Building Data Processing Platform For Sequencing Indica Rice Genomes Of Zhenshan 97 And Minghui 63

Rice is not only an important food crop,but also a model plant for biological research.Currently,the genome ofNipponbare(Oryza sativa L.ssp.japonica cv.Nipponbare),9311(Oryza sativa L.ssp indica cv 9311)and Oryza glaberrima have been obtained.Nipponbare can be a reference genome in study of japonicfa.However,there is no ndica genome of high quality available for indica researcher.Based on the BAC libraries and physical maps of Zhenshan 97(ZS97)and Minghui 63(MH63),using the strategy of sequencing large fragments separately,all the Minimum Tiling Path(MTP)BACs(Bacterial Artificial Chromosome,BAC)of ZS97 and MH63 were sequenced with SMRT technology on the PacBio RS II platform.The whole genome sequence of ZS97 and MH63 were acquired by assembling the contigs based on their physical map and reference genome.In order to manage the BAC library,physical map and sequencing data efficiently and systematically,our study established a sequencing data management platform,and processed our data using this platform.1)A laboratory information management system was developed,and all the BAC library and physical mapping data were stored in MySQL database.postHGAP is an important tool in our platform,which is used for vectors elimination and circularization of unitig sequences generated by HGAP assembly.It also be used in match acquired sequences and their BAC Ids.A total of 4,714 and 4,751 MTP BAC clones were picked for ZS97 and MH63,respectively.After running ’postHGAP’ for each HGAP assembly,we were able to identify 4,571 and 4,488 BAC sequences(4,415 and 4,320 of these were fully circularized)from ZS97 and MH63,respectively.The average lengths of sequenced BACs were 121 kb for ZS97 and 151 kb for MH63.Notably,the overall full-circularization rates for BAC pool sequencing were 94%(ZS97)and 91%(MH63).2)Gap sizes and sequence accuracy of assembled ZS97 and MH63 genomes were evaluated.The estimated amount of gap regions of each genome assembly was～37 Mb for ZS97 and-26 Mb for MH63.According to BAC overlapping of ZS97 and MH63,the sequencing accuracy of our study is over 99.9%.3)Structural variation analyses of the two genomes.131 Inversions between ZS97 and MH63 genome assemblies were detected,in which the inversion length is 1,960,828 bp for ZS97 and 1,848,622 bp for MH63.357 Inversions between ZS97 and Nipponbare genome assemblies were detected,in which the inversion length is 4,660,163 bp for ZS97 and 3,217,139 bp for Nipponbare.402 Inversions between MH63 and Nipponbare genome assemblies were detected,in which the inversion length is 5,642,744 bp for MH63 and 4,284,365 bp for Nipponbare.5,188 translocations were detected between ZS97 and MH63,and the corresponding length in ZS97 and MH63 is 8,943,636 bp and 8,942,631 bp,respectively.