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Figure S6. Structural comparison of green lineage plastid genomes based on MUMmerplot result. All plastid genome architectures are compared with the plastid genome of Ostrya rehderiana as recent diverged species.
Figure S7. Structural comparison of 58 green algal plastid genomes based on MUMmerplot result. All plastid genome architectures are compared with the plastid genome of Nephroselmis astigmatica as one of early diverged species. Empty spaces indicate inverted repeat (IR) regions.
Zygnema circumcarinatum NC_008117.1
Staurastrum punctulatum NC_008116.1
Roya anglica NC_024168.1
Mesotaenium endlicherianum NC_024169.1
Mesostigma viride NC_002186.1
Koliella corcontica NC_025536.1
Klebsormidium flaccidum NC_024167.1
Interfilum terricola NC_025542.1
Chlorokybus atmophyticus NC_008822.1
Chara vulgaris NC_008097.1
Chaetosphaeridium globosum NC_004115.1
Charophytes plastid genomes (11 spp.)
20Kbp
Figure S8. Structural comparison of 11 charophytes plastid genomes based on MUMmerplot result. All plastid genome architectures are compared with the plastid genome of Chaetosphaeridium globosum as one of recent diverged species. Empty spaces indicate inverted repeat (IR) regions.
Bryophytes plastid genomes (12 spp.)
Pteridophytes plastid genomes (18 spp.)
Tetraphis pellucida NC_024291.1
Syntrichia ruralis NC_012052.1
Sanionia uncinata NC_025668.1
Ptilidium pulcherrimum NC_015402.1
Physcomitrella patens NC_005087.1
Pellia endiviifolia NC_019628.1
Orthotrichum rogeri NC_026212.1
Nyholmiella obtusifolia NC_026979.1
Nothoceros aenigmaticus NC_020259.1
Marchantia polymorpha NC_001319.1
Anthoceros angustus NC_004543.1
Aneura mirabilis NC_010359.1
Selaginella moellendorffii NC_013086.1
Pteridium aquilinum NC_014348.1
Psilotum nudum NC_003386.1
Osmundastrum cinnamomeum NC_024157.1
Ophioglossum californicum NC_020147.1
Myriopteris lindheimeri NC_014592.1
Marsilea crenata NC_022137.1
Mankyua chejuensis NC_017006.1
Lygodium japonicum NC_022136.1
Isoetes flaccida NC_014675.1
Huperzia lucidula NC_006861.1
Equisetum hyemale NC_020146.1
Equisetum arvense NC_014699.1
Diplopterygium glaucum NC_024158.1
Angiopteris evecta NC_008829.1
Angiopteris angustifolia NC_026300.1
Alsophila spinulosa NC_012818.1
Adiantum capillus veneris NC_004766.1
IRa IRbSSCLSC20Kbp
IRa IRbSSCLSC20Kbp
Figure S9. Structural comparison of 12 bryophytes and 18 pteridophytes plastid genomes based on MUMmerplot result. Empty spaces indicate inverted repeat (IR) regions. Between IR regions, there is small single copy (SSC) region in plastid genomes. LSC indicates long single copy region in plastid genomes. All bryophytes and pteridophytes plastid genome architectures are compared with the plastid genome of Aneura mirabilis and Adiantum capillus-veneris respectively as the most popular genome structure contained species.
A1 and rest 17 types gymnosperm plastid genomes (67 spp.)
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5
6
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89
10-17
Figure S10. Structural comparison of 67 gymnosperm plastid genomes based on MUMmerplot result. Empty spaces indicate inverted repeat (IR) regions. Between IR regions, there is small single copy (SSC) region in plastid genomes. LSC indicates long single copy region in plastid genomes. All plastid genome architectures are compared with the plastid genome of Bowenia serrulata as one of A1-type plastid genome architectures contained species. Fourteen species show A1-type plastid genome architectures.
Type 1 (A1) of angiosperm plastid genomes (437 / 703 angiosperm spp.)
IRa IRbSSCLSC20Kbp
Figure S11. A1-type of angiosperm plastid genomes from MUMmerplot result using 437 angiosperm species. Empty spaces indicate inverted repeat (IR) regions. Between IR regions, there is small single copy (SSC) region in plastid genomes. LSC indicates long single copy region in plastid genomes. All plastid genome architectures are compared with the plastid genome of Amborella trichopoda as one of popular genome architecture contained species in angiosperms.
Type 2 (A2) of angiosperm plastid genomes (181 / 703 angiosperm spp.)
IRa IRbSSCLSC20Kbp
Figure S12. A2-type of angiosperm plastid genomes from MUMmerplot result using 181 angiosperm species. Empty spaces indicate inverted repeat (IR) regions. Between IR regions, there is small single copy (SSC) region in plastid genomes. LSC indicates long single copy region in plastid genomes. All plastid genome architectures are compared with the plastid genome of Amborella trichopoda as one of popular genome architecture contained species in angiosperms.
Type 3 (A3) of angiosperm plastid genomes (28 / 703 angiosperm spp.)
Figure S13. A3-type of angiosperm plastid genomes from MUMmerplot result using 28 angiosperm species. Empty spaces indicate inverted repeat (IR) regions. Between IR regions, there is small single copy (SSC) region in plastid genomes. LSC indicates long single copy region in plastid genomes. All plastid genome architectures are compared with the plastid genome of Amborella trichopoda as one of popular genome architecture contained species in angiosperms.
Rest-type of angiosperm plastid genomes (57 / 703 angiosperm spp.)
Figure S14. Rest-type of angiosperm plastid genomes from MUMmerplot result using 57 angiosperm species. Empty spaces indicate inverted repeat (IR) regions. Between IR regions, there is small single copy (SSC) region in plastid genomes. LSC indicates long single copy region in plastid genomes. All plastid genome architectures are compared with the plastid genome of Amborella trichopoda as one of popular genome architecture contained species in angiosperms.
Volvox carteri f. nagariensis GU084820 (Volvocaceae)
Pleodorina starrii NC_021109 (Volvocaceae)
Gonium pectorale NC_020438 (Goniaceae)
Volvocine algal plastid genomes
Figure S15. Structural comparison of volvocine algal plastid genomes based on MUMmerplot result. All plastid genome architectures are compared with the plastid genome of Volvox carteri f. nagariensis.