Reconstructing the complex evolutionary history of mobile ... · Different individuals of Gelidium elegans, Porphyra pulchra and Sporolithon durum were used to check the presence

Supplementary information

Reconstructing the complex evolutionary history of mobile

plasmids in red algal genomes

JunMo Lee1, Kyeong Mi Kim2, Eun Chan Yang3, Kathy A. Miller4, Sung Min Boo5,

Debashish Bhattacharya6, & Hwan Su Yoon1,*

List of Tables

Table S1. Information about the NGS data for five newly sequenced red algal plastid

genomes.

Table S2. Gene compositions of red algal plastid genomes.

Table S3. List of 193 plastid protein-coding genes used in the ML tree search.

Table S4. Newly annotated genes from previously published red algal plastid genomes.

These genes have been overlooked, underestimated or mis-annotated in previous studies.

Table S5. Results of BLASTx search using plasmid-derived regions in plastid genomes.

Cutoff of e-value is 1.0e-05 and two cases of relaxed e-value (2.0e-01 and 3.0e-03) are adapted

to Gle4293 orf4 of Sporolithon and Gro4059 orf2347 of Grateloupia. Abbreviations: HyP

indicates hypothetical protein as in orf for the open reading frame, PG for the pseudogenized

gene. In the plastid genome region of Sporolithon durum, between argB and ftsH gene, 4.2

kb (non-coding) includes two plasmid-derived pseudogenized genes. In the plastid genome of

S. durum, the region between rRNAs and ycf27 pm_orf86 shows uncertain mixed plasmid

signals from BLASTx search results. The plastid genome of Gracilariopsis tenuistipitata var.

liui also shows uncertain plasmid signals between leuD and psbD gene.

Table S6. Samples used in this study.

Table S7. Combined and pseudogenized cases of plasmid-derived regions. Several partial

regions of plasmid-derived regions were combined into each single or pseudogenized gene

based on their alignment as complementary parts. Detailed information about these sequences

is shown below the table. In the genome of Moorea producens, hypothetical protein (GI:

332351884) and both flanking regions were combined and these bacterial sequences were

translated using the Bacterial, Archaeal and Plant Plastid Code (codon table 11). In the

mitochondrial genome of Marchantia polymorpha, orf196 (GI: 11467138) and orf207 (GI:

11467137) were combined with their flanking non-coding regions respectively, and their two

regions were also combined as a single pseudo-gene (89 bp interval between two regions).

For phylogenetic analysis, these plant mitochondrial sequences have been translated to amino

acids using a standard code (codon table 1). In red algae, each part of pseudo-gene regions

was translated using the codon table 11 and combined serially.

Table S8. Contents of subfamily groups in DNA polymerase type-B family catalytic domain

(POLBc) superfamily from conserved domain database (CDD).

Table S9. List of published red algal plasmids. 13 species out of a total 36 red algal species

surveyed contain plasmids (marked as “present [O]”). Among 13 species, 14 plasmid

sequences were reported from only 5 species (Porphyra pulchra, Pyropia tenera, Gracilaria

chilensis, Gracilaria robusta and Gracilariopsis lemaneiformis) in the NCBI database. 14

plasmid sequences encoded 56 open-reading frames (orf).

Table S10. Primer information for population analysis. Different individuals of Gelidium

elegans, Porphyra pulchra and Sporolithon durum were used to check the presence or

absence of the plasmid-derived region. The plasmid-derived regions of G. elegans (between

ycf27 and psbD gene), P. pulchra (between orf121 and apcF gene) and S. durum (between

pseudogenized syfB and rps1 gene) were confirmed by PCR.

List of Figures

Fig. S1. Plastid genome map of Porphyra pulchra. Functional gene groups are color-coded.

Genes drawn inside of the circle indicate the transcriptionally clockwise strand, and genes on

outside indicate the counter-clockwise strand.

Fig. S2. Plastid genome map of Sporolithon durugm. Functional gene groups are color-coded.



Fig. S3. Plastid genome map of Gelidium elegans. Functional gene groups are color-coded.



Fig. S4. Plastid genome map of Gelidium vagum. Functional gene groups are color-coded.



Fig. S5. Plastid genome map of Gracilaria chilensis. Functional gene groups are color-coded.



Fig. S6. Maximum likelihood tree based on aligned amino acid sequences of concatenated

193 protein encoding genes from 16 published and 5 new (underlined) plastid genomes (2000

replications, bootstrap support > 50%).

Fig. S7. Synteny of all plasmid-derived regions in red algae. Colored boxes indicate each

homolog region in red algal plasmid and plastid genomes. Porphyra pulchra plasmid Pp6859

orf4 and orf5 homolog regions are also presented with two cyanobacterial species.

Fig. S8. Maximum likelihood tree based on aligned amino acid sequences of Gracilariopsis

lemaneiformis plasmid GL3.5 orf2 related genes and its homologs from BLASTp search

(cutoff e-value 1.0e-03) (2000 replications, bootstrap support > 50%). Taxon information and

their sequence localities are color-coded as follows: bacteria (black), red algae (red), virus

(violet), plastid (green) and plasmid (brown).

