堇花槐与苦豆子叶绿体基因组特征及其序列比较分析

[Objective]Based on the comparative analysis of chloroplast genome sequences,to accelerate the development and utilization of Sophora specific germplasm resources.[Method]Sophora japonica var.violacea and S.alopecuroides,which are flower color specific Germplasms of Sophora genus,were selected as the research objects.The chloroplast genome assembly,structural characteristics and genome annotation were carried out by using Illumina hiseq high-throughput sequencing.[Result]the chloroplast genomes of S.japonica var.violacea and S.alopecuroides were typical circular structures composed of four parts.The cpDNA length of S.japonica var.violacea was 158837 bp,and the length of its reverse repeat IRA and IRB was 25398 bp.The 88983 bp large single copy region(LSC)and 19058 bp small single copy region(SSC)were separated.The cpDNA length of S.alopecuroides is relatively short,which is 154108 bp.The length of its reverse repeat IRA and IRB is 25874 bp,which separates 84221 bp large single copy region(LSC)and 18139 bp small single copy region(SSC).Both Sophora japonica var.violacea and S.alopecuroides has more base substitutions(17464 bp)and less insertion deletions(1688 bp).The total GC content of S.japonica var.violacea was 36.13%,which was lower than that of S.alopecuroides(36.57%).In the reverse repeat region,the GC content of S.japonica var.violacea was 43.17%,which was higher than that of S.alopecuroides(42.79%);In the large single copy region,the GC content of S.japonica var.violacea was 33.51%,which was lower than that of S.alopecuroides(34.17%);In the small single copy region,the GC content of S.japonica var.violacea was 29.61%,which was lower than that of S.alopecuroides(30%).The total content of AT was different from that of GC.The content of small single copy region was higher,the content of large single copy region was medium,and the content of reverse repeat region was the lowest.The total AT content of S.japonica var.violacea was 63.87%,which was higher than that of S.alopecuroides(63.43%).In the small single copy region,the AT content of S.japonica var.violacea was 70.39%,which was higher than that of S.alopecuroides(70%).In the large single copy region,the AT content of S.japonica var.violacea was 66.49%,which was higher than that of S.alopecuroides(65.83%).In the reverse repeat region,the AT content of S.japonica var.violacea was 56.83%,which was higher than that of S.alopecuroides(57.21%).The number of co-coding genes in the chloroplast genome of S.japonica var.violacea and S.alopecuroides were 130 and 129,respectively.In the IR,IRA and IRB regions,the number of co-coding genes in the chloroplast genome was 38(19,19)and 35(18,17),respectively;In the LSC region,the number of chloroplast genome co-coding genes was 80 and 82,respectively;In SSc region,the number of co-coding genes in the chloroplast genome of the two genes was 12.Compared with S.alopecuroides,S.japonica var.violacea has a self-replicating rps19 gene,a conserved reading frame gene ycf1 gene and a trnfm-CAU gene;S.alopecuroides has a unique trnt-CGU gene.Among the 65 codons used by S.japonica var.violacea,the number and proportion of codons used in different amino acids were different.Among them,the GCT in ALa(a)uses 634 codons,accounting for 1.85%;There are also 8 codons with more than 3%,which are ATT(4.22%),AAA(4.21%),GAA(3.89%),TTT(3.79%),AAT(3.82%),GAT(3.32%),TTA(3.18%)and TAT(3.02%),respectively.Except that ATT and TTA codons are less used than S.alopecuroides,the other 6 codons are more than S.alopecuroides.The lowest codons used were tag and TGA,accounting for 0.07%,which was different from S.alopecuroides.In the cpDNA of S.japonica var.violacea and S.alopecuroides,the number of SSRs with single nucleotide repeat motifs was 110 and 79 respectively,accounting for 64.33%and 69.91%of the total SSRs,respectively;The number of dinucleotide repeat motif SSRs was 43 and 14,accounting for 25.15%and 12.39%of the total SSRs,respectively;The sum of single nucleotide repeat motifs and dinucleotide repeat motifs accounted for 89.47%(153)and 82.30%(93)of all chloroplast nuclear genomic SSRs,respectively.The SSRs of trinucleotide,tetranucleotide and pentanucleotide repeat motifs were less and they were all 1;The SSRs with trinucleotide and tetranucleotide repeat motifs were relatively more in S.alopecuroides.The SSRs with trinucleotide repeat motifs accounted for 6.19%(7)of the total SSRs,and those with tetranucleotide repeat motifs accounted for 11.50%(13)of the total SSRs,while those without pentanucleotide repeat motifs.[Conclusion]The homology of chloroplast genomes of S.japonica var.violacea and S.alopecuroides and the differences in sequence characteristics,coding gene distribution,codon usage frequency and SSR distribution between the two chloroplast genomes were identified,which laid a foundation for their chloroplast gene mining and development and utilization.