Exploring Research On The Mitochondrial Genome, Transcriptome And Nuclear Genome Of Okterbi

Pielomastax octavii is a representative specie of Eumastacoidea.But the molecular information of Pielomastax octavii are sparse,which are great hindrance to the study of classification and functional rsearch of Pielomastax octavii.Genome and transcriptome are the main data sources of many biological research,such as species evolutionary relationship and molecular mechanism of biological process.So this study carried the mitochondrial genome,transcriptome,and genome survey sequencing of Pielomastax octavii by using the high throughput sequencing technology.The main conclusions of study are as follow:1.Mitochondrial genome research(1)The complete mitochondrial genome of Pielomastax octavii is 15,628bp,contain 37 genes including 13 protein coding genes,2 rRNA genes,22 tRNA genes and 1 control region.AT biase is found in each part of the genome.(2)Among 13 potein genes,9 are coded by J chain,4 are coded by N chain.All protein genes use the typical start codon ATN.The stop codon falls in two categories,one of which is complete stop codon,including TAG and TAA.And the other one is incomplete stop codon,which has only one base T.Among all available codons,the most frequently used codon is UUA,while the least is CGC.And the highest among the amino acid composition is Leu(Leucine),the least is Cys(Cysteine).(3)All of the tRNAs are folded into a typical clover-leaf secondary structure except trn SAGN,whose DHU stem are lost.The anti-codons are consistent with the most insects.The secondary structure of two rRNA genes is similar to the other Orthopteran species,while several stem loops lost.A Poly(A)(T-strech)exist in the D-Loop region,which can form a stem loop structure,and it is related to the origin of replication.(4)The phlogenetic tree of Eumastacoidea were constructed by maximum likelihood method based on COI sequence fragment.The result show the relationships among families as follow:(((Morabidae+Episactidae)+(Chorotypidae+Eumastaci dae))+Thericleidae),which support the monophyly of Episactidae,and Episactidae and Morabidae are sister groups.2.Transcriptome research(1)The transcriptome sequencing of Pielomastax octavii generated 6.6Gb data.After de novo assembling these data,we obtained 48,831 Unigenes,with total lenght 49,475,997bp.The average length of all unigenes is 1,103bp,and N50 is 1,799bp.(2)After annotated the 36,149 Unigenes whose length great than 300bp,totally 20,727 Unigenes were matched with follow databases,19,178 with Nr,10,818 with Swiss-Prot,6,761 with COG,13,287 with KOG,18,530 with eggNOG,and 14,670 with Pfam database.Then we obained 8,731 annotation informations with GO function classification and 8,604 annotation informations with KEGG pathway analysis,while 15,422 Unigenes remain without annotation informations,which provide a major source of future gene discovery.(3)The result of GO classification analysis show that 8,737 Unigenes were classified into three functional category,including biological process,molecular function and cellular component,and gained 20,819,10,726,and 12,273 annotation informations respectively.By KEGG pathway analyses,we identified some Unigenes which related to innate immune signaling pathways.Among these genes,23 genes related to Jak-STAT signaling pathway(ko04630)and 17 genes related to MAPK signaling pathway-fly(ko04013).(4)The FPKM of all Unigenes is caluculated.Among the 20 most abundantly expressed genes,a lot of cellular skeleton protein coded genes such as actin,myosin,tropomyosin,troponin and paramyosin are identified.Besides some protein coded genes involved in electron transport chain are identified too,such as cytochrome oxidase subunit I and ADP/ATP carrier protein 2.(5)For screening Unigenes to do SSR analysis,a total of 6,129 SSR were identified and the total length is 95,715bp,while the shortest is l0bp and the longest is 216bp,including 4,038 mononucleotide repeats,1,105 dinucleotide repeats,691 trinucleotide repeats,25 tetranucleotide repeats,1 pentanucleotide repeats,2 hexanucleotide repeats,252 compound repeats and 15 tandem repeats.(6)The results of mitochondrial transcript mapping showed that only 37 bases in D-Loop region are not covered,and the reads coverage of Pielomastax octavii's mitochondrial genome is high about 100%.Among all genes,16S-rRNA,COI have the highest expression level and the lowest are ND4L and ATP 8.In addition,ATP8/ATP6 and ND4/ND4L are two pairs of overlapping genes,pherhaps,transcribed by bicistronic mRNA.3.By genome survey anlysis,we estimated the genome size of Pielomastax octavii about 6.16Gb.And the repetitive content is 81.61%,and the heterozygosity is 0.22%,which show that the genome of Pielomastax octavii is complex.The distribution figure of GC-depth showed that there is no obvious biaes in GC base,but because of heterozygosis the GC has divided into two layers.The acquisition of mitochondrial genome,transcriptome and genome sequence information of Pielomastax octavii provided a lot of valuable information for further study on the Eumastacoidea.And provided an important basis for grasping and exploiting the potential genetic resources of Pielomastax octavii,classification of orthoptera species and functional research.