Green lineage plastid genomes

20Kbp

Atropa belladonna (Solanales)

Cupressus gigantea (Cupressales)

Gloeotilopsis sterilis (Ulotrichaels)

Dioscorea elephantipes (Dioscoreales)

Oenothera argillicola (Myrtales)

Arundinaria fargesii (Poales)

Euonymus japonicus (Celastrales)

Machilus balansae (Laurales)

Cicer arietinum (Fabales)

Botryococcus braunii (incertae sedis)

Marchantia polymorpha (Marchantiales)

Podococcus barteri (Arecales)

Osyris alba (Santalales)

Francoa sonchifolia (Geraniales)

Lonicera japonica (Dipsacales)

Ettlia pseudoalveolaris (Chlorococcales)

Hevea brasiliensis (Malpighiales)

Illicium oligandrum (Austrobaileyales)

Drimys granadensis (Canellales)

Cycas revoluta (Cycadales)

Platanus occidentalis (Proteales)

Nerium oleander (Gentianales)

Rheum palmatum (Caryophyllales)

Acacia ligulata (Fabales)

Triticum monococcum (Poales)

Berberis bealei (Ranunculales)

Gossypium anomalum (Malvales)

Nephroselmis astigmatica (Pseudoscoufieldiaels)

Araucaria heterophylla (Araucariales)

Chaetosphaeridium globosum (Coleochaetales)

Piper cenocladum (Piperales)

Angiopteris angustifolia (Marattiales)

Liquidambar formosana (Saxifragales)

Cypripedium formosanum (Asparagales)

Larrea tridentata (Zygophyllales)

Lysimachia coreana (Ericales)

Liriodendron tulipifera (Magnoliales)

Buxus microphylla (Buxales)

Chara vulgaris (Charales)

Petrosavia stellaris (Petrosaviales)

Physcomitrella patens (Funariales)

Phaseolus vulgaris (Fabales)

Ceratophyllum demersum (Ceratophyllales)

Trillium cuneatum (Liliales)

Megaleranthis saniculifolia (Ranunculales)

Artemisia frigida (Asterales)

Campynema ineare (Liliales)

Boea hygrometrica (Lamiales)

Ananas comosus (Poales)

Viscum minimum (Santalales)

Erodium texanum (Geraniales)

Hirtella physophora (Malpighiales)

Pyramimonas parkeae (Pyramimonadales)

Pinellia ternata (Alismatales)

Carludovica palmata (Pandanales)

Vitis rotundifolia (Vitales)

Chloranthus japonicus (Chloranthales)

Allium cepa (Asparagales)

Ostrya rehderiana (Fagales)

Fragaria vesca (Rosales)

Musa textilis (Zingiberales)

Pteridium aquilinum (Polypodiales)

Silybum marianum (Asterales)

Nuphar advena (Nymphaeales)

Tetracentron sinense (Trochodendrales)

Klebsormidium flaccidum (Klebsormidiales)

Allosyncarpia ternata (Myrtales)

Carnegiea gigantea (Caryophyllales)

Kalopanax septemlobus (Apiales)

Acorus americanus (Acorales)

Amborella trichopoda (Amborellales)

Rhizanthella gardneri (Asparagales)

Corynocarpus laevigata (Cucubitales)

Sapindus mukorossi (Sapindales)

Cannabis sativa (Rosales)

Ginkgo biloba (Ginkgoales)

Hibiscus syriacus (Malvales)

Arabidopsis thaliana (Brassicales)

Isoetes flaccida (Isoetales)

Picea sitchensis (Pinales)

Mesostigma viride (Mesostigmales)Chlorokybus atmophyticus (Klebsormidiales)

Land

plan

t (Em

bryo

phyte

s)

Gymnosperm

PteridophytesBryophytes

Charophytes

Green algae

Angiosperm

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.

Xylochloris irregularis NC_025534.1Watanabea reniformis NC_025526.1

Tydemania expeditionis NC_026796.1Trebouxiophyceae sp. NC_018569.1

Stigeoclonium helveticum NC_008372.1Stichococcus bacillaris NC_025527.1

Schizomeris leibleinii NC_015645.1Pyramimonas parkeae NC_012099.1

Pycnococcus provasolii NC_012097.1Pseudochloris wilhelmii NC_025547.1

Pseudendoclonium akinetum NC_008114.1Prasinoderma coloniale NC_024817.1

Pleodorina starrii NC_021109.1Planctonema lauterbornii NC_025541.1

Picocystis salinarum NC_024828.1Pedinomonas tuberculata NC_025530.1

Pedinomonas minor NC_016733.1Paradoxia multiseta NC_025540.1

Parachlorella kessleri NC_012978.1Pabia signiensis NC_025529.1

Ostreococcus tauri NC_008289.1Oltmannsiellopsis viridis NC_008099.1Oedogonium cardiacum NC_011031.1

Neocystis brevis NC_025535.1Myrmecia israelensis NC_025525.1

Monomastix sp. NC_012101.1Microthamnion kuetzingianum NC_025537.1

Micromonas sp. NC_012575.1Micromonas pusilla FJ858269.1

Marvania geminata NC_025549.1Lobosphaera incisa NC_025533.1Leptosira terrestris NC_009681.1

