Indica Rice CO39 Genome Assembly, Annotation And Analysis

Rice is one of the most important crops and a staple food for more than half of the population in the world.It is urgently needed to enhance grain yield of rice to meet the population increase in the world.But rice plants are always growing under the environmental stresses,including biotic and abiotic stresses,which might cause large loss of rice yield.CO39 is one variety of indica rice.Previous researches indicated that CO39 was highly susceptible to blast disease,but resistant to abiotic stress,such as high temperature.Therefore,CO39 has been used as parent line to develop a lot of rice populations.However,the genome and annotation of CO39 is not available till now,which limits the research on CO39 populations.In this study,CO39 genome DNA was re-sequenced.Then,CO39 genome DNA was assembly and annotated in detail.The results in this study were summarized in the following.1.The genome DNA of CO39 was re-sequenced by using the advanced next-generation sequencing(NGS)technologies.The sequencing reads were mapped to O.sativa L.&japonica var.Nipponbare genome.The results showed that 356 Mb of CO39 genome DNA was consensus on Nipponbare genome DNA,showing 82.43%genome coverage.However,61Mb contigs could not be anchored to Nipponbare genome.2.Among the contigs of CO39 genome,we annotated 3,244 protein-coding genes.A database,CO39 genome database,was developed to deposit the DNA sequences,annotation and SNPs of CO39 genome.Researchers could open-access to the database at http://localhost/snp2gene/snp.php to use the CO39 genome information.3.When Nipponbare genome was used as reference genome,2,111,981 single nucleotide polymorphisms(SNPs)and 40,980 large Insertion/Deletion(InDel)sites(>100 bp)were detected in CO39 genome.Over 69.5Mb inserted sequences and 50.4Mb deleted sequences were also existed in the CO39 genome.After analyzing on the SNPs and Structural Variations(SVs),we found some deleted genes in CO39 genome.4.The NGS short reads of 50 publicly available rice accession genome were downloaded and mapped to Nipponbare,9311 and CO39 genome,respectively.The genome coverage of different rice variety genomes based on Nipponbare,9311 and CO39 were compared.The result showed that the assembly quality of 5 rice variety genome based on CO39 was better than that based on Nipponbare or 9311,indicating that CO39 genome was valuable as a reference genome.In this study,we assembled and analyzed the an indica rice,CO39 genome.This was supplement to the rice reference genome data,also helpful for the genetic research of CO39 rice population.