Mitochondrial Genome Assembly And Analysis Of Saussurea Involucrate In Xinjiang

Saussurea involucrata is distributed in the alpine regions of Xinjiang,Qinghai,Gansu,Sichuan,Yunnan and Tibet.It is mainly produced in the Tianshan and Kunlun Mountains of Xinjiang.It is a plateau perennial rare herb.S.involucrata not only has strong cold resistance and physiological function of utilizing effective accumulated temperature,but also has a set of morphological and anatomical ventilation structure which can grow vigorously on glaciers at high altitude and adapt to hypoxic environment,so as to maintain its respiratory function and ensure its morphological formation and physiological function regulation.The assembly and analysis of S.involucrata mitochondrial genome can lay a solid foundation for further analysis of its low temperature respiratory mechanism and the mechanism of nuclear matter interaction and tolerance under low temperature.The main contents of this study are as follows: Two different assembly methods are used to assemble the mitochondrial genes of Saussurea involucrata,and the results are analyzed and compared.The advantages and disadvantages of the two methods are analyzed,which lays a foundation for the next analysis of genome.The first method is to remove reads from the nuclear genome and chloroplast genome alignment from the sequencing data,and then use the remaining reads to assemble the S.involucrata mitochondrial genome.However,because the nuclear genome of S.involucrata is unknown,we used the nuclear genome of sunflower,which is closely related to S.involucrata of Compositae,instead of the nuclear genome of S.involucrata,and screened the mitochondrial reads of S.involucrata.The second method utilizes the long reading length of pacbio data to compose with illumine data.Mitochondrial contigs are screened out and scoffolds are assembled of the S.involucrata.The results of the above two methods are analyzed by non-coding RNA,repeat sequence analysis,gene prediction and annotation respectively.The advantages and disadvantages of the two methods are compared by annotation results,and analysing the possible reasons.Main results: statistical results of the first method showed that 1243 scaffold are assembled,the total base length is 668887 bp,the maximum length is 2685 bp,the N50 size was 575,the GC content was 39.20%,and the number of unknown bases was 0.01%.From the annotation results,986 coding genes,2 non-coding RNAs,119 simple repeat sequences,1 short dispersed repeat sequence,3 long dispersed repeat sequences and 31 low complexity sequences are predicted.Functional annotation shows that most of the genes are unknown functional genes,and no genes are annotated to the KEGG database,and there are few mitochondrial genes of plant.The results of the second methods of assembly statistics shows that a total of 3 contigs are assembled,with a maximum length of 208197 bp,a total base length of 287164 bp,a N50 size of 208197,a GC content of 44.48%,and an unknown base number of 0.19%,The annotation results shows that the number of predicted coding genes is 181,the number of non coding RNA is 27,and the result of repetitive sequence analysis is 0.The results showed that the second assembly method is more closely and consistent with the characteristics of plant mitochondrial genome.In total,there were 2,24 and 15 DEGs were found in Saussurea involucrata,Arabidopsis thaliana and Lycopersicon esculentum.These genes were mainly focused on mitochondrial ribosomal and electron transfer chain complex subunits.A few genes were seemed to relate to the cold adaptation that the expression level was positive to the ability of cold tolerance of the three plants,especially for the NAD1 and NAD5 gene.Further analysis on the conserved motif sequence of these genes,the sequences of S.involucrata showed closer relationship with the alpine plants such as Climacium dendroides and Anomodon minor than the other compositae plants.