| Oryza coarctata is the only wild salt organism species in the genus Oryza and it is considered to be one of the important species in ecological succession,mainly distributed in the coastal areas of Southeast Asian country.Mitochondria and chloroplasts are important places for plant life activities.As an important part of plant genetic information,mitochondrial genome and chloroplast genome play important roles in the study of system evolution,species identification,and nuclear-cytoplasmic interaction.In this study,Nanopore original sequencing data of O.coarctata in the NCBI database was used to complete the assembly and analysis of its organelle genome.The main research results are as follows:1)The assembly and annotation of the O.coarctata organelle genome:The mitochondrial genome size of O.coarctata is 547,438 bp,with an average CG content of 42.38%,encoding 84 genes,including 34 protein coding genes,47 t RNA genes and3 r RNA genes.The chloroplast genome size of O.coarctata is 136,282 bp,showing a typical four segment structure,including a large single copy(LSC)which length is82,044 bp,a small single copy(SSC)which length is 12,642 bp,and a pair of reverse repeat regions(IR),which length is 20799 bp.The average CG content is 38.93%,encoding 128 genes,of which 109 unique genes.2)Characteristics of the O.coarctata organelle genome: 496 simple sequence repeats(SSRs)had been detected,51.81% were single nucleotide repeats,50 pairs of tandem repeats,and their lengths were all greater than 500 bp.It is predicted that 428 RNA editing sites,which are mainly distributed on the cytochrome C synthase gene,resulting in the conversion of neutral amino acids into hydrophobic amino acids.There were 139 simple sequence repeats(SSR),73.38% were single nucleotide repeats,and 15 pairs of tandem repeats greater than 30 bp were found,a total of 27 RNA editing sites in the O.coarctata chloroplast genome.Compared with the chloroplast genome,the mitochondrial genome has more repetitive sequences and RNA editing sites.The analysis of the site of RNA editing shows that RNA editing usually occurs at the first and second positions of the codon,and can change the start and stop sites of the gene sequence,and even change the function of the gene.3)Gene communication and phylogenetic relationship: Comparative analysis between the genomes revealed that the O.coarctata mitochondrial genome was highly rearranged,indicating that a large number of repeated sequences can cause gene rearrangement or mutation.So,it is speculated that the mechanism of this genome rearrangement may be the salt tolerance of O.coarctata in the swamp environment is related.There were 3186 sequences of mitochondrial gene origin in the nuclear genome of O.coarctata,with a total length of 1876,146 bp,accounting for 0.33% of the total nuclear genome sequence.There were 1567 sequences of chloroplast gene origin in the nuclear genome of O.coarctata,with a total length 906,467 bp,accounting for 0.16% of the total nuclear genome sequence.There were 114 sequences of chloroplast gene origin in the mitochondrial genome of O.coarctata,with a total length of 261,198 bp.There are 20 chloroplast-derived mitochondrial t RNA genes,14 of which have migrated to the nucleus.The above results indicate that gene migration is continuous.Mitochondrial genes form the center of integration.Gene migration is frequent,and there are multiple migration and integration phenomena.The high-quality O.coarctata organelle genome was obtained in this study,which provided new data and ideas for the study of O.coarctata salt tolerance adaptability,and was of great significance to the genetic background of rice germplasm resources and genetic breeding.The de novo assembly of organelle genomes constructed by this research will provide a new method for the assembly of plant organelle genomes in the future.Discussions based on repetitive sequences,RNA editing,and gene exchange will also provide data support for future research on organelle genomes. |
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