Characteristic Analysis Of 162 Nematode Mitochondrial Genomes And Phylogenetic Study

Nematoda belongs to the Nematode phylum and are type of widely distributed invertebrates.There are many types of nematodes,either parasitic on animals and plants,or living freely in soil,freshwater and seawater environments.Parasitic nematodes can seriously endanger host health or even cause death.To control parasites,we must first understand their taxonomic status and phylogenetic relationships.Therefore,studying the phylogeny of nematodes based on the mitochondrial genome(mitogenome)has important biological significance.In this study,we systematically analyzed the basic characteristics of the mitochondrial genome of 162 species of nematodes in 5 orders,41 families,80 genera,including genome size,AT content,base preference,usege of synonymous codons,gene number,gene overlap,genome rearrangement,etc.In order to systematically understand the phylogenetic relationships of 162 nematode species,the nucleic acid sequence of 12 protein encoding genes(PCG123),the nucleic acid sequence without the third position of the codon(PCG12),amino acid sequence of 12 proteins(AA)were concatenated.The Bayesian Interference(BI)and Maximum Likelhood(ML)were used to reconstruct and analyze the phylogenetic tree.The findings are as follows:1.Basic characteristics of the nematode mitochondrial genomeThe nematode mitochondrial genome has a high AT content(ranging from 60% to85%)and the base usage shows a clear AT bias(T%> A%> G%> C%).The 12protein-coding genes in the genome all use complete start codons(mostly ATT and TTG),and prefer to use codons ending in A and U.The gene numbers in mitogenomes of nematode Mermithida is the largest(more than 39 genes),while nematode Dorylainida has the least(less than 36 genes).The molecular mechanism for the increase or deletion of genes may be due to gene duplication-random loss or due to improper replication of certain t RNA genes.2.Rearrangement of mitochondrial genomesBy comparing the gene arrangement,a total of 42 types of arrangements were found in 162 mitogenomes(GA1-GA42).Among them,83 nematodes belong to the GA3 type.In the Order with highly rearranged,the rearrangements were observed int RNA genes,protein coding genes,and r RNA genes.They are mainly distributed in Dorylaimida,Mermithida,and Rhabditida.In moderately rearranged Orders,only a few genes are rearranged and concentrated in Strongylida and Trichinellida.Although a large number of gene rearrangements occurred at the Order level,the order of genes in the same Family was relatively stable.3.Mitochondrial genome characteristics and phylogenyPrincipal component analysis was performed for 34 genomic features and the resetult showed that the principal component 1(PC1)can explain 96.39% of all data,then 15 feature data were extreacted,including total length of mitogenomic,length of AT region,unspecified region,base content,gene numbers,chain skew,gene rearrangement rate,codon adaptation index,codon effective number,GC content,number of synonymous amino acids,etc.Using effective features can better separate Dorylaimida,Mermithida,Trichinellida and the Family of them,but not for Strongylida,Rhabditidaand and the corresponding Family.The results show that the basic characteristics of mitogenomes are relatively conservative only in the low-taxonomic level,while the variation is high in the high-taxonomic level.4.Mitogenome and nematode phylogenyFrom the taxonomy level Order,the phylogenetic tree constructed based on the data PCG123 shows that Mermithida,Dorylaimida and Trichinellida are sister groups to each other.Nematodes from the same Family are clustered separately into a group(BS>80,PP> 0.90).It is worth noting that H.bacteriophora(Strongylida)is clustered with P.pacificus(Rhabditida)and Koerneria sudhausi(Rhabditida).S.venezuelensis(Strongylida)is clustered in a group with A.besseyi(Rhabditida),B.mucronatus(Rhabditida),and B.xylophilus(Rhabditida).While,Wellcomia siamensis and S.obvelata(Rhabditida)are grouped together.In the ML phylogenetic tree,nematode in Famliy Onchocercidae(Rhabditida),Gnathostomatidae(Rhabditida),Meloidogynidae(Rhabditida),Oxyuridae(Rhabditida)are grouped together with the nematodes in Dorylaimida,but their phylogenetic relationship is far from other nematode species in the same Order.In BI tree,nematodes in Family Meloidogynidae are phylogenetically closer to the nematodes in Order Dorylaimida.Our results show that the Bayesian method is more suitable for nematode phylogenetic analysis.This may be that the maximum likelihood method uses the maximum probability of the data to fit the phylogenetic tree,while the Bayesian method uses the maximum probability of fitting the data and the evolution model to fit the phylogenetic tree.In the phylogenetic treebased on the data PCG12,there is no clustering phenomenon between some Families in Rhabditida and Dorylaimida.The phylogenetic tree based on the data AA shows that nematodes in the same Order are grouped together,and nematodes in Mermithida,Dorylaimida,Strongylida and Rhabditida are all monophylic(BS> 80,PP > 0.90).At the taxonomic level of Family,the phylogenetic tree based on the data PCG123 and PCG12 shows that G.pulchrum(Gnathostomatidae)and nematodes in Thelaziidae are clustered together.T.circumcincta(Haemonchidae)is clustered with C.oncophora(Cooperidae).In addition to the above problems,U.sanguinis(Angiostrongylidae)and Metastrongylidae are clustered in a group in the AA-based phylogenetic tree,and Wellcomia siamensis and Strongylidae are clustered.P.azarasi(genus Pseudoterranova)is grouped with nematodes in genus Anisakis.Therefore,we think that the data PCG12 and Bayesian inference(BI)are more suitable for nematode phylogenetic studies at the low-taxonomy level.This may be that the third nucleotide in codons has a fast evolution rate and is prone to substitution saturation.5.Nematode population and phylogenetic evolution(1)Aphelenchoididae is phylogenetically far from the Meloidogynidae family,Pratylenchidae family,Steinernematidae family in Order Tylenchina,and they are polyphyletic groups,but it is phylogenetically close to Spirurina.Therefore,this result supports that the sub-Order Slugrina should be divided from the sub-Order Tylenchina,rather than belonging to the Family Aphelenchoididae in sub-Order Tylenchina.(2)Although the results show that nematodes in Dracunculoidea is phylogenetically close to Philometridae(BS = 100,PP = 100),but nematode species in Dracunculoidea is less,so their real phylogenetic relationship needs to be further studied.The results of this study will provide a reference for the taxonomic research of Superfamily of Dracunculoidea.(3)The results show that nnematdoes in Strelkovimermis and Romanomermis,nematodes in Thaumamermis and Agamermis are phylogenetically close.This result is inconsistent with the results of phylogenetic analysis based on 18 Sr DNA and cox1.The possible reason is that the genetic information contained in a single gene is limited,and it is only suitable for exploring the phylogenetic relationship of limited nematode species within a certain taxonomy level.The multiple mitogenome data used in this paper contain rich genetic information and are more reliable.(4)Both ML and BI phylogenetic trees based on multiple data show that Cylicostephanus and Poteriostomum are monophyletic groups.Therefore,this studysupports the reorganization of them into the same genus.