Genomic Sequencing And Phylogenetic Analysis Of 8 Species Of Cangidae Fish

The Carangidae family boasts a diverse array of species,delectable meat,and substantial nutritional value,making it a prime focus for both deep-sea fishing and aquaculture development in the future.To comprehensively comprehend the characteristics of Carangidae,it is imperative to conduct a thorough investigation of their genomic information while simultaneously exploring their developmental processes through evolutionary genetics.Doing so will provide a molecular foundation for taxonomic studies of Carangidae,the creation of premium germplasm resources,and the sustainable use of fishery resources.In this study,we successfully assembled the mitochondrial genomes of eight Carangidae species using second-generation sequencing and bioinformatics analysis.Combining mitochondrial genomic data from NCBI,we established the phylogenetic tree of Carangidaeusing the Maximum Likelihood method,Bayesian Inference,and Neighbor Joining method.Our analysis also revealed the genetic structure and phylogenetic characteristics of themitochondrial genomes of these eight species.Furthermore,we conducted a preliminary genome-wide assembly and evaluation to enhance the genomic information of Carangidae,improve their taxonomic system,and provide a reliable basis for biodiversity research and species identification.The following comprise the key findings of this study.1.We determined and preliminarily assembled a total of eight newly sequenced mitochondrial genomes belonging to the following Carangidae species: Megalaspis cordyla,Elagatis bipinnulatus,Scomberoides tol,Selaroides leptolepis,Decapterus maruadsi,Alepes kalla,Caranx sexfasciatus,and Carangoides orthogrammu.These mitochondrial genomes ranged in size from 16540 bp to 16689 bp and contained two ribosomal genes,13 protein-coding genes,and 22-23 transfer RNA genes,respectively.The mitochondrial genomic structure was consistent with that of other Carangidae fishes,with the exception of S.tol,which had an additional t RNA-Met structure,and a gene rearrangement.2.Based on the mitochondrial genomic data of 41 Carangidae species,our analysis yielded the following results:(1)the genetic distance between Uraspis secunda and Uraspis helvola is0.002,suggesting that they might be the same species.(2)The genetic distance of 0.082 between A.kalla and Alepes djedaba is less than the genetic distance of 0.107 between A.kalla and Atule mate,providing support for grouping A.kalla with Alepes.(3)The genetic distance between Carangoides equula and C.orthogrammu showed intra-genus distances greater than inter-genus distances,contradicting traditional taxonomic status.(4)Our analysis revealed the evolutionary relationships among the four subfamilies: Seriolinae diverged earliest,beginning in the middle Eocene(46.80 Mya),followed by Caranginae in the late Eocene(40.34 Mya),then Chorineminae in the early Miocene(15.31 Mya),and finally Trachinotinae in the late Miocene(12.05 Mya).Seriolinae and Caranginaeare most closely related as a group,while Trachinotinae and Chorineminae are most closely related as a group.3.Our initial assembly of the whole genomes of the eight Carangidae species revealed a size range from 831.4 Mb to 1539.7 Mb.The lengths of Contigs N50 and Scaffolds N50 ranged from 173 bp to 967 bp and 532 bp to 27044 bp,respectively.We identified 2280271,2658378,2216617,2525579,3722730,2520241,2024608,and 2061702 repeat sequence units in the whole genomes of the eight Carangidae species,respectively.Notably,D.maruadsi exhibited the most repetitive sequences,C.sexfasciatus had the least.