Fig. S9. Maximum likelihood tree based on aligned amino acid sequences of red algal

replicase genes from Pyropia tenera (GI: 254029132, 17980119) plasmids, Porphyra pulchra

plasmid (GI: 7108461, 7108459, 7108457) and their homologs from BLASTp search (cutoff

e-value 1.0e-05) (2000 replications, bootstrap support > 50%). Taxon information and their

sequence localities were indicated with color-code as follows: parasitic bacteria (blue), plant

(green), red algae (red), rhizaria (cyan), stramenopile (brown), plasmid (violet), mitochondria

(orange) and nucleus (black).

Table S1. Information about the NGS data for five newly sequenced red algal plastid

genomes.

No. Taxa

Total bases of NGS

sequencing data (Mbp)

Size of complete

plastid genome (bp)

Total bases of mapped

plastid genome (bp)

Average coverage of

plastid genome (X)

1 Gelidium elegans 1,529 Mbp 174,749 bp 44,027,950 bp 228X

2 Gelidium vagum 990 Mbp 179,852 bp 66,802,278 bp 339X

3 Gracilaria chilensis 506 Mbp 185,637 bp 87,006,562 bp 445X

4 Porphyra pulchra 263 Mbp 194,175 bp 12,007,987 bp 52X

5 Sporolithon durum 3,190 Mbp 191,464 bp 32,008,868 bp 159X

Table S2. Gene compositions of red algal plastid genomes.

Species Reference GC (%)

Coding genes

tRNAs rRNAs Introns

Cyandiophyceae Cyanidioschyzon merolae (NC_004799)

Ohta et al. 2003 37.6 207 31 3 0

Cyanidium caldarium (NC_001840)

Glöckner et al. 2000

32.7 199 (2*) 30 3 0

Galdieria sulphuraria (NC_024665)

Jain et al. 2014 28.5 182 39 6 0

Porphyridiophyceae

Porphyridium purpureum (NC_023133)

Tajima et al. 2014 30.3 224 29 6 43

Bangiophyceae

Porphyra pulchra This study 33.3 207 37 6 0 Porphyra purpurea (NC_000925)

Reith & Munholland 1995

33.0 209 37 6 0

Porphyra umbilicalis (JQ408795)

Smith et al. 2012 32.9 208 (1*) 37 6 0

Pyropia fucicola (KJ776837)

Hughey et al. 2014 32.7 207 (4*) 35 3 0

Pyropia haitanensis (NC_021189)

Wang et al. 2013 33.0 213 (2*) 37 6 0

Pyropia kanakaensis (KJ776836)

Hughey et al. 2014 32.8 210 (4*) 35 3 0

Pyropia perforata (NC_024050)

Hughey et al. 2014 32.9 211 (2*) 35 3 0

Pyropia yezoensis (NC_007932)

Wang et al. 2013 33.1 213 37 6 0

Florideophyceae Calliarthron tuberculosum (NC_021075)

Janouškovec et al. 2013

29.2 201 31 3 2

Sporolithon durum This study 29.3 202 30 3 2 Chondrus crispus (NC_020795)

Janouškovec et al. 2013

28.7 204 30 3 1

Gelidium elegans This study 30.2 202 30 3 1

Gelidium vagum This study 29.9 201 30 3 1

Gracilaria chilensis This study 29.3 203 30 3 1 Gracilaria salicornia

(NC_023785) Campbell et al.

2014 28.8 203 (1*) 30 (1*) 3 1 (1*)

Gracilaria tenuistipitata var. liui (NC_006137)

Hagopian et al. 2004

29.2 205 (2*) 30 (1*) 3 1 (1*)

Grateloupia taiwanensis (NC_021618)

DePriest et al. 2013

30.6 234 (1*) 30 (1*) 3 1 (1*)

*: including un-annotated genes in previous reports

Table S3. List of 193 plastid protein-coding genes used in the ML tree search.

See the file “Table_S3_S4_S7_supplementary_tables.xlsx” (sheet Table S3).

Table S4. Newly annotated genes from previously published red algal plastid genomes.

These genes have been overlooked, underestimated or mis-annotated in previous studies.

Detailed information is shown in remarks.


Table S5. Results of BLASTx search using plasmid-derived regions in plastid genomes. Cutoff of e-value is 1.0e-05 and two cases of relaxed e-

value (2.0e-01 and 3.0e-03) are adapted to Gle4293 orf4 of Sporolithon and Gro4059 orf2347 of Grateloupia. Abbreviations: HyP indicates

hypothetical protein same as in orf for the open reading frame, PG for the pseudogenized gene. The plastid genome region of Sporolithon durum

between argB and ftsH gene is 4.2 kb non-coding part that includes two plasmid-derived pseudogenized genes. Between rRNAs and ycf27 in

plastid genome of S. durum, pm_orf86 shows uncertain mixed plasmid signals from BLASTx search results. The plastid genome of

Gracilariopsis tenuistipitata var. liui also shows uncertain plasmid signals between leuD and psbD gene.

