Volume 10, Issue 4, Pages 649-651 (April 2017) Brassica rapa Genome 2.0: A Reference Upgrade through Sequence Re-assembly and Gene Re-annotation  Chengcheng Cai, Xiaobo Wang, Bo Liu, Jian Wu, Jianli Liang, Yinan Cui, Feng Cheng, Xiaowu Wang  Molecular Plant  Volume 10, Issue 4, Pages 649-651 (April 2017) DOI: 10.1016/j.molp.2016.11.008 Copyright © 2017 The Author Terms and Conditions

Figure 1 Comparisons of Genomic Components between the B. rapa Genome Assemblies V1.5 and V2.0. (A) Percentage of genomic components in V1.5 (left) and V2.0 (right). (B) Size of genomic components in the two assemblies. (C) Distributions of insertion time dated by divergence rate of full-length LTRs (the rate of neutral mutation sites accumulated in the two terminal repeat sequences of LTRs). This was calculated in the two genome assemblies of B. rapa and the genome of B. oleracea. y-Axes on the left and right are the number and frequency distributions of LTRs, respectively. A new TE expansion event (∼6.5 million years) was observed in V2.0. (D) An example showing an extra annotated gene BraA01001064 in V2.0, compared with gap sequences in V1.5. (E) BraA03003780 is not present between genes Bra001448 and Bra001449 in V1.5, indicating the improved sequence assembly in V2.0. (F) The extra gene BraA03002268 in V2.0 showed high sequence similarity (identity, 100%; coverage, 100%) to intergenic sequences between Bra000197 and Bra000198 in V1.5, indicating a more comprehensive gene annotation in V2.0. Gene models colored in yellow are extra genes annotated in V2.0. Red arrows denote counterpart gene pairs that keep a perfect syntenic relationship in the two assemblies. Orange rectangles denote gap positions (Ns). Figures were plotted using the GEvo module in CoGe (https://genomevolution.org/coge/). Molecular Plant 2017 10, 649-651DOI: (10.1016/j.molp.2016.11.008) Copyright © 2017 The Author Terms and Conditions