Assembly And Analysis Of Oryza Australiensis Genome

As the ancestor of cultivated rice,wild rice has accumulated many excellent traits in the process of evolution to adapt to the complex ecological and geographical environment.Wild rice has accumulated a large number of excellent traits and become a natural gene pool through long-term survival pressure and natural pressure selection.For breeders,wild rice has many genes that are not present in the genome of cultivated rice or have been degraded or disappeared.It has very rich genetic diversity and is of great significance to breeding work.Strengthening the development and utilization of the genetic diversity of wild rice can effectively help rice production and quality improvement breeding.Oryza australiensis,an Australian wild rice originated from northern Australia and belongs to the rice species of the Oryza EE genome.Compared with the AA genome of Asian cultivated rice（Oryza sativa L）,there are many differences.In this study,the Australian wild rice was used as material to obtain the third-generation Oxford Nanopore,second-generation Illumina and RNA-seq sequencing data.Then the third-generation combined with the secondgeneration data genome assembly method was used to complete the Australian wild rice genome assembly.Genes and transposons were also annotated,and related genomics researches were carried out.The main results of this study are as follows:1.The genome assembly of Oryza australiensis was completed using third generation data genome assemble software.After assembly,the contig N50 was 33.394 Mb.The assembled genome size was 890.8 Mb,of which 99.22%was anchored to 12 pseudochromosomes.2.Gene structure annotation and function annotation were performed and then intergrated to the final annotation results.In all,39,680 genes were successfully annotated.Repeat annotation software was used to annotate the repetitive sequences of the genome.The repeat sequence accounted for 68.29%of Australian wild rice genome,and the number was significantly higher than that in Nipponbare rice（13.75%）.3.LTR retrotransposons was identified and the divergence of the two LTR sequences in each complete LTR retrotransposon was calculated and the insertion time of LTR was estimated using the rate of molecular colck.A LTR retrotransposon burst was identified within 0.4-0.6 Mya,which directly caused the expansion of the genome of Oryza australiensis.4.The collinearity between the genome of Oryza australiensis and its relatives was calculated,and a phylogenetic analysis between Oryza australiensis and other rice varieties was carried out.