Species Locality Region Feature Size Matched results E-value Identities GI Remarks

Porphyra pulchra orf121-apcF - PG 585 bp Pp6427 orf3 1.E-39 45% 11466611

Pyropia haitanensis

petG-rps14 - PG 414 bp Pp6859 orf7 3.E-44 63% 11466621 petG-rps14 - PG 291 bp Pp6859 orf 6 3.E-22 48% 11466620 petG-rps14 pm_orf72 orf 216 bp Pp6859 orf 5 9.E-12 55% 11466341 un-annotated gene previously

ycf12-ftrB - PG 399 bp Pp6859 orf 4 4.E-36 51% 11466618 ycf12-ftrB pm_orf93 orf 279 bp Pp6427 orf 1 1.E-12 59% 11466609 un-annotated gene previously

Sporolithon durum

PG(syfB)-rps1 pm_orf185 orf 555 bp Gle4293 orf 4 2.E-01 26% 11465618 relaxed e-value, Pp6859 orf1 region mixed PG(syfB)-rps1 pm_orf73 orf 219 bp Pp6859 orf 6 4.E-06 37% 11466620 PG(syfB)-rps1 pm_orf819 orf 2457 bp Calothrix sp. HyP 1.E-146 36% 668693613 Pp6859 orf4 and orf5 homolog

argB-ftsH - PG 312 bp Calothrix sp. HyP 8.E-09 78% 668693613 copy region of pm_orf819 argB-ftsH - PG 381 bp Gch7220 orf 5 5.E-14 36% 11465596

Gelidium elegans ycf27-psbD - PG 831 bp Pp6859 orf 5 2.E-38 36% 11466341

Gelidium vagum rps6-rRNAs - PG 2091 bp Calothrix sp. HyP 2.E-107 34% 66863613 Pp6859 orf4 and orf5 homolog

rps6-rRNAs - PG 555 bp Gro4970 orf 5 2.E-12 25% 11466341

Grateloupia taiwanensis ycf27-psbD - PG 306 bp GL3.5 orf 1 1.E-05 35% 18514 overlapped to unique orf31 & orf32

rRNAs-ycf27 - PG 183 bp GL3.5 orf 2 3.E-12 74% 18515 overlapped to unique orf06

ycf27-psbD - PG 303 bp Gro4059 orf 2347 3.E-03 27% 11466334 relaxed e-value, overlapped to unique orf32

Gracilaria salicornia ycf27-psbD orf139 orf+PG 495 bp Gro4970 orf 1 3.E-24 50% 11466337 Gracilaria tenuistipitata var. liui rRNAs-ycf27 - PG 441 bp Gle4293 orf 1 5.E-14 64% 11465615

Gracilaria chilensis leuD-psbD - PG 606 bp Gle4293 orf 1 7.E-37 61% 11465615

leuD-psbD - PG 300 bp Gle4293 orf 2 6.E-08 36% 11465616 leuD-psbD - PG 408 bp Gle4293 orf 3 1.E-23 52% 11465617

Table S6. Sampling information used in this study.

No. Taxa Strain No. Date Locality

1 Gelidium elegans

SKKU18 Oct. 27, 2012 Anin, Gang-reung, Korea

SKKU22 Oct. 27, 2012 Gamchusa, Donghae-si, Korea

SKKU28 Oct. 22, 2012 Wando, Jungdo-ri, Korea

2 Gelidium vagum - Jul. 23, 2012 Manripo, Tae-an, Korea

3 Gracilaria chilensis - Feb. 1, 2003 Ancud, Chile

4 Porphyra pulchra UC1879714 Jun. 20, 1970 Moss Beach, California, USA

UC1454976 Jun. 20, 1970 Moss Beach, California, USA

5 Sporolithon durum

SKKU_SD01 Nov. 6, 2012 Army Bay, Whangaparaoa, New Zealand

SKKU_SD02 Aug. 28, 2014 Army Bay, Whangaparaoa, New Zealand

SKKU_SD03 Aug. 28, 2014 Army Bay, Whangaparaoa, New Zealand

Table S7. Information about the combination and separation of plasmid-derived regions.

Several partial orf regions were combined into one single orf, while an orf was separated into

two genes based on the complementary alignment. In the genome of Moorea producens,

hypothetical protein (GI: 332351884) and its flanking regions (both of sides) were combined

and these bacterial sequences were translated using the Bacterial, Archaeal and Plant Plastid

Code (codon table 11). In the mitochondrial genome of Marchantia polymorpha, orf196 (GI:

11467138) and orf207 (GI: 11467137) were combined with their flanking non-coding regions,

respectively, and their two regions were also combined as a single orf (89 bp interval between

two regions). For phylogenetic analysis, these plant mitochondrial sequences have been

translated to amino acids using a standard code (codon table 1). In red algae, each part of

sequences were translated. All these red algal sequences were translated using the codon table

11.


Table S8. Contents of subfamily groups in DNA polymerase type-B family catalytic domain

(POLBc) superfamily from conserved domain database (CDD).

