rRNA are widely used, the gene is applied to initially identify, once the species in question has been assigned to lower taxonomic rank, appropriate COI primers for the taxon may be got. Therefore, combined COI with partial of the rDNA region meets most needs of DNA barcoding in monogeneans.