Volume 8, Issue 3, Pages 489-492 (March 2015) De Novo Plant Genome Assembly Based on Chromatin Interactions: A Case Study of Arabidopsis thaliana  Ting Xie, Jue-Fei Zheng, Sheng Liu, Cheng Peng, Yong-Ming Zhou, Qing-Yong Yang, Hong-Yu Zhang  Molecular Plant  Volume 8, Issue 3, Pages 489-492 (March 2015) DOI: 10.1016/j.molp.2014.12.015 Copyright © 2015 The Author Terms and Conditions

Figure 1 Results of Chromatin Interaction-based Assembly of Ler. (A) Clustering predictions for the de novo assembly of Ler. The 896 scaffolds in the prediction shown on the x axis are aligned with the reference genome (Col). The prediction for each scaffold is marked by a dot and colored according to its true chromosome. The y axis shows the five groups that were created by the clustering assembly with the order chosen for the purposes of clarity. (B) Comparison between the clustering results of the chromatin interaction-based approach and genetic mapping. Blue and red colors indicate agreement and disagreement with the genetic map predictions, respectively. The gray color indicates that the scaffolds were not clustered in Lachesis. (C–G) Ordering and orienting predictions on five chromosome groups in the de novo assembly. For each ordering, only the scaffolds with greater than 15 HindIII restriction sites that were considered informative by Lachesis on the chromosome are shown. The value that is displayed on the x axis is the order of the predictions for these scaffolds. The value that is displayed on the y axis is the true position of these scaffolds along the Ler chromosomes (the scaffolds that could not be aligned to the reference genome were identified by 0 bp). The identity of the chromosome, the number of scaffolds in the ordering, and the reference length of the chromosome are also listed in each panel. (H) Comparison between the ordering results of the chromatin interaction-based approach and genetic mapping. Blue and red colors indicate agreement and disagreement with the genetic map predictions, respectively. The gray color indicates that the scaffolds were not ordered in Lachesis. (I–M) Distribution of assessment for the chromatin interaction-based assembly in low-interaction sample levels. Different percentages (x axis) of the total interactions are randomly shown 1000 times in the chromatin interaction-based assembly. The y axis represents the distribution of the length proportion of the sum of the scaffolds that were clustered into groups (I), mis-clustered (J), ordered (K), mis-ordered (L), or mis-oriented (M). Molecular Plant 2015 8, 489-492DOI: (10.1016/j.molp.2014.12.015) Copyright © 2015 The Author Terms and Conditions