Volume 10, Issue 6, Pages (June 2017)

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Volume 10, Issue 6, Pages 895-898 (June 2017) BioNano Genome Map Resource for Oryza sativa ssp. japonica and indica and Its Application in Rice Genome Sequence Correction and Gap Filling Ping Chen, Xinyun Jing, Baosheng Liao, Yan Zhu, Jiang Xu, Renyi Liu, Yinhong Zhao, Xuan Li Molecular Plant Volume 10, Issue 6, Pages 895-898 (June 2017) DOI: 10.1016/j.molp.2017.02.003 Copyright © 2017 The Author Terms and Conditions

Figure 1 Genome Structural Issues Detected by BioNano Genome Maps in Nipponbare and 93-11. (A) Discrepancies detected between BioNano genome maps and corresponding reference genomes of Nipponbare (left) and 93-11 (right). There were 58, 120, 3, and 81 discrepancies found for groups I, II, III, and IV (defined in the main text) in Nipponbare, and 1414, 852, 15, and 1138 found in 93-11 (Supplemental Datasets 3 and 4). (B) Discrepancies detected in the old and latest versions of Nipponbare and 93-11 reference genomes. In Nipponbare, an erroneous inversion was detected in IRGSPv5 (chr10:7894177-7974664) but corrected in the latest version IRGSP1.0 (upper left), whereas another inversion was detected in IRGSP1.0 (chr11:19826358-19840926) but not in the old version IRGSPv5 (lower left). In 93-11, an erroneous insertion was found in 93-11v1 (chr02: 33054748-33127908) but corrected in the latest version 93-11v2 (upper right), whereas an erroneous translocation was found in 93-11v2 (chr10:24114686-24135570) but not in the old version 93-11v1. (C) Examples of complex sequence structure in gaps. Sequence repeat units are marked with red or purple arrows (more details in the main text). (D) Analyses of tandem repeats in comparison of rice reference genomes and the BioNano maps. (E) The BAC scaffolding error in Chr11 of IRGSP1.0 found in alignment with the BioNano map. Based on BioNano map contig640, the BAC_3335 (AC120507) was reconstructed from 23 contigs to form four repeats units (black box). BAC_3335 lay between BAC_3334 (AC112658) and BAC_3336 (AC145319) according to BioNano contig640 but was missing in IRGSP1.0 (Chr11: 28547360-28644282). (F) An example of a defect region in 93-11v2 for which the BioNano map (contig788) aligned perfectly with IRGSP1.0. A 23-kb fragment with six gaps was erroneously anchored in 93-11v2 (chr12:1174639-1197895). In 93-11v2Plus, the 23-kb fragment was reduced to a 28-bp sequence (in box), confirmed by PCR product and its sequencing result. Molecular Plant 2017 10, 895-898DOI: (10.1016/j.molp.2017.02.003) Copyright © 2017 The Author Terms and Conditions