Koliella longiseta NC_025531.1Gonium pectorale NC_020438.1

Gloeotilopsis sterilis NC_025538.1Geminella minor NC_025544.1

Fusochloris perforata NC_025543.1Floydiella terrestris NC_014346.1

Ettlia pseudoalveolaris NC_025532.1Elliptochloris bilobata NC_025548.1

Dunaliella salina NC_016732.1Dictyochloropsis reticulata NC_025524.1

Dicloster acuatus NC_025546.1Coccomyxa subellipsoidea NC_015084.1

Choricystis parasitica NC_025539.1Chlorella vulgaris NC_001865.1

Chlorella variabilis NC_015359.1Chlorella sorokiniana NC_023835.1

Chlorella mirabilis NC_025528.1Chlamydomonas reinhardtii NC_005353.1

Bryopsis plumosa NC_026795.1Bryopsis hypnoides NC_013359.1

Botryococcus braunii NC_025545.1Bathycoccus prasinos NC_024811.1

Auxenochlorella protothecoides NC_023775.1Acutodesmus obliquus NC_008101.1Nephroselmis olivacea NC_000927.1

Nephroselmis astigmatica NC_024829.1

Green algal plastid genomes (58 spp.)

IRa IRb20Kbp

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.

Pseudotsuga sinensis NC_016064.1 PinalesPicea abies NC_021456.1 Pinales

Abies koreana NC_026892.1 PinalesCedrus deodara NC_014575.1 Pinales

Keteleeria davidiana NC_011930.1 PinalesPicea morrisonicola NC_016069.1 Pinales

Cathaya argyrophylla NC_014589.1 PinalesNageia nagi NC_023120.1 Araucariales

Podocarpus lambertii NC_023805.1 AraucarialesCephalotaxus oliveri NC_021110.1 Cupressales

Cephalotaxus wilsoniana NC_016063.1 CupressalesTaiwania cryptomerioides NC_016065.1 Cupressales

Taiwania flousiana NC_021441.1 CupressalesLarix decidua NC_016058.1 Pinales

Podocarpus totara NC_020361.1 AraucarialesRetrophyllum piresii NC_024827.1 Araucariales

Taxus mairei NC_020321.1 CupressalesMetasequoia glyptostroboides NC_027423.1 Cupressales

Cunninghamia lanceolata NC_021437.1 CupressalesAmentotaxus argotaenia NC_027581.1 CupressalesAmentotaxus formosana NC_024945.1 Cupressales

A1-type

IRa IRbSSCLSC20Kbp

Bowenia serrulata NC_026036.1 CycadalesCeratozamia hildae NC_026037.1 Cycadales

Cycas revoluta NC_020319.1 CycadalesCycas taitungensis NC_009618.1 CycadalesDioon spinulosum NC_027512.1 Cycadales

Encephalartos lehmannii NC_027514.1 CycadalesLepidozamia peroffskyana NC_027513.1 Cycadales

Macrozamia mountperriensis NC_027511.1 CycadalesStangeria eriopus NC_026041.1 CycadalesZamia furfuracea NC_026040.1 Cycadales

Ginkgo biloba NC_016986.1 GinkgoalesAgathis dammara NC_023119.1 Araucariales

Araucaria heterophylla NC_026450.1 AraucarialesWollemia nobilis NC_027235.1 Araucariales

Picea sitchensis NC_011152.3 PinalesPinus bungeana NC_028421.1 Pinales

Pinus contorta NC_011153.4 PinalesPinus gerardiana NC_011154.4 PinalesPinus koraiensis NC_004677.2 Pinales

Pinus krempfii NC_011155.4 PinalesPinus lambertiana NC_011156.4 Pinales

Pinus longaeva NC_011157.3 PinalesPinus massoniana NC_021439.1 PinalesPinus monophylla NC_011158.4 Pinales

Pinus nelsonii NC_011159.4 PinalesPinus strobus NC_026302.1 Pinales

Pinus taeda NC_021440.1 PinalesPinus taiwanensis NC_027415.1 Pinales

Pinus thunbergii NC_001631.1 PinalesCallitropsis vietnamensis NC_026298.1 Cupressales

Juniperus virginiana NC_024024.1 CupressalesJuniperus monosperma NC_024022.1 CupressalesHesperocyparis glabra NC_026297.1 Cupressales

Cupressus sempervirens NC_026296.1 CupressalesCupressus gigantea NC_028155.1 Cupressales

Callitropsis nootkatensis NC_026295.1 CupressalesGnetum gnemon NC_026301.1 Gnetales

Gnetum montanum NC_021438.1 GnetalesGnetum parvifolium NC_011942.1 Gnetales

Ephedra equisetina NC_011954.1 EphedralesWelwitschia mirabilis NC_010654.1 Welwitschiales

Cryptomeria japonica NC_010548.1 CupressalesJuniperus cedrus NC_028190.1 Cupressales

Juniperus scopulorum NC_024023.1 CupressalesJuniperus bermudiana NC_024021.1 CupressalesCalocedrus formosana NC_023121.1 Cupressales

1

A1 and rest 17 types gymnosperm plastid genomes (67 spp.)

