Mechanisms Of Plant Organelle Genome Variation And Evolution

Chloroplasts and mitochondria are respectively the major executors of photosynthesis and respiration in plant cells.They are not only the bases that organisms rely on for existence,but also predominant media for global carbon-oxygen cycle.Since endosymbiosis,genomes of plant chloroplasts and mitochondria have experienced substantial variations during the long evolutionary cause from unicellular algae to angiosperms.Nowadays,large numbers of plant nuclear as well as organelle genomes have been sequenced along with the boom of high-throughput genome sequencing technologies,which provides us insight into the variation laws of plant organell genomes,and basis for further study their physiological functions in photosynthesis and respiration on the whole genome level.In this study,we sequenced and assembled the complete chloroplast genome of a representative woody oil plant in the family Rosaceae Prinsepia utilis Royle for the first time.It is 156,328 bp in length and encodes for 131 genes.Genome-wide sequence comparisons with other complete chloroplast genomes in Rosaceae showed conserved genome structure,gene order,essential gene content,and corresponding gene functions.We also analyzed the sequence characters and evolution patterns of different genes and found that some can play important roles as molecular markers in plant evolutionary analysis.Accoridng to the sequence alignment of several angiospermous chloroplast genomes,we found that the GC content variation was the primary cause for different variation pattern of chloroplast coding and noncoding regions.That is,with the increase of GC content,the sequence was more conserved(e.g.,rRNA,tRNA,rbcL,matK genes were with high G+C content and more conserved than others);on the contrary,the genomic sequence tend to be more variated(e.g.,the Poly A or Poly T SSRs were quite common in non-coding regions).According to genome wide comparisons of Poaceae and other plants,the same situation was also found,which suggest that GC content variation was the primary cause for angiosperm chloroplast genome variation.To study the plant mitochondrial genome variation,we assembled and analyzed the cultivated rice Oryza saiva spp.aromatic mitochondrial and nuclear genome sequences.Its mitochondrial genome is 498676 bp coding for 64 genes;the assembled nuclear genome is 336 Mbp and codes for 39,860 genes.Genome-wide comparisons showed plenty of rearrangements and repeat sequences,resulting very low colinearity of the mitochondrial genome while its protein coding genes were relatively conserved.While its protein coding genes were relatively conserved.In addition,we also found rice mitochondrial genome integrated some genes that come from chloroplast genome.At the same time,it transfers substantial genome sequences to the nuclear chromosomes.Combined with some results from other studies,we proposed a new model for plant mitochondrial genome function and evolution.That is,plant mitochondrial genome served as a vector of plant entire horizontal genome transfer(EHGT)during plant evolution.Firstly,plant mitochondrial genome captured foreign genes or complete genomes of its own species or other species via repeat sequence mediated genome fusion.Then the mitochondrial genome transfer its genomic sequences to the nucleus.This model explained that angiosperm mitochondrial complex genome size and structure variations.So,continus transfers of plant mitochondrial genome sequences to the nucleus added angiosperm nuclear genome diversity and complexity,which provide basis for angiosperm evolution of species diversity.The developments of genome sequencing technologies have released more and more genomic big data of environmental biology.However,how to analyze and apply these initial data with the decline of sequencing cost has become an bottleneck.With the basis of above plant chloroplast and mitochondrial genome analyzing methods,wo continued improve data analyzing pipeline and created an intact organell genomes analyzing method-direct obtain complete chloroplast and mitochondrial genomes from animal and plant DNA sequencing data.We used this method obtain at least 92 complete chloroplast genomes from 3000 rice genome sequencing data;we analyzed some model plants chloroplast genome such as foxtail millet,green foxtail and Prunus mume;the animal mitochondrion genome of black flying fox;and also 19 complete mitochondrial genome sequeces of different watermelon accessions.These results confirms importance of better analyzing genomic big data,which provide basis for further data mining come from genomic big data of environmental biology.Finally,we also tried to isolate DNA from the inclusions of 100 million's years old Burmese ambe.Although the DNA was difficult to examined by using custom CTAB isolation method,further small amount genome sequencing technology may be aid ancient genome sequencing of ancient DNA come from amber,wich provide opportunity to study species paleogenomic evolution.