| Pleuronectiformes (Vertebrate: Osteichthyes) are remarkable because they undergo a dramatic metamorphosis from bilaterally symmetrical larvae to laterally compressed adults with both eyes on one side of the head. These species are primarily distributed in marine environments and a few inhabit freshwater and estuaries, some of these species are of great commercial importance.Molecular phylogenetic analyses of the sister-group to and within the order Pleuronectiformes have been explored in some studies. Most of these studies focused on phylogenetic relationships within the Acanthomorpha or Teleostei and included few flatfish species; other molecular phylogenetic studies were devoted to intra- and inter-family relationships within the order. However, the phylogenic position of the flatfishes in Teleostei based on the molecular data has not been detailed reported to date.On the other hand, our lab have determined the complete mitochondrial DNA sequences of Cynoglossus semilaevis and a striking finding is that the tRNA-Gln gene is translocated from the light to heavy strand. This is accompanied by shuffling of the tRNA-Ile gene and long-range translocation of the putative control region (CR); and the CRs sequences have altered significantly. To further explore sister-group relationships to Pleuronectiformes and inversion local, translocation of tonguefishes, we have completed the following work:1. We first determined the complete sequence of mitochondrial genome of Psetta maxima (17,583 bp), which contained 13 protein-coding genes, 2 rRNA genes ?(srRNA, lrRNA), 22 tRNA genes and a putative CR as most of other fish mitogenomes. However, a striking characteristic of this genome is the surprising length of ND2 gene of 1100 bp, which is the longest among 700 teleost mitogenomes sequenced up to now. In order to better understand the sister-group relationships of Pleuronectiformes, extensive and intensive phylogenetic analyses were conducted by Maximum-likelihood and Bayesian inference based on the first and second codon positions of the 12 concatenated protein-coding genes with 22 tRNA genes from 41 teleost mitochondrial genomes. The results showed that Pleuronectiformes is a monogenetic group. Phylogenetic analyses supported the suggestion that this group shares a recent common ancestor with carangids and also provided the evidence for the"lower-percoid"origins. It indicated that the results didn't support the hypothesis that flatfishes derived from the ancestor species which was recent common one to Clupeiformes, Zeiformes or Beryciformes. The comparisons of phylogenetic analyses between the tRNA genes and protein-coding gene indicated that the tRNA genes, especially the unpaired regions, could provide useful and specific information for inferring phylogenetic relationships, and the topology of phylogenetic trees based on each region of the tRNA genes did not show large deviations to acknowledged relationships in Pleuronectiformes. Therefore, we suggest that tRNA genes can be included when mitochondrial genomes data is used for phylogenetic analysis in the taxonomic level of teleost orders.2. The complete CRs of mtgenomes were amplified and then sequenced using PCR method from three species Cynoglossus macrolepidotus, Cynoglossus bilineatus, Paraplagusia bilineata and Paraplagusia blochi under Cynoglossinae. The lengths of CR fragments ranging from 655 bp to 1155 bp were exhibited obvious length heteroplasmy. Comparison the configurations of CR regions with that of four representive species of other families of the order Pleuronectiformes were carried out. The conserved blocks of CSB-A and TAS were observed, but the CSB1-3 and CSB B-F are absent in soles CRs, which have been found in other flatfishes. The AT contents of four tongue soles mtgenomes are little higher than that of other flatfishes. Both mutations mentioned above might be the result of the related fast evolution of CR regions in those species. The tandem repeats at 5'end of CRs were detected and could be capable of forming secondary structures in all four tongue soles, in which the conserved block of extended termination associated sequence domain (ETAS) were presented. The presumed secondary structures and the ETAS blocks provided an evidence for illegitimate elongation model. Furthermore, we speculated the elongation process of those tandem repeat by using this model.3. We determined the complete mitochondrial genomes of two Soleidae fishes: Zebrias quagga and Heteromycteris japonicus; five Cynoglossus fishes: Cynoglossus puncticeps, Cynoglossus itinu, Cynoglossus bilineatus, Cynoglossus abbreviatus and Cynoglossus sinicus; three Paraplagusia fishes: Paraplagusia blochii, Paraplagusia japonica and Paraplagusia bilineata. The full-lengths of complete mitochondrial genomes of ten soles range from 16417bp (Cynoglossus abbreviatus) to 17142bp (Cynoglossus puncticeps). Compared to other teleosts mitogenomes, in all eight Cynoglossus and Paraplagusia fishes mitogenomes, the tRNA-Gln gene is translocated from the light to heavy strand, and accompanied by shuffling of the tRNA-Ile gene and long-range translocation of the putative CR. The duplication/random-loss model was employed to explain: the CR is translocated to the downstream of ND1, and the transposition of CR effects the mitochondrial replication unstable, which leads the sideward tRNA genes IQM (Ile,Gln and Met) to inverted copy. After that, duplicated tRNA would degenerate one randomly by natural selection, consequently, current genes arrangement was formed.4. In the study of control regions of Pleuronichthys cornutus, we found its tandem repetitive sequences (mtTRs) was complex and regular, therefore, 109 monoclonal mtTRs of Pleuronichthys cornutus was determined to discuss the characteristics and pattern of its. All 1358 complete mt genomes sequences of vertebrates available from NCBI genome data base (http://www.ncbi.nlm.nih.gov) in April 2010 and then extracted out the mtTRs, from which we tried to decrypt the ?generation, insertion and deletion of mtTRs of vertebrates.The changes of mtTRs can be interpreted by several hypotheses, such as intra- or inter- molecular recombination, slipped-strand mispairing and illegitimate elongation model. But the rationality and scope of the application of various models have not been all-sided evaluated. Even more, still many characteristics of mtTRs could not be explained by the existing models, for example, longer motifs in mtgenomes were found to be more than shorter ones, and mtTRs could be generated at any positions of the whole mt genome, and a lot of VNTRs were not in CRs but in all kinds of genes.Based on the characteristics of mtTRs in vertebrates and former various hypotheses, we proposed a new model to explain the generation, insertion and deletion of mtTRs of vertebrates: Pause-Melting Misalignment model. In its simplest form, Pause-Melting Misalignment model involves melting of the nascent and template strands which may be induced by dynamic competition between the nascent and displaced strand when elongation of nascent strands was arrested at any position, after the nascent strand rebind with template strand, mispairing would easily happened due to the same strong hydrogen bonding forces between multiple repeated sequences, and the following replication would indel one or several repeat units.
|
PDF Full Text Request