Complete Mitochondrial Genome And Phylogenetic Analysis Of16Gobies In East China Sea

Gobies refer to all the fishes under Gobioidei and it represents the biggest group ofpresent living Perciformes fishes. They are widely distributed and inhabited in differentmarine or freshwater warm-water ecological environment. As a huge biological group,gobies play an important role in the water ecological environment. Due to its small sizetogether with the morphological degradation and specialization in different degree, makestraditional morphological identification of gobies very difficult, which leads to theconfusion of its names and classification as well as the serious synonyms phenomenon andthe controversial of phylogentic. At present, due to its advantages, mitochondrial gene hasbeen videly used in the research of identification, classification and evolution of fish and soon. Compared to the partial gene fragments, the whole mitochondrial genome sequencecpossess more abundant information, therefore the results could be more comprehensiveand accurate. In this study, the complete mitochondrial genome of16gobies, which thesamples were collected from the East China Sea, were determined by the method of LongPCR and common PCR and the structure characteristics were analyzed. Combined thecomplete mitochondrial genome sequences of the other10species of gobies, which havebeen published in GenBank, the phylogenetic relationship and evolution of26species ofgobies were discussed, aimed at providing new perspectives of identification andclassification of gobies and accumulating molecular information.The main conclusions are as follows:1.16speices of gobies share similar characteristics with most vertebrates in basecomposition, gene order and codon usage of the mitochondrial genome, but there isobvious variation in noncoding region. The origin of light strand replication (OL) of16speices of gobies can fold into a stable stem-loop secondary structure and two conservedmotif were found in the5’ region:5’-GCCGG-3’ and5’-ACCGG-3’. The main noncodingcontrol region (CR) was varied, and the core sequence (ACATATATGT) of thetermination-associated region, the conserved motif GTGGG of CSB-E, CSB-D and CSB-1,2,3were recognized in most species, except CSB-F, which absented in all fishes. Differentrepetitive seqences were found in CR of4speices of gobies (Odontamblyopus rubicundus, Trypauchen vagina, Acentrogobius chlorostigmatoide, Oxuderces dentatus) and itsmechanism is not yet clear. All these featrues were in accord with the characteristic that CRwas not under coding pressure and evolve quickly, and provdie a favorable materia forresearching the production, extension and deletion mechanisms of repetitive sequences ofvertebrate mitochondrial genome.2. The phylogenetic trees showed that different families and genera of gobiesgenerally clustered together, except for Lophiogobius ocellicauda, which is a Gobiinae fish,clustered in the Gobionellinae group. Rhyacichthys aspro was rooted in the tree and thenext were the Odontobutidae and Eleotridae species. Within the Goiidae, two clades arerecovered. One includes the fishes of Amblyopinae, Gobionellinae, Oxudercinae andSicydiinae, the other contains the fishes of gobiinae. These results were different form thetraditionally classification of Gobiidae, but support the6family phylogenetic taxonomy ofThacker (2009). The results of genetic distance and phylogenetic tree showed thatAcanthogobius ommaturus and Acanthogobius hasta, Glossogobius olivaceus andGlossogobius circumspectus are synonyms respectively.3. Molecular clock results, which based on all the encoding genes of mitochondrialgenome, revealed that the divergence time of the fishes of Gobiidae probably originated inthe late Eocene to Oligocene time period and further evoled to modern characteristic gobyspecies in Miocene.