Indica Kasalath Whole Genome Assemble Annotation And Comparative Analysis Of Different Rice Subspecies

In the process of long-term natural selection and artificial domestication, significant changes have taken place in the genome of rice, there is a major difference in different rice subspecies genomes. Different rice subspecies genome have large structural variations and SNPs in the rice population. Based on these differences between the genome sequences, we could compare differences in characters among different individuals, revealing the similarities and differences between the rice accessions, analyzing gene functional expression, epigenetic regulation functions, rice origin and evolutionary relationships and molecular breeding.Kasalath (Kacha Lota Dhan) is an important representative of indica rice genome. In molecular biology research, the callus of Kasalath can easily serve as a receptor, which has the vital significance in terms of genetic transformation. Features readily transformed in Kasalath have successfully put many high yields and quality agricultural traits transformed into other rice subspecies, which dramatically enhance disease resistance, increases yield and improves quality.In this study, Kasalath genome sequences were sequenced through high-throughput sequencing technologies, filtered with strict quality control, adopted the de novo assemble strategy, combined with BAC-end released on the internet. Finally, we obtained a high-quality draft genome sequence of Kasalath genome size of360Mb, which covered90%of estimated Kasalath genome (406.3Mb).The Kasalath genome N50length is up to318KB, scaffolds with position information of genome size is253.4Mb. Based on the de novo and homologous method, it is estimated that repeat elements account for about28.01％of the genome, which was involved with a relatively high proportion of the DNAtransposon, LTR and dispersed repetitive sequence. A total of37,266protein-coding genes was identified by gene prediction modeling, most of which were supported by cDNA and RNA sequencing data. The total GC content of genes is45.66%. On average, each gene contains3.88exons, and exons GC content is55.57%. We also identified616tRNAs,2471miRNA sites and668C/D box snoRNAs. We also annotated the functions of all the coding genes, the GO enrichment and the metabolic pathways.In the rice population, we respectively aligned the Kasalath,93-11and50subspecies rice resequencing data to Nipponbare genome, identified high quality SNP and transposon element information. Ultimately, we found out the Kasalath specific SNP among rice population, then annotated the SNP loci and clustered the related genes. The results showed that most of the SNP sites were retrotransposon proteins and the majority of genes were significantly involved in ’response to biotic stimulus’,‘response to stress’,response to stimulus’,‘signaling’and‘transferase activity.’...