Conserved domain database Accession

POLBc superfamily cl10023

DNA polymerase type-B family catalytic domain (POLBc) cd00145

DNA polymerase type-B B1 subfamily catalytic domain (POLBc B1) cd05530


DNA polymerase type-B alpha subfamily catalytic domain (POLBc alpha) cd05532

DNA polymerase type-B delta subfamily catalytic domain (POLBc delta) cd05533

DNA polymerase type-B zeta subfamily catalytic domain (POLBc zeta) cd05534

DNA polymerase type-B epsilon subfamily catalytic domain (POLBc alpha) cd05535


DNA polymerase type-II subfamily catalytic domain (POLBc Pol II) cd05537

DNA polymerase type-II B subfamily catalytic domain (POLBc Pol II B) cd05538

Table S9. List of published red algal plasmids. 13 species out of a total 36 red algal species

surveyed contain plasmids (marked as “present [O]”). Among 13 species, 14 plasmid

sequences were reported from only 5 species (Porphyra pulchra, Pyropia tenera, Gracilaria

chilensis, Gracilaria robusta and Gracilariopsis lemaneiformis) in NCBI database. 14

plasmid sequences encoded 56 open-reading frames (orf).

Order Species Present (O), Absent (X)

No. of plasmids

Reported plasmid

sequences

NCBI GI (retained proteins)

References

Erythropeltidales Smithora naiadum O 3 X Goff and Coleman 1990

Glaucosphaerales Glaucosphaera vaculolata X Goff and Coleman 1990

Bangiales

Porphyra linearis X Villemur 1990a

Porphyra pulchra O 5 5

11466614 (7), 11466608 (5), 7108460 (1), 7108458 (1), 7108456 (1)

Moon and Goff 1996, 1997

Pyropia perforata X Goff and Coleman 1990

Pyropia tenera O ? 2 17980118 (1), 254029130 (2) Choi et al. 2001

Wildemania miniata O 3 X Villemur 1990a

Ceramiales Asterocolax gardneri X

Goff and Coleman 1990

Campylaephora californica X

Choreocolax polysiphoniae X

Harveyella mirabilis X

Janczewski gardneri X

Micorcladia coulteri X

Odonthalia floccosa X

Odonthalia washigtoniensis X

Osmundea spectabilis O ? X

Polyneura latissima X

Polysiphonia elongata X Vertebrata lanosa X

Gigartinales Gardneriella tubifera X Goff and Coleman 1990

Gymnogongrus sp. O 2 X Villemur 1990a

Sarcodiotheca gaudichaudii X Goff and Coleman 1990

Gracilariales Gracilaria chilensis (1) O

4 1 18476 (1) Villemur 1990a

Gracilaria chilensis (2) ? 2 11465608 (5), 11465591 (16) Goff and Moon (unpublished)

Gracilaria pacifica O 4 X Goff and Coleman 1990

Gracilaria robusta (1) O

? 2 11466336 (7), 11466333 (2) Goff and Moon (unpublished)

Gracilaria robusta (2) 1 X Goff and Coleman 1990 Gracilaria textorii O 2 X

Gracilaria tikvahiae O 3 X Villemur 1990a

Gracilariophila oryzoides O 2 X Goff and Coleman 1990

Gracilariopsis langissima X Villemur 1990a

Gracilariopsis lemaneiformis O 3 2 18513 (2), 11465614 (5) Goff and Coleman 1990

Gracilariopsis sp. X Villemur 1990a

Halymeniales Prionitis lanceolata X Goff and Coleman 1990

Plocamiales Plocamiocolax pulvinata X Goff and Coleman 1990

Plocamium cartilagineum X

Rhodymeniales Lomentaria divaricata X Goff and Coleman 1990

Table S10. Primer information for population analysis. Different individuals of Gelidium

elegans, Porphyra pulchra and Sporolithon durum were used to check the presence or

absence of plasmid-derived region. The plasmid-derived regions of G. elegans (between

ycf27 and psbD gene), P. pulchra (between orf121 and apcF gene) and S. durum (between

pseudogenized syfB and rps1 gene) were confirmed by PCR.

Speices Strain Primer set

Gelidium elegans

SKKU18 [Forward 1] Gele_F1_1: 5'-ATTCAGTCTTCTAGAACTACTAGTAA-3' Gele_F1_2: 5'-AAAGACATGTTGATACAAGAGTTGTC-3' [Reverse 1] Gele_R1_1: 5'-CTTGTCCAATTGCTATGGTCATATTA-3' Gele_R1_2: 5'-AACCTTCTAGATAAGAACTAGCTAA-3'

SKKU22

SKKU28

Porphyra pulchra

UC1879714 [Forward 1] Pp_F1_1: 5'-TCTAGATTATAGATAGATTTAGTGCTC-3' Pp_F1_2: 5'-AAGACTAGTATATTTGTTAGTGCATCA-3' [Reverse 1] Pp_R1_1: 5'-AACTTTGAAGCTTTATTAGATGCAAGA-3' Pp_R1_2: 5'-GCTTAGGATATTAGAATTCACAGATAA-3'

UC1454976

Sporolithon durum

SKKU_SD01 [Forward 1] Spo_F1: 5’-CTGACACTGAGACAGATATAGAAAATTA-3' [Reverse 1] Spo_R1: 5’-AATTATTCATCGATCTTTCATTAGACAC-3' [Forward 2] Spo_F2: 5’-GTGCTAGTGTATTTAAGCTATATGAAG-3' [Reverse 2] Spo_R2: 5’-TTATTAAATAGAAGTTTAGCTCCATCT-3'

