Comparative Plastome Structural Analysis

Whole-genome alignments were performed to examine the arrangement of locally colinear blocks (LCBs) of different cactus plastome structural types using progressiveMauve (v2.3.1) [76 (link)] with default parameters. Before this, we manually removed the last IR region of plastomes. The plastome syntenies were plotted using Mcscan (v.2) [77 (link)] implemented in TBtools (v.1.106) [78 (link)]. Specifically, we first obtained BLASTn results between the pairs of plastomes (IR removed), and the e-value was set as 1e-5. Then, the alignments were split into 10 bp fragments, which were forced to be used as a ‘gene’ in TBtools (v.1.106). The dot plots of plastomes were drawn using MAFFT online version [79 (link)] or Gepard (v1.40) [80 (link)]. Boundary changes in the IR regions were drawn manually.

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Yu J., Li J., Zuo Y., Qin Q., Zeng S., Rennenberg H, & Deng H. (2023). Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae). BMC Plant Biology, 23, 132.

Publication 2023

Cactus Gene Genome Syntenies

Corresponding Organization : Southwest University

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Variable analysis

independent variables

Arrangement of locally colinear blocks (LCBs) of different cactus plastome structural types

dependent variables

Plastome syntenies

control variables

Default parameters of progressiveMauve (v2.3.1) used for whole-genome alignments
Last IR region of plastomes manually removed before whole-genome alignments
E-value of 1e-5 set for BLASTn results between pairs of plastomes (IR removed)
Alignments split into 10 bp fragments and forced to be used as a 'gene' in TBtools (v.1.106)
Dot plots of plastomes drawn using MAFFT online version or Gepard (v1.40)

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