Studies On Complete Mitochondrial Genome Of Parabramis Pekinensis Strenosoma And Codon Usage Patterns Of Megalobrama Amblycephala

Parabramis pekinensis strenosoma and Megalobrama amblycephala are both high quality herbivorous aquaculture fishes for their rapid growth, disease resistance, high nutritive quality in China. P. pekinensis strenosoma, a subspecies of P. pekinensis with greater fatness than common P. pekinensis, shows higher economic value and has more cultured potential. Meanwhile, the morphological variation might make it a good organism to study the relationship between genetic variation and phenotypic plasticity. As a consequence of environmental disruption and over-fishing, biomass of M. amblycephala was decreasing and body size smaller. Meanwhile cultured population of M. amblycephala is gradually exhibiting early sexual maturity, low growth rate and disease susceptibility due to its inbreeding. For scientific development of P. pekinensis and M. amblycephala seed industry, their genetic resource conservation and genetic improvement work appears to be very important. However their were little study foucs on complete mitochondrial genome of P. pekinensis strenosoma and codon usage patterns of M. amblycephala from omics perspective.(1) Fourteen amplification primers were designed to amplify the whole mitogenome based on the P. pekinensis’ s mitochondrial nucleotide conserved sequences. The complete mitogenome sequence of P. pekinensis strenosoma is 16,623 bp in length, with with a slight A+T bias of 55.93%. The sequence analysis revealed the typical gene content found in cyprinidae mitogenomes, including 37 genes and 2 main non-coding regions. The mitogenomes nucleotide sequence identity between P. pekinensis and P. Pekinensis strenosoma is high, indicating only a tiny of variance within genera. Phylogenetic tree of Culterinae relationships based on 13 PCGs was robust. Species in each genus were well clustered, consistent with their morphological classification.(2) Based on the mitogenome data of 14 culterinae, their codon usage bias were investigated and compared. M. amblycephala has evidently codon usage bias, containing 25 preferential codons and preferred A-end codons for synonymous selection. The variance of codon usage between M. amblycephala and P. pekinensis, Sinibrama macrops was smaller, Hemiculter leucisculus, Culter recurviceps, Culter alburnus, Chanodichthys erythropterus bigger, Pseudolaubuca engraulis biggest. The variance reflected the evolutionary relationship in culterinae.(3) A comprehensive analysis on usage bias of genetic codon and codon pairs in M. amblycephala were performed based on RNA-seq. Five high-frequency codons were identificated and NUA and NCG codons were underrepresented. 724 high-frequency codon pairs were identified encoding 335 amino acid pairs, as well as 14 preferred and 199 avoided codon pairs. Position-dependent heterogeneity of codon usage apparently lied close to start and stop codons and had its flanking sequence feature or its preferential codon. Codon usage bias may be driven by GC3, and meanwhile six GO categories and methylation regulation were both influenced by GC3. Among vertebrate species, GC content, RSCU and codon context pattern all had species specificities and codon context was relatively better for vertebrate evolution estimating.Our study provided molecular information for germplasm resources of P. pekinensis evaluating and utilizating, genetic variation exploring in Parabramis and its breeding work. It also provided insight into fish codon biology, vertebrate evolution and fish breeding project, such as codon optimization and transgene fish establishment, and the extensive application of RNA-Seq data.