The Study Of Mitochondrial Genome In Undaria Pinnatifida And Comparative Analysis Of Algal Mitochondrial Genomes

Undaria pinnatifida belongs to Eukaryota, Chromista, Heterokontophyta,Phaeophyceae, Laminariales, Alariaceae, Undaria. U. pinnatifida which is mainlydistributed in China, Japan and South Korea is an annual kelp living in warm climate.It is an important edible seaweed with high economic value. As an representativespecies of Alariaceae, molecular systematics research of U. pinnatifida falls behindLaminariaceae. Among the69algal species which has completed mitochondrialgenome sequencing, only11species belonging to Laminariaceae are reported inLaminariales (Phaeophyceae). None mitochondrial genome sequencing has beenreported in Alariaceae species.In this study, we amplified and sequenced the mitochondrial genome of U.pinnatifida for the first time, and discussed the algae mitochondrial genome evolutionon the whole. Compared with the vascular plants, algae mitochondrial genomeshowed significantly differences, and thus can be divided into three evolutionarytypes: reduction, conservative and expansion. The genome size of algae rangedfrom13bp-201.8kbp with the average size of45.87kbp. The configuration was circularor linear. The A+T content varied between44.6-77.8%with the average of65.51%,and the ratio of gene spacer region was between3.6%-55.5%with an average of17.2%. The number of function identified genes ranged from10-77with the averagenumber53.97and coding density code was0.35-1.99.Mitochondrial DNA of U. pinnatifida is circular in structure, and the wholegenome length is37402bp with AT content of67.5%. The heavy chain (H) contains19.2%guanine (G),13.4%cytosine (C),30.1%adenine (A) and37.4%thymine (T).66genes were coded by U. pinnatifida mitochondrial genome,35of which wereprotein coding genes,3of which were ribosomal RNA gene (rRNA),25of which were transfer RNA gene (tRNA) and3were ORFs. Most of the coding genes weredistributed in the heavy chain (H chain), and only6genes (including ORF130, rpl2,rpl16, rpl3, rps19, tatC) were distributed in the light chain (L). None of the codinggenes contain any introns. The length of coding genes varied from123-3870bp in U.pinnatifida mitochondrial genome. All the coding gene use ATG as start codon andmost of the genes use TAA as stop codon with the exception of5genes (ORF377,nad4, rpl5, rpl14, rps12) using TAG and3genes (nad3, rps7, rps8) using TGA as thestop codon.The gene arrangement of mitochondrial genome was highly conservative inPhaeophyceae, and so were the distribution of coding chain and transcription polarityof each gene. But the gene arrangement of mitochondrial genome in Dictyotadichotoma made an exception. Four protein coding genes (atp8, rpl31, rps10and atp9)in total showed differences with other brown algae. We construct the Bayesianphylogenetic tree based on the amino acids of29shared protein coding genes ofPhaeophyceae mitochondrial genomes and7shared protein coding genes of70algaespecies, and the result showed that the phylogenetic tree shared good consistencywith the cluster relation. The phylogenetic tree which is constructed based onmitochondrial genome can truly reflect the evolution process of species evolution. Inthe Laminariales, Laminariaceae and Costariaceae have closer genetic relationshipand can be considered as sister group mutually, then they clustered into one branchwith Alariaceae.The Variation rate of proteins whose function is known is between25.00%and74.21%in brown algae with the average mutation rate55.31%. Among them, themost conservative gene is atp9, with the length of228bp and sequence variation of25%, and by contrast rpl31gene is the most mutative gene with the length of201-210bp and mutation rates high as74.21%. Comparing U. pinnatifida (Alariaceae)with Laminariaceae we discovered that the mutation rate of the shared protein codinggens varied between4.82%(atp9) and31.35%(rps11) and the average mutation rateis19.47%. By comparing U. pinnatifida (Alariaceae) with Costariaceae, we foundthat the mutation rate was between4.98%(atp8) and18.55%(rpl31) with an average rate of12.73%; Finally by comparing Costariaceae and Laminariaceae together, themutation rate ranged from7.02%(atp9) to28.20%(rps11), and the average rate is18.55%.