Table S1. List of primers for quantitative RT-PCR. All primers were designed by Primer Express software
(Applied Biosystems). Slope and amplification efficiency (E) of each primer pair in quantitative-PCR are also
shown
Primer name
Sequence (5' to 3')
CMA030C-F
CMA030C-R
CMA040C-F
CMA040C-R
CMA145C/CMC188C/CMI306C/CMJ002C/
CMK006C-F
CGTGTCCGCAGTCGTTCA
GGCGGTCGCGTCTTGA
GCGAACGGCGCATCAG
GGTCTTCCAGTGCTCGCTTCT
CMA145C/CMC188C/CMI306C/CMJ002C/
CMK006C-R
CMC021C-F
CMC021C-R
CMC120C-F
CMC120C-R
CMD041C-F
CMD041C-R
CMD058C-F
CMD058C-R
CMD113C-F
CMD113C-R
CME095C-F
CME095C-R
CME145C-F
CME145C-R
CMF068C-F
CMF068C-R
CMF117C-F
CMF117C-R
CMH052C-F
CMH052C-R
CMH132C-F
CMH132C-R
CMI049C-F
CMI049C-R
CMI084C-F
CMI084C-R
CMI162C-F
CMI162C-R
CMI196C-F
CMI196C-R
CMI224C-F
CMI224C-R
CMI273C-F
CMI273C-R
CMJ042C-F
CMJ042C-R
CMJ051C-F
CMJ051C-R
CMJ055C-F
CMJ055C-R
CMJ173C-F
CMJ173C-R
GCGGAATAATGCCTTTGAACA
Slope
Ea
-3.66
0.88
-3.61
0.89
-3.39
0.97
-3.26
1.03
-3.47
0.94
-3.36
0.98
-3.59
0.90
-3.47
0.94
-3.61
0.89
-3.39
0.97
-3.43
0.96
-3.68
0.87
-3.49
0.93
-3.71
0.86
-3.41
0.97
-3.71
0.86
-3.49
0.94
-3.63
0.89
-3.52
0.92
-3.71
0.86
-3.32
1.00
-3.76
0.85
-3.58
0.90
-3.40
0.97
CCCGGAGAAAGTCGTCTTGA
AGGGTGTCGCGGTGAAAG
CCGCATAGCTGACACCGACTA
GGGCACACGGCCTCTCT
TTGCCTCGGGTGCAGATC
TTCAACCCACGCGATGTG
AGAGTGCATAACCTGCACCAACT
CTGCGCGATCTCCGAAAC
GCCGATTTTAATGATGTCCTCAA
TTGCTCTTGGAGCCGGTTT
TGCCGCCTTCGTGTTGTT
GCTCGCAAAGGCCGATAC
GTCGGGATCCGGAACCA
CACGCTACGGTGCTATTTCACA
TGAGGACTTCGGGCTCGAT
TCACCACGGACCCAAAGC
CCGACACATTTCGCCACAT
TGCTTGGATGATTGGCATAATC
TCCAAAGCCGTGATGTTATCCT
CGTTGTTTCCCCACGTTCA
TTGGCTTCTCACCGTCATGA
ACGGCTTGAACGCACACA
TGGAGAATACCCGGGCAAT
TGGCATGACGGAGGAAGAG
TTGCGTGGACGGCTGTT
AAGCCGCTATCGATGAAATCC
TCGTTCCCGAATTCACTGTAGA
TTGTCCCCACGAGAAAACCT
TGCGGGACGCCAAACTT
CGGCAAAGCTTCGTGTACTCT
CGGCGCGCTCGATTAG
CATCAGCGACGCCCAGAT
TTTCAGGGCAGGGTCGAA
TTCCCGTGGGCACCTTAA
GCAACGCGGATACGTGTTC
GGAATTCGGCATCGTTTCC
GACGCTGGTCCCCGGTAT
CAGGCGAATAACGTTTATTGCTT
GCACCCGCCAGATGGA
GCCGAGGGTGACAACGTT
TGTGCGCCCACCTCAAC
AATGCTCGTCGCTGTTTGG
GGCAGGCTTTATGCCTTTCTG
1
CMJ250C-F
CMJ250C-R
CMJ272C-F
CMJ272C-R
CMJ293C-F
CMJ293C-R
CMJ305C-F
CMJ305C-R
CMK041C-F
CMK041C-R
CMK131C-F
CMK131C-R
CMK188C-F
CMK188C-R
CML036C/CML059C/CMM231C-F
CML036C/CML059C/CMM231C-R
CML209C-F
CML209C-R
CMM068C-F
CMM068C-R
CMM167C-F
CMM167C-R
CMM196C-F
CMM196C-R
CMM299C-F
CMM299C-R
CMN017C-F
CMN017C-R
CMN233C-F
CMN233C-R
CMN285C-F
CMN285C-R
CMO121C-F
CMO121C-R
CMO124C-F
CMO124C-R
CMO128C-F
CMO128C-R
CMO229C-F
CMO229C-R
