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Table 1 List of species/strains of 12 lineages of the Chlamydomonadales [14] used for comparison of hydrophobicity scales of RBCS helices (Fig. 3)

From: The Rubisco small subunits in the green algal genus Chloromonas provide insights into evolutionary loss of the eukaryotic carbon-concentrating organelle, the pyrenoid

Lineage or strongly supported primary clade [14] Species Strain Sequencea Source of rbcS Accession number of rbcS Hydrophobicityb
Chloromonadinia (Reticulata group with pyrenoid) Chloromonas chlorococcoides SAG 15.82 5 mRNAc LC547865  − 23.6
LC547866  − 23.6
LC547867  − 23.0
LC547868  − 25.9
LC547869  − 26.3
SAG 12.96 1 mRNAc LC547870  − 25.9
SAG 16.82 3 mRNAc LC547871  − 23.6
LC547872  − 23.0
LC547873  − 26.3
SAG 72.81 2 mRNAc LC547874  − 23.6
LC547875  − 23.0
Chloromonas difformis NIES-2215 3 mRNAc LC547876  − 26.6
LC547877  − 29.6
LC547878  − 26.6
Chloromonas typhlos NIES-2243 2 mRNAc LC547879  − 22.8
LC547880  − 24.3
SAG 26.86 4 mRNAc LC547881  − 22.8
LC547882  − 19.6
LC547883  − 27.7
LC547884  − 27.7
Chloromonadinia (Reticulata group without pyrenoid) Chloromonas reticulata SAG 29.83 2 mRNAc LC547885  − 30.5
LC547886  − 31.2
SAG 26.90 4 mRNAc LC547887  − 31.6
LC547888  − 30.5
LC547889  − 30.5
LC547890  − 31.2
SAG 32.86 4 mRNAc LC547891  − 30.5
LC547892  − 30.5
LC547893  − 31.2
LC547894  − 31.2
Chloromonas rosae SAG 51.72 2 mRNAc LC547895  − 31.4
LC547896  − 33.6
Chloromonadinia (snow Chloromonas) Chloromonas krienitzii NIES-3753 3 mRNAc ICPW01000006  − 23.4
ICPW01000007  − 23.4
ICPW01000008  − 23.4
Chloromonas muramotoi NIES-4284 2 mRNAc ICPX01000119  − 15.7
ICPX01000120  − 15.7
Crucicarteria Carteria crucifera SAG 8-7a 1 mRNAd VIAU scaffold 2059943  − 25.6
  Carteria cerasiformis NIES-424 2 mRNAc ICQZ01000174  − 34.5
ICQZ01001652  − 30.6
NIES-425 1 mRNAc ICRA01000128  − 34.5
Chlorogonia Haematococcus lacustris NIES-144 4 gDNA BLLF01000007  − 24.2
BLLF01000015  − 24.2
BLLF01001246  − 24.2
BLLF01002948  − 24.2
CCAC 0055 2 mRNAd AGIO scaffold 2001898  − 24.2
ODXI scaffold 2002606  − 24.2
Dunaliellinia Dunaliella parva   1 mRNA HQ315783  − 23.8
Dunaliella salina   1 mRNA AY739272  − 24.4
Dunaliella tertiolecta   1 gDNA AY530155  − 32.2
CCMP 364 1 mRNAd ZDIZ scaffold 2000214  − 32.2
Asteromonas gracilis CCAC 0049 2 mRNAd MNPL scaffold 2000234  − 13.6
NTLE scaffold 2002920  − 13.6
Hafniomonas Hafniomonas reticulata CCAC 0530/1 1 mRNAd FXHG scaffold 2070561  − 37.2
Moewusinia Chlamydomonas moewusii   1 mRNA X13974  − 29.7
Chlamydomonas bilatus SAG 7.72 2 mRNAd OVHR scaffold 3000834  − 25.3
OVHR scaffold 3000835  − 25.3
Chlamydomonas eustigma NIES-2499 1 gDNA BEGY01000097  − 37.2
Chlamydomonas sp. HS-5 1 mRNA AU066498  − 20.1
Chlamydomonas sp. W80 3 mRNA DC847488  − 20.1
