Phylogenetic Evolution Of Gobioninae（Teleostei: Cyprinidae） Inferred From Mitochondrial Genomes And Reduced Representation Genomes

Due to abundant species,wide distribution and different living environment in Gobioninae,whichcause the researches of the genera and intergeneric relationships,origin and evolution facing great challenges.In this study,the mitochondrial genomes of four species of Gobioninae were sequenced and annotated increasing the number of the subfamily Gobioninae public databases.Combined with the complete mitochondrial genomes of Gobioninae downloaded from the public database,we compared and analyzed the sequences to understand the characteristics.In addition,based on mitochondrial gene database and reduced-representation sequencing which were obtained a large number of SNPs database at the whole genome through Rad-seq technology,construct the phylogenetic tree and estimate the divergence time for Gobioninae.So as to further understand the phylogenetic relationship,origin and evolution of Gobioninae from a higher level by means of genomics.The main conclusions are as follows:1.The complete mitochondrial genomes of four species were sequenced and annotated,lengths were 16603bp,16603bp,16604bp and 16609bp,respectively.They all had a typical circular double stranded,which is composed of 37 genes.The composition and order of genes are similar with other Gobioninae.The whole genome sequence and different regions all showed the phenomenon that A+T was higher than G+C.Heavy chain showed obvious A and C base preference,while the L chain showed obvious G and T base preference.For PCGs,codons containing A and U bases are frequently used.According to the calculation and analysis of effective codon usage statistics,Codon adaption index and composition of bases,there was significant codon usage bias in PCGs of four species of Gobioninae.Except t RNA^Ser（GCT）,the t RNA of four species of Gobioninae can form typical cloverleaf secondary structure.The base variation mostly occurs in the secondary structure ring in t RNA,and the base variation in OL region is also similar.2.Combine 85 mitochondrial genome sequences of Gobioninae were downloaded from the public database for comparative analysis.The results showed that the mitochondrial genome sequences of Gobioninae ranged from 1.65 Kb to 1.67 Kb,which was mainly caused by the variation of non-coding regions of different species,especially the variation of D-loop region.Besides,overlaps also affect the length of sequences.The base composition of Gobioninae also shows a significant A+T preference,which is consistent with that of other teleost fishes.In addition to ATG and GTG,ATA also used in the start codons of protein coding genes,and the usage of stop codons shows diversity.The 13 PCGs were subjected to different selection pressures and showed different evolution rates and nucleotide diversity.Among them,nad2 was suffered from the least selection pressure,the fastest evolution rate,and the highest nucleotide diversity.Cox1and cox3 were endured higher selection pressure,which bring about the slower evolution speed and relatively conservative.3.Based on the mitochondrial genome database,the phylogenetic relationships of 89 species of Gobioninae belonging to 27 genera were reconstructed by using molecular phylogenetic methods,and the divergent time was estimated by the molecular clock theory and five fossil records.According to the phylogenetic results,89 species of Gobioninae were divided into four monophyletic groups:“Hemibarbus-Squalidus”group,Coreius,tribe Sarcocheilichthys and tribe Gobioninii.Among them,the“Hemibarbus-Squalidus”group is located at base of the phylogenetic tree of subfamily Gobioninae,and the earliest divergent time is in the Oligocene of 33.51 Mya.The genus Coreius forms a separate branch,constituting a sister group with Sarcocheilichthys and Gobioninii and the divergent time happened in 29.32 Mya.Two lineages,Sarcocheilichthys and Gobioninii,foremed a sister group and their divergent time was in the late Oligocene before 28.65 Mya.According to the results of the divergent time,the origin of subfamily Gobioninae was in the late Eocene of 35 Mya,the separation of different groups occurred in the Oligocene,and the differentiation of most genera also occurred in the Miocene of 15-28 Mya.Based on the time tree,we reconstructed the ancestral distribution area of Gobioninae,and the results showed that Gobioninae probably originated in China,spread to Japan,Korean Peninsula and Mongolia in East Asia and then spread to other parts of Asia.4.Phylogenetic tree,divergent time and ancestral character states were reconstruction based on SNPs which obtained by RAD-seq technology.The results showed that Gobioninae can be divided into three lineages:“Hemibarbus-Squalidus”group,tribe Sarcocheilichthys and tribe Gobioninii.Similar to the mitochondrial results,“Hemibarbus-Squalidus”group is located at the base of the phylogenetic tree and have earliest divergent time.The Sarcocheilichthys and Gobioninii constitute a sister group and the divergent time happened in 29Mya.The divergence of groups occurred in the early Oligocene and the divisions of most genus happened in the Miocene of 10-26 Mya.Based on the divergent time,the evolution of seven characters of Gobiinae was inferred.The results showed that the original morphology of Gobiinae might be living in the lower or middle dweller with developed swim bladder,anal close to anal fin,scaly abdomen,and no papillae in the lower mouth.Evolutionary trend of Gobioninae from the original morphology to cylindrical fish with lived in the bottom dweller,with degenerated swim bladder,anal close to anal fin,scaleless abdomen,and developed papillae.In order to adapt to living environment,the Gobioninae with diversity characteristics were formed.