Complete Mitochondrial Genome And Comparative Genomics Analysis Of The Three Species Of Acheilognathinae

The complete mitochondrial genome sequences of Rhodeus lighti, Paracheilognathus imberbis and Paracheilognathus meridianus were determined and annotated in detail. These sequences would have enriched the database of mitochondrial genome sequences. The sequences of 14 species of Acheilognathinae mitochondrial genome which were published in GenBank were also used to infer the GC composition, codon usage biases and the phylogenetic relationships among the subfamilies. The main conclusions were as follows:(1) The whole mitochondrial genome sequence for the Rhodeus lighti, Paracheilognathus imberbis and Paracheilognathus meridianus Were determined. These mtDNA were closed-circular molecule and 16,677 bp、16,819 bp、16,563 bp in length, include 2 rRNA,22 tRNA,13 protein coding genes and D-Loop control region respectively; Gene arrangment and transcription direction were consistent with other Cyprinidae mitochondrial genomes.(2) The overall A+T% content in mtDNA of Rhodeus lighti、Paracheilognathus imberbis and Paracheilognathus meridianus was 56.09%,56.98% and 57.88%. The A+T% content in 13 protein coding genes was 56%,56.8% and 58.1%; The nucleotide composition showed A+T bias in mtDNA and 13 protein codon genes of three fish.(3) The total length of 13 peotein coding genes in the Rhodeus lighti, Paracheilognathus imberbis and Paracheilognathus meridianus was 11422bp、 11422bp and 11423bp. All protein-coding genes in Rhodeus lighti, Paracheilognathus imberbis and Paracheilognathus meridianus share the same start codon ATG except COX1,which begins with GTG. However,there was different in stop codon among four fish. Seven protein-coding genes(ND1、COX1、ATPase8、ATPase6、ND4L、 ND5 and ND6) in these fish used TAA as complete stop codons except ND5 in P. imberbis, and the ND5 in P. imberbis using TAG as stop codons. The ND4 in R. lighti, P. imberbis and P. meridianus and the ND3 in P. meridianus were end with incomplete stop codons TA, The rest protein coding genes end with incomplete stop codons T.(4) All four fish in this study tRNA genes formed typical clover-leaf structure; D-Loop control region were 1015bp、1172bp、910bp and 1214 bp in length respectively.(5) The nucleotide composition, relative synonymous codon usage and the effective number of codon in mtDNA of the four fish were determined. The results showed, all Acheilognathinae fish prefer NNA codons over any other codons, and NNG was least preferred. The strong mutational pressures along with other weak selective constraints influence codon usage bias in Acheilognathinae fish.(6) The Phylogenetic analyses results based on rRNA & PCGs and PCGs sequence showed:① P. meridianus, A. macropterus and A. barbatus have more close relationships, and the R. lighti, R. sinensis and R. ocellatus have the same status.② The four species including A. signifer, A. koreensis, A. somjinensis and A. intermedia have a close relationshiop with the species which belonged to the genus Rhodeus.