DC847494  − 20.1
DC847626  − 19.1
Oogamochlamydinia Oogamochlamys gigantea SAG 44.91 1 mRNAd XDLL scaffold 2047213  − 18.1
Lobochlamys segnis SAG 50.84 1 mRNAd OFUE scaffold 2045013  − 18.1
Phacotinia Phacotus lenticularis SAG 61–1 1 mRNAd ZIVZ scaffold 2002271  − 34.9
Radicarteria Carteria obtusa SAG 39.84 3 mRNAd RUIF scaffold 2001762  − 29.6
RUIF scaffold 2001763  − 32.4
RUIF scaffold 2001764  − 32.4
Reinhardtinia Chlamydomonas reinhardtii CC-503cw92mt+ 2 mRNA XM_001702354  − 13.4
XM_001702357  − 13.4
Chlamydomonas asymmetrica NIES-2207 2 gDNA BDDA01000282 (2 sequences)  − 13.4
   − 13.4
Chlamydomonas cribrum SAG 13.72 1 mRNAd BCYF scaffold 2001609  − 14.0
Chlamydomonas debaryana NIES-2212 3 gDNA BDDB01000073  − 14.0
BDDB01000328  − 14.0
BDDB01001769  − 14.0
Chlamydomonas globosae SAG 7.73 1 mRNA EC116339  − 13.4
Chlamydomonas sphaeroides NIES-2242 3 gDNA BDDC01000297 (2 sequences)  − 14.0
 − 14.0
BDDC01001831  − 13.4
Chloromonasoogama SAG 9.79 1 mRNAd IHOI scaffold 2001609  − 13.4
Gonium pectorale CCAC 0085 2 mRNAd KUJU scaffold 2000900  − 16.0
KUJU scaffold 2000901  − 16.0
Eudorina elegans CCAC 0011 3 mRNAd RNAT scaffold 2001381  − 16.0
RNAT scaffold 2001382  − 16.0
RNAT scaffold 2001383  − 16.0
Heterochlamydomonas inaequalis SAG 4.75 1 mRNAd IRYH scaffold 2037065  − 17.3
Lobomonas francei SAG 45–1 3 mRNAd JKKI scaffold 2001057  − 15.4
JKKI scaffold 2001059  − 15.4
JKKI scaffold 2001061  − 15.7
Neochlorosarcina sp. CCAC 0208 1 mRNAd USIX scaffold 2005162  − 14.0
Volvox aureus CCAC 1028 3 mRNAd JWGT scaffold 2000603  − 13.4
JWGT scaffold 2000604  − 13.4
JWGT scaffold 2000606  − 13.4
CCAC 2242 4 mRNAd WRSL scaffold 2000117  − 13.4
WRSL scaffold 2000118  − 13.4
WRSL scaffold 2000119  − 13.4
WRSL scaffold 2000120  − 13.4
Volvox carteri   3 gDNA AY205158 (3 sequences)  − 13.4
   − 13.4
   − 13.4
Volvox globator CCAC 2662 5 mRNAd ASPU scaffold 2003346  − 13.4
ASPU scaffold 2003347  − 13.4
ASPU scaffold 2003348  − 13.4
ASPU scaffold 2003349  − 13.4
ASPU scaffold 2003350  − 13.4
Stephanosphaerinia Chlorococcum microstigmatumf SAG 11–43 1 mRNAd QRTH scaffold 2038871  − 24.1
Spermatozopsisg Spermatozopsis similis CCAC 0013 2 mRNAd ENAU scaffold 2000800  − 28.8
ENAU scaffold 2000801  − 28.8
  1. aNumbers of RBCS paralogs used for comparison of hydrophobicity scales of helices A and B (Fig. 3)
  2. bHydrophobicity of RBCS helices A and B. For details, see Methods
  3. cFor details, see Additional file 3: Table S2
  4. dOne thousand plant transcriptome data (https://db.cngb.org/onekp/) [48]
  5. eFormerly identified as Chlamydomonas incerta [49]
  6. fFormerly identified as Chloromonas perforata [50]
  7. gNot identified as strongly supported primary clade because of its uncertain phylogenetic position [14]