2

3

4

5

6

7

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.)

IRa IRbSSCLSC20Kbp

Vigna unguiculata NC_018051.1Vigna radiata NC_013843.1

Vigna angularis NC_021091.1Wisteria floribunda NC_027677.1Phaseolus vulgaris NC_009259.1

Oenothera parviflora NC_010362.1Oenothera glazioviana NC_010360.1

Oenothera elata NC_002693.2Oenothera biennis NC_010361.1

Oenothera argillicola NC_010358.1Lotus japonicus NC_002694.1

Medicago papillosa NC_027154.1Medicago hybrida NC_027153.1

Millettia pinnata NC_016708.2Lens culinaris NC_027152.1

Glycyrrhiza glabra NC_024038.1Glycine tomentella NC_021636.1Glycine syndetika NC_021650.1

Glycine stenophita NC_021646.1Glycine soja NC_022868.1Glycine max NC_007942.1

Glycine falcata NC_021649.1Glycine dolichocarpa NC_021648.1

Glycine cyrtoloba NC_021645.1Glycine canescens NC_021647.1

Cypripedium formosanum NC_026772.1Cicer arietinum NC_011163.1

Astragalus nakaianus NC_028171.1

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.)

IRa IRbSSCLSC20Kbp

Pisum sativum NC_014057.1 (Fabales)Trifolium aureum NC_024035.1 (Fabales)Trifolium boissieri NC_025743.1 (Fabales)

Trifolium grandiflorum NC_024034.1 (Fabales)Trifolium glanduliferum NC_025744.1 (Fabales)

Trifolium meduseum NC_024166.1 (Fabales)Trifolium repens NC_024036.1 (Fabales)

Trifolium strictum NC_025745.1 (Fabales)Trifolium subterraneum NC_011828.1 (Fabales)

Vicia sativa NC_027155.1 (Fabales)Lathyrus clymenum NC_027148.1 (Fabales)

Lathyrus sativus NC_014063.1 (Fabales)Lupinus luteus NC_023090.1 (Fabales)

Lathyrus inconspicuus NC_027149.1 (Fabales)Lathyrus graminifolius NC_027074.1 (Fabales)

Lathyrus palustris NC_027078.1 (Fabales)Lathyrus davidii NC_027073.1 (Fabales)

Lathyrus pubescens NC_027079.1 (Fabales)Lathyrus odoratus NC_027150.1 (Fabales)

Lathyrus tingitanus NC_027151.1 (Fabales)Lathyrus venosus NC_027080.1 (Fabales)

Lathyrus japonicus NC_027075.1 (Fabales)Lathyrus littoralis NC_027076.1 (Fabales)

Lathyrus ochroleucus NC_027077.1 (Fabales)

Cuscuta exaltata NC_009963.1 (Solanales)Cuscuta reflexa NC_009766.1 (Solanales)

Orobanche ramosa NC_023465.1 (Lamiales)Sciaphila densiflora NC_027659.1 (Pandanales)

Vaccinium macrocarpon NC_019616.1 (Ericales)Carnegiea gigantea NC_027618.1 (Caryophyllales)

Petrosavia stellaris NC_023356.1 (Petrosaviales)

Erodium carvifolium NC_015083.1 (Geraniales)Erodium chrysanthum NC_027065.1 (Geraniales)

Erodium texanum NC_014569.1 (Geraniales)Erodium trifolium NC_024635.1 (Geraniales)

Geranium palmatum NC_014573.1 (Geraniales)Hypseocharis bilobata NC_023260.1 (Geraniales)

Viviania marifolia NC_023259.1 (Geraniales)Erodium crassifolium NC_025906.1 (Geraniales)

Monsonia speciosa NC_014582.1 (Geraniales)Erodium absinthoides NC_026847.1 (Geraniales)

Erodium gruinum NC_025907.1 (Geraniales)Pelargonium alternans NC_023261.1 (Geraniales)Pelargonium australe NC_028053.1 (Geraniales)

Pelargonium cotyledonis NC_028052.1 (Geraniales)Pelargonium x hortorum NC_008454.1 (Geraniales)

Pelargonium dichondrifolium NC_028051.1 (Geraniales)Silene noctiflora NC_016728.1 (Caryophyllales)Silene paradoxa NC_023360.1 (Caryophyllales)Silene conoidea NC_023358.1 (Caryophyllales)

Silene conica NC_016729.1 (Caryophyllales)

Adenophora remotiflora NC_026999.1 (Asterales)Campanula takesimana NC_026203.1 (Asterales)

Hanabusaya asiatica NC_024732.1 (Asterales)Trachelium caeruleum NC_010442.1 (Asterales)

Carex siderosticta NC_027250.1 (Poales)Stipa lipskyi NC_028444.1 (Poales)

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.

50Kbp