SKKU_SD02

SKKU_SD03

rnpB RNA

trnR

groEL

ycf17

rrstrnItrnA

rrlrrf

thiGtrpG

nblA cpeBcpeAccsApsaK

ycf61cpcApgmAsecAtrnEorf327psb30psaItrnVtrnRrrs

trnItrnA

rrlrrf

chlN

ycf37psaF psaJ apcD

fabHpsbXaccDpsbV

petJ

carA

orf1

08

rne

rpl2

7rp

l21

orf2

63rp

l32

psbY

ycf3

5

Pp64

27 o

rf3 re

gion

psaLrb

cL

orf62orf6

21orf287ycf24ycf16

rps18rpl33 glnB

ycf3atpBatpE

tatCpetA

preA

acsF

psaDorf68

psaApsaB

trnG

rps1

4

psbN

psaE

trnD

trnS

trnA

tnrM

trnT

trnY

trnV

rpl19

dnaB

rpl9

moeB

orf75

petD

petB

trnH

rps1

syfB

psbWtrnQsyhtrnR

orf148

orf198

ycf65rps16 ycf19

psbC

psbDorf27

rps6orf203

ccs1

orf240cpcG trnN

accAycf23psaC

gltB

trpA

ftrB psbJ

psbLpsbF psbE

ycf63chlIpsaM

ycf46rpl34

orf174

trnLor

f238

orf3

20rbcRps

bAtrnL

trxA

rpl28

or

f58trn

Tyc

f4trn

G rp

s4

ilvHtrn

McemA

trnL

ycf39

orf111

psbI

atpAatpDatpFatpG

atpI

atpH

tsfrps2

rpoC2

rpoC1

rpoB

rps20

infB

apcBapcA

apcE

odpB

petN secG ycf36 trnMbas1pbsA rpl35

rpl20

chlBacpP

orf565

rpl3 rpl4

rpl23 rpl2 rps19 rpl22

rps3 rpl16 rpl29 rps17

rpl14 rpl24

rpl5 rps8 rpl6

rpl18 rps5 secY

rpl36 rps13 rps11 rpoA

rpl13

rps9 rpl31 rps12

rps7 tufA

rps10

odpA

apcF

ycf2

0

trnP

ycf26

trnK

ycf22

ntcA

argB

trnSpe

tFpsbZ

accBtrnS

orf149

ycf34

trnL

trnC

infC

rbcScb

bX

orf1

21trn

R

orf1

14

orf4

50

chlL

orf107

ycf21

cpcB

Porphyra pulchra194,175 bp

GC content: 33.3 %

Fig. S1. Plastid genome map of Porphyra pulchra. Functional gene groups are color-coded. Genes drawninside of the circle indicate the transcriptionally clockwise strand, and genes on outside indicatethe counter-clockwise strand.

ribosomal RNAATP synthaseribosomal protein LSUOther genesIntrontrpB RNA

transfer RNAPhotosystemribosomal protein SSUORFpseudogenized genes

dnaK

psbK

petG

ycf3

8ps

bBps

bT

ftsH

psbH

ycf3

3

clpC

trnF

trnS

trnW

rpl11rpl

1

rpl12

ycf29

thiS

ilvB

cemA

trnMe(intronic orfs)

psbI

trnLycf39ycf41

orf360

ftsH

p

sbH

ps

bT

psbB

ycf3

8

rps10

t

ufA

rps7

rps

12 r

pl31

rps9

rpl13

rpoA

rps11

rps13

rpl36

secY

rps5

rpl18

rpl6

rps8

rpl5

rpl24

rpl14

rps1

7

rpl29

rp

l16

rps3

rpl22

rps19

rpl2

rp

l23

r

pl4

rpl3

Sporolithon durum191,465 bp

GC content: 29.3 %

Gch7220 orf5

regionycf33ilvB

clpC

trnStrnW

rpl11rpl1rpl12

ycf29thiS

rnpB RNA

groEL

ycf17

ycf6

0

rps6

ps

aM

chlI

yc

f63

ycf2

6ps

bEps

bF

psbL

ps

bJ

ftrB

trn

Ktrp

A

carA petJ psbV accD psbXfabHapcD psaJ psaF ycf37 chlN chlL

trxA rpl28 orf65

trnT petL ycf4

trnG

Fig. S2. Plastid genome map of Sporolithon durum. Functional gene groups are color-coded. Genes drawninside of the circle indicate the transcriptionally clockwise strand, and genes on outside indicatethe counter-clockwise strand.

