Quality Analysis Of Rice Nipponbare And93-11Reference Sequences

A complete and high-quality genome reference sequence of an organism provides a solid foundation for a wide research community and determines the outcomes of relevant genomic, genetic, molecular and evolutionary research. Rice is an important food crop and a model plant of grasses, and therefore, was the first chosen crop plant for whole genome sequencing. The genome of the yaponic-representative rice variety, Nipponbare, was sequenced using a golden standard map-based clone-by-clone strategy. However, although the Nipponbare RefSeq has the best quality of the existing crop genome sequences, it still contains many assembly errors and gaps.To improve the Nipponbare RefSeq, first a robust method is required to detect the hidden assembly errors. Through alignments between BESs embedded in the Nipponbare BAC physical map and the Nipponbare RefSeq(IRGSP build5), we detected locations on the Nipponbare RefSeq that were inversely matched with BESs and could therefore be candidates of spurious inversions of assembly. We performed further analysis of5potential locations and confirmed assembly errors at those locations;4of them,2on chr4and2on chr11of the Nipponbare RefSeq, were found to be caused by reverse repetitive sequences flanking the locations. Our approach is effective in detecting spurious inversions in the Nipponbare RefSeq and can be applied for improving the sequence qualities of other genomes as well.Gaps in Nipponbare RefSeq have also restricted the quality improvement of sequence. There still exist45gaps in the current version of Nipponbare RefSeq. Among them,9are centromeric sequences, while36are physical gaps on chromosome arms. For physical gaps, there is currently no effective solution to the closing of the gaps. In this research, we aligned physical maps of93-11, Zhenshan97, Minghui63and Zhonghua11to the Nipponbare RefSeq. We found that physical map contigs of those species could overlap gaps of Nipponbare RefSeq. Clones overlapping or bridging the gaps of the Nipponbare RefSeq can be discovered among the clone contigs. Through experiment, BAC clones overlapping7gaps of Nipponbare RefSeq can be obtained, which could provide valuable information and resource for the closing of the gaps in the Nipponbare RefSeq.In this research, we aligned indica93-11physical map to93-11and Nipponbare RefSeqs respectively, and found controversial clone contigs. The corresponding locations of those clone contigs in the93-11RefSeq chromosomes were identified through FISH analysis. It is found that the above alignment controversy was caused by the assembly errors in the93-11genome sequence.In sum, although the genome sequence of Nipponbare and93-11have been accomplished, there is still much room for the quality improvement of both sequences. Even for Nipponbare RefSeq which has the best quality in the existing crop genome sequences to date, there still exist assembly errors and gaps. In this research, we put forward a robust method for detecting and correcting spurious inversions in Nipponbare RefSeq, which can be applied to improving sequence qualities of other genomes as well. Through the analysis of alignment, related resources for closing gaps in Nipponbare RefSeq is constructed. Some errors in the93-11sequence are also verified.