Phylogeny Of Subfamily Oniscidea(Crustacea:Isopoda) Based On The Mitochondrial Genome

Subfamily Oniscida belongs to Arthorpod phylum,Crustacea and Isopoda,and is sole terrestrial crustacea,and with most biodiversities among isopods.However,monophyly of suborder Oniscidea is in dispute based on morphological characteristics.Next Generation Sequencing based on Illumina Mi Seq Sequencing platform are used to sequence and assemble annotations to obtain the complete mitochondrial genome sequence of Ligia exotica.The mitochondrial genome sequences of 12 species of Oniscidea,including the research sequence are analyzed,combined with 11 sequences published by NCBI.The bioinformatics methods including comparative genomics,pedigree genomics and evolutionary biology are used to analyze the sequences,and the results as follows:1.Structural Characteristics of Mitochondrial Genome of Ligia exoticaThe full length of the mitochondrial genome of the Ligia exotica is 14978 bp,including 13 protein-coding genes(PCGs),2 r RNA genes,21 t RNA genes,and one control regions.23 genes are encoded by the N chain,while the remaining 13 genes are encoded by the J chain.The AT contents of the whole genome sequence is 59.13%.Twelve of the 13 protein coding genes of the initiation codons are ATN,and the remaining Cox1 is CGA which is specially used.The total number of codons of 13 PCGs is 3692.The highest codon usage frequency is UUU,RSCU value is 1.43;UGC has the lowest usage frequency and the RSCU value is 0.54.Gly,Leu,Ser and Val are the most abundant amino acids,accounting for41.31% of all amino acid families.t RNA-G is missing from mitochondrial genome of Ligia exotica.Degradation of t RNA genes have been identified: t RNAC and t RNA-V are missing DHU arm.t RNA-F,t RNA-P,t RNA-M,t RNA-L2,t RNA-K and t RNA-D were deleted the T?C arm.2.Comparison and Pedigree Genome Analysis of OniscideaAmong the mitochondrial genes of oniscidea,the highest AT content is 75.3% of Mongoloniscus sinensis and the lowest is 59.1% of Ligia exotica.Nucleotides show obvious AT skew and GC skew.Cox1,Nad5,Cob,Nad4 and Nad2 were larger than 1000 bp.It turns out that the biggest change in length is Nad6,and the smallest is Cox1.The smaller difference in the longer genes.The amino acid composition of Oniscidea is also unbalanced.Among the13 protein coding genes,the percentage of conserved sites of Cob,Cox1,Cox2 and Cox3 genes in Ligiidae are all more than 70%.3.Phylogeny of subfamily Oniscidea and Natural selectionThe oniscidea is a polyphyletic group,the 12 species of the Oniscidea do not converge into one branch.The Ligia exotica and Ligia oceanica are one branch,in phylogenetic trees,it is closer to the species of marine Isopoda,which is the most primitive branch.In the BI and ML phylogenetic trees,except for Ligia exotica and Ligia oceanica,the remaining 10 species were clustered into a branch.The M.sinensis formed a clade with three species of Porcellionidae and they much closer in morphology and life environment.Based on the morphological and molecular data of the Oniscidea,the taxonomic status of the genus Ligia should up to the subfamily Ligiaidea.Among the 13 protein coding genes,the ratio of non-synonymous and synonymous substitution rates(w=d N/d S)varied significantly.The w values of Cob,Cox1,Cox2,Cox3,Nad1,Atp6 were lower.The w values of Nad2,Nad4,Nad4 l and Nad5 are medium.The ratio of Nad6 to Atp8 is relatively high.Species with strong diffusibility have higher dn/ds than weak diffusibility.This indicates that these genes and species are subject to different selective functional constraints.4.Divergence time of OniscideaAccording to the species divergence diagram of the Oniscidea,89.5361 Mya is divided into one of the Ligia and the other is the remaining Oniscidea.Most species of the Oniscidea began to differentiate into various branch species before 58.0177 Mya,such as Armadillidae,Porcellionidae and Agnaridae.The common ancestor of the three species of the Armadillidae appeared before 60 Mya,and the differentiation time of Armadillium nasatum and Armadillium vgareul were 24.4779 Mya.The two species of Ligia also began to evolve into branches around 50 Mya to adapt to different living environments.