The Research Of Chloroplast Genome Of Ginkgo Biloba

Ginkgo biloba,is the oldest surviving plant of the gymnosperms left behind after the quaternary glacial movement,has high medicinal value and economic value.In this study,the whole genome of Ginkgo biloba was sequenced based on Illumina Hiseq2500 platform.The genome sequence of the ginkgo chloroplast on NCBI was used as the reference sequence,and the short reads was assembled by BWA,Samtools and Newbler3.0 software and assembled into contig.Finally,the contig was spliced into a circular chloroplast sequence by Macvector software.The PCR genome of gap was verified and completed,thus,a complete sequence of Ginkgo chloroplast genome was obtained.After splicing validation,annotation analysis of Ginkgo biloba chloroplast genome was completed and compared with chloroplast genome of other plants.The results are:1.The content of chloroplast genome of Ginkgo biloba is 156,997 bp and GC is 60.44%.The chloroplast structure is similar to that of most plants,showing a typical four segment structure,in which LSC is 100,174 bp,SSC is 22,615 bp,and IR is 17,104 bp.The content of GC in IR region is the highest,up to 44.96%,while the content of GC in SSC area is the lowest(36.25%).It is obvious that the conservatism of IR is higher than that of LSC and SSC.2.A total of 134 genes were annotated in the whole sequence,and 117 genes remained after removed duplication,including 90 protein coding genes,36 tRNA and 8 rRNA.Among them,6 protein coding genes,10 tRNA and 8 rRNA genes are located in two IR regions,69 protein coding genes and 24 tRNA are located in the LSC region,while the SSC region contains only 15 protein coding genes and 2 tRNA.3.The total length of chloroplast genome CDS of Ginkgo biloba is 77,422 bp,which accounts for 49.3% of the total length of chloroplast genome and 39.03% of GC,owns 15,206 codons.Among them,there are 1627 codons encoding leucine,accounting for about 10.7% of the total use rate.4.The codon coded cysteine is the least,only 159,accounting for about 1.04% of the total utilization rate.11 introns,39 SSR,51 positive repeats,39 palindromic repeats and 23 tandem repeats were detected in Ginkgo chloroplast genome.5.Comparing Ginkgo biloba with other species,the gene composition and gene sequence is similar to Cycas.The variation of non-coding region is more obvious than coding region.The variation of LSC and SSC regions is obviously higher than that of IR,and the genes of rpl23?rpoC2?rpl20?rps15 and ycf1 are the highest.6.Compared with most gymnosperms,the IR area of Ginkgo obviously contracted,the contraction is about 8K.7.Phylogenetic analysis of chloroplast genome of Ginkgo biloba using 36 common protein coding genes from 23 species showed that ginkgo and Cycas were sister branches in evolution theory.