atpA

atpD atpFatpG atpH atpI

tsfrps2rpoC2

rpoC1rpoBrps20infB

apcBapcAapcEodpB

rpl20rpl35pbsAbas1

trnM ycf36secG petM petNch

lB(in

troni

cor

f476

)acpP

petGpsbKdn

aK

petF

psbNpsaE

trnD

trnMtrnS

trnYtrnT

rpl19

argB

trnFpseudo-dnaB

rpl9

petDpetBntcAtrnHrps1

pm_orf819

pm_orf173

pm_orf185

pseudo-syfB

psbW

uppycf19rps16ycf65

trnQ

psbCpsbD

ycf27pm_orf86

rpl34trnP

ycf52

ycf53ycf55

rbcR

psbA

trnL

trpG

thiG

trnR

trnV

psaI

ycf64

tilS

trnE

secA

pseu

do-yc

f21

pgmA

cpcA

cpcB

rpoZ

psaKccsAcpeAcpeBnblAycf20

rps4trnLtrnC

psaL

cbbXrbcSrbcL

infC

apcF

psb3

0

trnR

moeB

ycf4

5odpA

Sta7437_4988

region



rrs

rrfrrltrnAtrnI

rpl21rpl27

rne

ccdA

ccs1trn

N

gltB

cpcG

trnRycf80

ilvH

orf408ycf58

orf84orf134sufBsufC

psaC

pseudo-ycf23ycf22

accAycf54

psbYrpl32ycf56

rpl33

rps18ycf3atpBatpEtatCpetApreAacsFps

aDtr

nSorf6

8ac

cB

psaApsaBrps1

4ps

bZtrnG

sufCsufBycf92

ycf58orf621 trnG

ycf4petLtrnTCcr_orf64

rpl28

trxA

ilvH

ycf80

cpcG

accAycf23

ycf22

psaCgltB

trpAtrnKftrB

ycf26ycf63chlI psaM

rpl34 trnP

ycf53

ycf55

rbcR

psbA

trnL

trpG

thiG

rrf

rrl

rrs

trnA

trnI

ycf1

7

groE

L

rnpB R

NA

thiSycf29

trnW

rpl11rpl1

rpl12

clpC

ilvBycf33

ftsH

psbH

psbT psbB

ycf38

rpl3 rpl4

rpl23 rpl2 rps19 rpl22 rps3 rpl16 rpl29 rps17 rpl14 rpl24 rpl5rps8rpl6rpl18rps5 secY rpl36 rps13 rps11 rpoA rpl13 rps9 rpl31 rps12 rps7

tufA rps10

trnGpsbZ



rps14psaB

psaAaccB

trnS

preA

tatCpetA

atpEatp

Bycf3rp

s18

Gelidium elegans174,748 bp

GC content: 30.2 %

Fig. S3. Plastid genome map of Gelidium elegans. Functional gene groups are color-coded. Genes drawninside of the circle indicate the transcriptionally clockwise strand, and genes on outside indicatethe counter-clockwise strand.

psbJpsbLpsbF psbE

rpl33

psaDacsF

ycf46

ycf52

trnRycf91

atpI

apcB

apcA

odpB

odpA rpl20

rpl35

pbsAbas1trnM ycf36

secG petM petN

acpP

ycf45

petGpsbK

dnaK

petF

psbN

argB

rpl19 trnTtrnYtrnV

trnFdnaB

rpl9m

oeBpetDpetBntcAtrnHrps1

syfBpsbW

upp

ycf1

9rp

s16

ycf6

5or

f164

psbCpsbD

Pp68

59 o

rf5 re

gion

ycf2

7

rps6

ccs1ccdAycf

35

rne

psbY

rpl32

ycf56

rpl21

rpl27

ycf54

carApetJpsbVaccDpsbXfabHapcDpsaJpsaF

ycf37

trnVtrnR

psaIpsb30

tilS

trnE

secA

ycf21

pgmA

cpcAcpcBrpoZ

psaK

ccsAcpeA

cpeBnblA

ycf20

apcF

rps4infC

trnC

trnL

ycf34 rbcSrbcL

psaLtrnM

e

(intronic orf12) cemA

psbIycf41ycf39trnL at

pAat

pDat

pFat

pGat

pH

cbbX

ycf64

trnN

ycf60

syh

trnR

trnQ

trnDtnrStnrM

psaE

apcE

tsf rps2

rpoC

2

rpoC

1

rpoB

rps2

0inf

B

ycf33

sufCsufBorf256

ycf58orf614 trnG

ycf4petLtrnTCcr_orf64

rpl28

trxA

ilvHycf80cpcG

accAycf23

ycf22

psaCgltB



trpAtrnKftrB

ycf26ycf63chlI psaM

rpl34 trnP

ycf53ycf55

rbcR

psbJpsbLpsbF psbE

psbA

trnL

trpG

thiG

rrfGr

o497

0 orf5

regi

on

Sta7

437_

4988

regi

onrr

l

rrs

trnA

trnI

ycf1

7

groE

L

rnpB R

NA

thiSycf29

trnW

rpl11rpl1

rpl12

clpC

ilvB

ftsH

psbH

psbT psbB

ycf38

rpl3 rpl4

rpl23 rpl2 rps19 rpl22 rps3 rpl16 rpl29 rps17 rpl14 rpl24 rpl5rps8rpl6rpl18rps5 secY rpl36 rps13 rps11 rpoA rpl13 rps9 rpl31 rps12 rps7 tufA

rps10

trnGpsbZ

rps14psaB

psaAaccB

trnS

preA

tatCpetA

atpEatp

Bycf3rp

s18

Gelidium vagum179,853 bp

GC content: 29.9 %

rpl20

rpl35

pbsAbas1trnM ycf36

secG petM petN

Fig. S4. Plastid genome map of Gelidium vagum. Functional gene groups are color-coded. Genes drawninside of the circle indicate the transcriptionally clockwise strand, and genes on outside indicatethe counter-clockwise strand.