CMO245C-F
CMO245C-R
CMO276C-F
CMO276C-R
CMO291C-F
CMO291C-R
CMP129C-F
CMP129C-R
CMP193C-F
CMP193C-R
CMP260C-F
CMP260C-R
CMQ172C-F
CMQ172C-R
CMQ191C-F
CMQ191C-R
CTACCCGAAGCTTGACGGTAA
GATACAAGGGCCACCGGTATC
CGTTGTCCAGGTTCCAACGT
CGTGTGCGCTTTCGTATGC
GCGCGCTCTCGACATTCT
CACGCTGTCGAGCAGTTCAG
CGGACAAGGTATCGCATATCTCA
CCCGCCCCTCGATTAACT
CGGCAAGTCGGCGTCTT
CGACGCCAAAACGAATGTC
CGATCTCCTGGTTACGAATATCG
CGTTGCAGGCGCGTTT
TGTCAAGAGCTCGGCTACGTACT
GAGCATGCATTCCGCGTTA
GCAGGTCGCGCAATATCG
GTGCAAAGTTCTGACCCATGAC
ACGATGGCCAGATGGATGA
TAGCGCCGCCGTCACT
CATCAGCGGTGTCGGAATG
TCCTGAGGTACGCGTGCAT
TCGAGTCCACTGGCGTGTT
CGCACCGCCTTTCAGATG
TGCCGGCAAGTCAAATACC
GCCCACGGAACGAAACTTT
TGTAGCCCTGCCCATGCT
AGCGCTCCTGTCGACGAT
CACTTTCGGAGGTGCTTTGC
CCGGCATACGGAGCTTGAT
TCATTGCGTCGCCGTATG
GCAGGGTACGCAGGTCAATT
CTCGTATGCGATGCTTTTGG
GCAGCCTGGAGTGGTGTCA
TGCGCGGAGCGTACGT
GGATCACATCCGGGTGCTT
TGCCGATGGTGGAGAAGTTC
CCCGACCCAGTCCCAAA
TCAAGGATTGTGCGGCAAA
GCATTGCGCCGGAGACT
CCGTCGTTGCTCTCTTGTGA
GTCGAGCACGCGTTTCG
CCCGAGGACGCGGATATAA
TCGCACCCGGTTGCA
CCCCGACGCTGGTATGAG
AAACAATCCGCTCGGTATGC
CCATAGACGGAGCGGATGAG
GCACCACCGCGTCCTTT
GAAGCACAGGGCGACTTGAC
TCGATGACCTTACAGGCAAGCT
GTGCGTTTCCGCTGCTAAA
GCATCCGCAAAGCCCTTAT
CGACGGCACCGATTGC
TGCACCGGATAGAGACCTTTG
GCCATCGGTTTATGCCATGT
TGCAGTGCTACCCCGAAATC
GGGAACGATTCGGTGAAGAA
ATCCCACCGTAGGCCTGATT
2
-3.38
0.98
-3.57
0.90
-3.63
0.89
-3.54
0.92
-3.56
0.91
-3.51
0.93
-3.29
1.01
-3.46
0.95
-3.55
0.91
-3.51
0.93
-3.31
1.00
-3.65
0.88
-3.60
0.89
-3.71
0.86
-3.53
0.92
-3.43
0.96
-3.67
0.87
-3.59
0.90
-3.61
0.89
-3.75
0.85
-3.58
0.90
-3.76
0.85
-3.47
0.94
-3.60
0.90
-3.64
0.88
-3.83
0.82
-3.49
0.93
-3.72
0.86
CMQ234C-F
CMQ234C-R
CMR014C-F
CMR014C-R
CMR476C-F
CMR476C-R
CMS195C-F
CMS195C-R
CMS272C-F
CMS272C-R
CMS327C-F
CMS327C-R
CMT034C-F
CMT034C-R
CMT209C-F
CMT209C-R
CMT216C-F
CMT216C-R
CMT256C-F
CMT256C-R
CMT285C-F
CMT285C-R
CMT362C-F
CMT362C-R
CMT412C-F
CMT412C-R
CMT497C-F
CMT497C-R
CMT561C-F
CMT561C-R
CMT582C-F
CMT582C-R
CMT611C-F
CMT611C-R
CMT633C-F
CMT633C-R
CMV013C-F
CMV013C-R
CMV014C-F
CMV014C-R
CMV153C-F
CMV153C-R
CMV154C-F
CMV154C-R
CMW001C-F
CMW001C-R
CMW002C-F
CMW002C-R
a
GGCTGCGTTCCGTCAAAA
TTCGAAGCTCCCGGACTTT
CCGCGACATCATGCAGAAT
CCGGCTGTTCCATCGTAAAG
GGCTGCTGGTTATGTGTTCATG
CGCTCTCCACGAGAAAAGCT
TCGCCGCATGGAATGAA
TTGAGGATGTTGGCCGTTATC
ATTCCGAGCAATGTTCTGGATT
CAGCGGCCCCTTGATG
AGAAGACGCCAAGGGACTTCT
TTCAAGCACACAAACGGGATT
GGCAGCAACCAAGGAGGAA
TCGCGCTGCGCTTGA
TTGTGGATGCAGCAAAACGT
GCCTTCGAGCCGAACAATC
CGGACGACGGCGTTACC
TTAACCGCTGCGTGATGCT
AGGCCCGAGCGGAGAA
