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Fig. 6 | BMC Plant Biology

Fig. 6

From: Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

Fig. 6

Circos plot based on complete chloroplast genome alignment between eleven Avena species presented here available in Genome Warehouse database and two Avena species available in NCBI (NC031650.1 and NC027468.1) with A. sativa_Liu312 as a reference. All data in rings showing the location relationship between tandem repeats, insertions/deletions (indels) and single nucleotide polymorphisms (SNPs) by R package circlize [35] in the non-overlapping 150 bp bins. For plastome alignment, rings “a-b” show the location of substitutions and SNPs, respectively. Dots with a high relative positions in rings “a-b” represent more polymorphic loci in the 150 bp window. Rings “c-d” show the location of deletions and insertions, respectively. Ring “e” shows tandem repeat (7 bp–95 bp) location by Phobos [31] with parameters of repeat length ≤ 100 bp and sequence identify ≥85%. The relatively height of columns in rings “c-e” represent the relative number of polymorphic loci belonging to deletions, insertions, or tandem repeats within the 150 bp window, respectively. Ring “f” shows A. sativa_Liu312 chloroplast map with coding genes labeled in green, rRNAs in yellow and tRNAs in blue. Blue shadows denote the surrounding location of tandem repeats and deletions; Red shadows denote the surrounding location of tandem repeats and insertions. LSC, SSC, IRs denote large single-copy, small single-copy, and inverted repeat regions of Avena plastome alignment. Total 702 tandem repeats, 141 insertions, 100 deletions, 992 SNPs, and 33 substitutions shown in the diagram

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