rpl33

psaDacsF

ycf46

ycf52

trnRycf91

atpI

apcB

apcA

odpB

odpA

acpP

ycf45

petGpsbK

dnaK

petF

psbN

argB

rpl19 trnTtrnYtrnV

trnFdnaBrpl9m

oeBpetDpetBntcAtrnHrps1

syfB

psbW

upp

ycf1

9rp

s16

ycf6

5or

f164

psbCpsbDycf2

7

rps6

ccs1ccd

Aycf35

rnepsbY

rpl32

ycf56

rpl21

rpl27

ycf54

carApetJpsbVaccDpsbXfabH

apcDpsaJpsaF

ycf37

trnVtrnR

psaIpsb30

tilS

trnE

secA

ycf21

pgmA

cpcAcpcBrpoZ

psaKccsA

cpeA

cpeBnblA

ycf20apcF

rps4infC

trnC

trnL

pseudo-ycf34 rbcSrbcL

psaL

cbbX

ycf64

trnN

ycf60

syh

trnR

trnQ

trnDtnrStnrM

psaE

apcE

tsf rps2

rpoC

2

rpoC

1

rpoB

rps2

0inf

B

cemA

trnMe

(intronic orfs)

trnL

ycf39

orf109psbI

atpAatpF

atpGatpH

atpItsf

rps2

rpoC2

rpoC1

rpoB

rps20rps18rpl33 yc

f3

tatC

preA

acsF

psaD

trnS

accB

psaA

psaB

rps14psbZ

trnG

rpl3

rpl4

rpl23

rpl2

rps19

rpl22 rps3 rpl16 rpl29 rps17

rpl14 rpl24

rpl5rps8rpl6rpl18

rps5secY rpl36 rps13 rps11 rpoA

rpl13

rps9

rpl31

rps12

rps7

tufA

rps10

ycf38

psbB

psbT

psbH

syfBrps1trnHntcApetBpetDmoeBrpl9groELycf17

rrstrnI

trnA

rrl

rrfthiGtrn

Lps

bA

rbcRyc

f55

ycf5

3

trpA

trnK

ftrB

psbJ

psbL

psbF

psbE

ycf26

ycf63

chlI psaM

pseudo-yc

f46

rpl34

trnP

ycf5

2

gltB

psaC

cpcGorf73trnRycf80

ilvH

trnG ycf4petLtrnTorf65 rpl28 trxA

orf220ycf58

orf245ycf24

ycf16

Gracilaria chilensis185,637 bp

GC content: 29.3 %

Fig. S5. Plastid genome map of Gracilaria chilensis. Functional gene groups are color-coded. Genes drawninside of the circle indicate the transcriptionally clockwise strand, and genes on outside indicatethe counter-clockwise strand.



orf446

pseudo-ycf23ycf22accA

trpG

trnFpsbW

ftsH

ycf33ilvB

orf149dnaB

petAat

pEatpB

atpD

orf198orf197

infB

apcB

apcA

apcE

odpB

odpA

rpl

20 rp

l35

pseu

do-p

bsA

bas1

trnM

ycf3

6 yc

f47

petM

petN

acpP

ycf45

petG

dnaK

petF

psbNpsaE

argB trnDtrnS

trnM

rpl19 trnTtrnY trnV

clpC

rnpB RNAycf40ycf29

rpl12trnWtrnQsyhtrnR orf160

ycf65

rps16

ycf19

upp

psbDGle4293 orf3 region

Gle4293 orf2 region

Gle4293 orf1 region

leuDleuC

ycf27rps6cc

s1ds

bDycf3

5trn

N

rne

psbY

rp

l32

ycf5

6rp

l21

rpl2

7

ycf5

4carApe

tJpsbVac

cD

psbX

apcD

psaJ

ycf37

trnV

trnR

psaIpsb30tilStrnE

secAycf21

pgmAcpcAcpcB

ycf61

psaKccsAcpeAcpeBnblAycf20apcF

rps4infC

rbcL rbcS cbbXtrnCtrnL ycf34

psaL

psaF

fabH

ycf6

0

psbC

rpl1rpl11

psbK

Fig. S6. Maximum likelihood tree based on aligned amino acid sequences of concatenated 193 protein encoding genes from 16 published and 5 new (underlined) plastid genomes (2000 replications, bootstrap support > 50%).

Fig. S8. Maximum likelihood tree based on aligned amino acid sequences of Gracilariopsis lemaneiformis plasmid GL3.5 orf2 related genes and its homologs from BLASTp search (cutoff e-value 1.0e-03) (2000 replications, bootstrap support > 50%). Taxon information and their sequence localities are color-coded as follows: bacteria (black), red algae (red), virus (violet), plastid (green) and plasmid (brown).