CAGTGCGAACGGTGAAAGTTC
GCGATTATGCCGTGCTTGA
CGTAAAATCATCGGCAACGA
GCACCGGATGTCTTCCAAA
CCGGAACACTCGGATTACAGA
TTGTTGATGCGACCTGTATGC
GGTTCGGCAACAGTACAACGT
CGGCCTTAACCCGGAAA
CGCGGTCGTGAAGGTTTT
GCATGCGGGCCCTGTA
TGTTTTTGACGCCCTTTGGT
CGTCCTTCCGACGGTTCA
GGACTTCACCTCGCCAGTTG
GGCCATCGGCGACCAT
CGATCTCGTTTTCCGTTTGG
CGCATGGGTGTGGAAAGG
ATGGAAGGTGCAACCACAACT
GCATCTGGCGAAGTCAAAGG
CGCAAATTCTGCTCTCTTATAACATT
TGGCATTCAACTCGACTAAAGG
TTCGTTTGCAGGTCGATTCA
ATGGCCGAATTATTCGGAAA
GGTGCTGAAAATAAATGCATCGA
TGCAGGCATGTTGCATTATACA
TCCGGGACCTCGAATCACTA
TGTTTTTCTTTAAATTTTATTCGCCTACT
CTTTATTAAATAACCATAAAAAACTTACACACATT
TTGGTGGAATGGTGATCGTTATT
GCGCTGTCACGACTATCTATAATCC
-3.66
0.88
-3.57
0.91
-3.45
0.95
-3.62
0.89
-3.39
0.97
-3.78
0.84
-3.67
0.87
-3.62
0.89
-3.46
0.94
-3.33
1.00
-3.62
0.89
-3.54
0.92
-3.44
0.95
-3.55
0.91
-3.54
0.92
-3.60
0.90
-3.39
0.97
-3.69
0.87
-3.85
0.82
-3.44
0.95
-3.83
0.82
-3.24
1.04
-3.46
0.94
-3.58
0.90
Amplification efficiency (E) for each gene was determined from following equation: E = 10-1/Slope -1.
3
Figure S1 Changes in cell size and shape of C. merolae cell in the flat-plate culture. (a) A plot for areas of a
plastid and an extraplastid at 0, 1, 3, and 6 h in the culture. Compartmentation of the plastid and extraplastid is
explained in Figure 1f. Plots for lateral and longitudinal diameters of a plastid (b) and an extraplastid (c). Areas
and diameters were measured for 30 cells in each culture time
4
Figure S2 Changes in expression level of genes involved in central carbon metabolism in the flat-plate culture.
The transcript level of each gene was measured by quantitative RT-PCR, and corrected using transcript levels of
18S rRNA gene as an internal standard, and then normalized to the transcript level of each gene at 0 h. Genes are
classified into six classes with respect to the peak of transcript level; genes of <2-fold change (a), 2 to 4-fold
changes (b), 4 to 8-fold changes (c), 8 to 16-fold changes (d), 16 to 32-fold changes (e), and >32-fold change (f).
Each value is an average ± standard deviation of three independent assays
5
Figure S3 Culture under the darkness with addition of organic substances. C. merolae was cultured in a flask
with rotary-shaking under the dark condition with addition of 200 mM glucose, 200 mM glycerol, 200 mM
succinic acid, or 5 mM L-lactic acid for four weeks and OD750 was measured every one week. In the assay, the
cells were exposed to room light at the sampling time for a short period of time.
6