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1.
Figure 1

Figure 1. From: Unleashing the Genome of Brassica Rapa.

Phylogeny of Brassica and relatives marking the relative placement of lineage divergence and polyploidy events. Polyploidies are named according to the Arabidopsis convention of α (most recent in the linage of Arabidopsis), β (second most recent), and γ (eudicot paleohexaploidy).

Haibao Tang, et al. Front Plant Sci. 2012;3:172.
2.
Figure 3

Figure 3. From: Unleashing the Genome of Brassica Rapa.

(A) Histogram of log 10 transformed Ks values of syntenic gene pairs identified in Figure 2. (B) Syntenic dotplot of self–self Brassica rapa comparison with gene pairs colored by their Ks values shown in (A). Results may be regenerated: http://genomevolution.org/r/4sr4

Haibao Tang, et al. Front Plant Sci. 2012;3:172.
3.
Figure 2

Figure 2. From: Unleashing the Genome of Brassica Rapa.

Syntenic dotplot of self–self Brassica rapa comparison. Horizontal and vertical gray lines separate chromosomes. Green dots are syntenic gene pairs identified through collinearity. Red dashed lines band and red arrows point to large intra-genomic syntenic signal showing a 3:3 syntenic relationship. Results may be regenerated: http://genomevolution.org/r/4srl

Haibao Tang, et al. Front Plant Sci. 2012;3:172.
4.
Figure 4

Figure 4. From: Unleashing the Genome of Brassica Rapa.

Syntenic dotplots of Brassica rapa (y axis) vs. Arabidopsis thaliana (x axis). Vertical and horizontal gray lines separate chromosomes and contigs. Syntenic gene pairs are colored dots on the dotplot. Red dashed lines highlight sets of syntenic regions. (A) Syntenic gene pairs colored green. Results may be regenerated: http://genomevolution.org/r/4skv. (B) Syntenic gene pairs colored based on their synonymous rate values. Results may be regenerated: http://genomevolution.org/r/4sl1. (C) Syntenic gene pairs after screening for a 3:1 (rapa:thaliana) syntenic depth. These are orthologous gene pairs. Results may be regenerated: http://genomevolution.org/r/4sl5. (D) Histogram of synonymous rate values for all syntenic gene-paris. Colors in this histogram are mapped to dotplot shown in (B). (E) Histogram of synonymous rate values for syntenic gene pairs screened for a 3:1 syntenic depth. Colors are mapped to dotplot shown in (C).

Haibao Tang, et al. Front Plant Sci. 2012;3:172.
5.
Figure 6

Figure 6. From: Unleashing the Genome of Brassica Rapa.

Conserved non-coding sequence analysis of Arabidopsis TOC1 gene and orthologs from Brassica rapa using GEvo. (A) Gene models are composite arrows where green or yellow regions represent protein coding sequence, blue is mRNA, and gray is the full extent of the gene. Regions of sequence similar are as in Figure 5 and were identified using BLASTN; such regions are in the opposite orientation if drawn below the dashed line. The bottom Brassica region has GEvo’s slider bars adjusted to border the two most 5′ CNSs. Results may be regenerated: http://genomevolution.org/r/4t5e (B) HSPView’s report on the BlastN HSP containing Evening Element (AAAATATCT). (C) Using SeqView to visualize the sequence encompassing the two most 5′ CNSs in Bra035933 with the Evening Element highlighted. Sequence can be obtained: http://genomevolution.org/r/4t6t

Haibao Tang, et al. Front Plant Sci. 2012;3:172.
6.
Figure 5

Figure 5. From: Unleashing the Genome of Brassica Rapa.

Comparing orthologous syntenic genomic regions between Brassica rapa (Br) and Arabidopsis thaliana (At) with GEvo. Each panel represents a genomic region with the dashed line separating the top and bottom strands of DNA. Orange in the background signifies unsequenced gaps. Gene models are drawn above and below dashed line as composite colored arrows. The At TOC1 gene and its Br orthologs are colored yellow (blue arrows). Regions of sequence similarity are drawn as colored boxes, and may be connected using transparent wedges. (A) Syntenic pattern of collinear regions of sequence similarity as identified by LASTZ. Results may be regenerated: http://genomevolution.org/r/4sma. (B) Fractionation of Br’s gene content; LASTZ comparison to At’s gene content. Genes covered by a region of sequence similarity are colored purple. Note that At’s gene content is represented among the combined Br regions. Results may be regenerated: http://genomevolution.org/r/4smb. (C) Picking the wrong algorithm for the comparison. BLASTN with settings for detecting CNSs used to compare sequences results in too many non-syntenic regions of sequence similarity. Results may be regenerated: http://genomevolution.org/r/4smc

Haibao Tang, et al. Front Plant Sci. 2012;3:172.

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