Plan

t

Red algaeRhizaria

Stramenopile

Para

sitic

Bac

teria

0.7

uncultured marine virus [replication protein, gi444297942]Odonata-associated cirular virus-7 [replication-associated protein, gi744824944]

Avon-Heathcote Estuary associated circular virus 25 [replication-associated protein, gi765702697]Odonata-associated circular virus-15 [replication-associated protein, gi744824968]

1 ssDNA virus and 3 unclassified viruses4 ssDNA viruses

70 ssDNA viruses

uncultured marine virus [replication protein, gi444298144]Odonata-associated circular virus-8 [replication-associated protein, gi744824948]

Phytophthora sojae [mitochondrial orf98, gi145932354, mitochondria]Pyropia tenera [putative replicase (plasmid), gi254029132, plasmid]Pyropia tenera [replication associated protein (plasmid), gi17980119, plasmid]Porphyra pulchra [replicase (plasmid), gi7108461, plasmid]

Porphyra pulchra [replicase (plasmid), gi7108459, plasmid]Porphyra pulchra [replicase (plasmid), gi7108457, plasmid]

Reticulomyxa filosa [hypothetical protein RFI_31564, gi569354614, nucleus]Reticulomyxa filosa [rep, gi569382219, nucleus]

McMurdo Ice Shelf pond-associated circular DNA virus-2 [rep-associated protein, gi667699509]

‘Chrysanthemum coronarium’ phytoplasma [hypothetical protein, gi754689944]Onion yellow phytoplasma [replication associated protein, gi51172577]Onion yellow phytoplasma [replication protein, gi501877271]Onion yellow phytoplasma [replication protein, gi499583384]Onion yellow phytoplasma [replication protein, gi504873008]Onion yellow phytoplasma [geminivirus-like replication protein, gi504873005]

Candidatus Phytoplasma australiense [replication associated protein, gi501453683]Italina clover phyllody phytoplasma [hypothetical protein, gi515760571]Phytoplasma sp. [hypothetical protein, gi4468959]Vaccinium witches’-broom phytoplasma [hypothetical protein, gi515761095]Wheat blue dwarf phytoplasma [replication-associated protein, gi504896643]Paulownia witches’-broom phytoplasma [replication-associated protein, gi501254467]Wheat blue dwarf phytoplasma [replication-associated protein, gi504896653]Periwinkle little leaf phytoplasma [replication-associated protein, gi504873735]Candidatus Phyoplasma australiense [replication associated protein, gi501453688]Chrysanthemum yellow phytoplasma [hypothetical protein, gi735683554]Chinaberry witches’-broom phytoplasma [replication associated protein, gi503512976]Paulownia witches’-broom phytoplasma [replication-associated protein, gi501254473]Chrysanthemum yellows phytoplasma [hypothetical protein, gi735684243]Wheat blue dwarf phytoplasma [replication-associated protein, gi504896657]New Jwersey aster yellows phytoplasma [Rep protein, gi307902848]Aster yellows witches’-broom phytoplasma [hypothetical protein, gi499732216]Aster yellows witches’-broom phytoplasma AYWB [conserved hypothetical protein, gi84789653]Aster yellows witches’-broom phytoplasma AYWB [conserved hypothetical protein, gi84789536]Aster yellows witches’-broom phytoplasma [hypothetical protein, gi499732224]

Niminivirus [Rep, gi603013937]Grapevine red-blotch associated virus [C1 protein, gi528746544]

Sewage-associated circular DNA virus-18 [replication-associated protein, gi751868117]Sewage-associated circular DNA virus-28 [replication-associated protein, gi751868297]Sewage-associated circular DNA virus-14 [replication-associated protein, gi664651390]

Rhynchosia yellow mosaic virus [replication associated protein, gi256996647]

Nicotiana tomentosiformis [uncharacterized protein LOC104099148, gi697190578, nucleus]

Dalechampia chlorotic mosaic virus [replication associated protein, gi408355352]Tomato mottle leaf curl virus recombinant [replication-associated protein, gi85665888]

8 ssDNA viruses4 ssDNA viruses

3 ssDNA viruses38 ssDNA viruses

6 ssDNA viruses

Nicotiana tomentosiformis [uncharacterized protein LOC104086178, gi697159806, nucleus]Nicotiana tomentosiformis [uncharacterized protein LOC104092751, gi697175541, nucleus]Nicotiana tomentosiformis [uncharacterized protein LOC104099147, gi697190576, nucleus]Nicotiana tomentosiformis [uncharacterized protein LOC104115566, gi697140845, nucleus]Nicotiana tomentosiformis [uncharacterized protein LOC104119210, gi697149473, nucleus]

Asystasia mosaic Madagascar virus [replication-associated protein, gi761719712]Asystasia mosaic Madagascar virus [replication-associated protein, gi756558185]

137 ssDNA VirusesNicotiana tomentosiformis [uncharacterized protein LOC104099419, gi697190580, nucleus]Nicotiana tabacum [AL1 protein, gi1587991, nucleus]

100

55100

81

76

65

86100

78

100

100

98

75100

52

73100

100

85

100100

10066

70866688

Fig. S9. Maximum likelihood tree based on aligned amino acid sequences of red algal replicase genes from Pyropia tenera (GI: 254029132, 17980119) plasmids, Porphyra pulchra plasmid (GI: 7108461, 7108459, 7108457) and their homologs from BLASTp search (cutoff e-value 1.0e-05) (2000 replications, bootstrap support > 50%). Taxon information and their sequence localities were indicated with color-code as follows: parasitic bacteria (blue), plant (green), red algae (red), rhizaria (cyan), stramenopile (brown), plasmid (violet), mitochondria (orange) and nucleus (black).

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Reconstructing the complex evolutionary history of mobile ... · Different individuals of Gelidium elegans, Porphyra pulchra and Sporolithon durum were used to check the presence