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

Matsuzaki, Ryo; Suzuki, Shigekatsu; Yamaguchi, Haruyo; Kawachi, Masanobu; Kanesaki, Yu; Yoshikawa, Hirofumi; Mori, Toshiyuki; Nozaki, Hisayoshi

doi:10.1186/s12862-020-01733-1

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	Sequence^a	Source of rbcS	Accession number of rbcS	Hydrophobicity^b
Chloromonadinia (Reticulata group with pyrenoid)	Chloromonas chlorococcoides	SAG 15.82	5	mRNA^c	LC547865	− 23.6
					LC547866	− 23.6
					LC547867	− 23.0
					LC547868	− 25.9
					LC547869	− 26.3
		SAG 12.96	1	mRNA^c	LC547870	− 25.9
		SAG 16.82	3	mRNA^c	LC547871	− 23.6
					LC547872	− 23.0
					LC547873	− 26.3
		SAG 72.81	2	mRNA^c	LC547874	− 23.6
		SAG 72.81	2	mRNA^c	LC547875	− 23.0
	Chloromonas difformis	NIES-2215	3	mRNA^c	LC547876	− 26.6
					LC547877	− 29.6
					LC547878	− 26.6
	Chloromonas typhlos	NIES-2243	2	mRNA^c	LC547879	− 22.8
		NIES-2243	2	mRNA^c	LC547880	− 24.3
		SAG 26.86	4	mRNA^c	LC547881	− 22.8
					LC547882	− 19.6
					LC547883	− 27.7
					LC547884	− 27.7
Chloromonadinia (Reticulata group without pyrenoid)	Chloromonas reticulata	SAG 29.83	2	mRNA^c	LC547885	− 30.5
		SAG 29.83	2	mRNA^c	LC547886	− 31.2
		SAG 26.90	4	mRNA^c	LC547887	− 31.6
					LC547888	− 30.5
					LC547889	− 30.5
					LC547890	− 31.2
		SAG 32.86	4	mRNA^c	LC547891	− 30.5
					LC547892	− 30.5
					LC547893	− 31.2
					LC547894	− 31.2
	Chloromonas rosae	SAG 51.72	2	mRNA^c	LC547895	− 31.4
	Chloromonas rosae	SAG 51.72	2	mRNA^c	LC547896	− 33.6
Chloromonadinia (snow Chloromonas)	Chloromonas krienitzii	NIES-3753	3	mRNA^c	ICPW01000006	− 23.4
					ICPW01000007	− 23.4
					ICPW01000008	− 23.4
	Chloromonas muramotoi	NIES-4284	2	mRNA^c	ICPX01000119	− 15.7
	Chloromonas muramotoi	NIES-4284	2	mRNA^c	ICPX01000120	− 15.7
Crucicarteria	Carteria crucifera	SAG 8-7a	1	mRNA^d	VIAU scaffold 2059943	− 25.6
	Carteria cerasiformis	NIES-424	2	mRNA^c	ICQZ01000174	− 34.5
		NIES-424	2	mRNA^c	ICQZ01001652	− 30.6
		NIES-425	1	mRNA^c	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	mRNA^d	AGIO scaffold 2001898	− 24.2
		CCAC 0055	2	mRNA^d	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
	Dunaliella tertiolecta	CCMP 364	1	mRNA^d	ZDIZ scaffold 2000214	− 32.2
	Asteromonas gracilis	CCAC 0049	2	mRNA^d	MNPL scaffold 2000234	− 13.6
	Asteromonas gracilis	CCAC 0049	2	mRNA^d	NTLE scaffold 2002920	− 13.6
Hafniomonas	Hafniomonas reticulata	CCAC 0530/1	1	mRNA^d	FXHG scaffold 2070561	− 37.2
Moewusinia	Chlamydomonas moewusii		1	mRNA	X13974	− 29.7
	Chlamydomonas bilatus	SAG 7.72	2	mRNA^d	OVHR scaffold 3000834	− 25.3
	Chlamydomonas bilatus	SAG 7.72	2	mRNA^d	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	mRNA^d	XDLL scaffold 2047213	− 18.1
Oogamochlamydinia	Lobochlamys segnis	SAG 50.84	1	mRNA^d	OFUE scaffold 2045013	− 18.1
Phacotinia	Phacotus lenticularis	SAG 61–1	1	mRNA^d	ZIVZ scaffold 2002271	− 34.9
Radicarteria	Carteria obtusa	SAG 39.84	3	mRNA^d	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
	Chlamydomonas reinhardtii	CC-503cw92mt+	2	mRNA	XM_001702357	− 13.4
	Chlamydomonas asymmetrica	NIES-2207	2	gDNA	BDDA01000282 (2 sequences)	− 13.4
	Chlamydomonas asymmetrica	NIES-2207	2	gDNA		− 13.4
	Chlamydomonas cribrum	SAG 13.72	1	mRNA^d	BCYF scaffold 2001609	− 14.0
	Chlamydomonas debaryana	NIES-2212	3	gDNA	BDDB01000073	− 14.0
					BDDB01000328	− 14.0
					BDDB01001769	− 14.0
	Chlamydomonas globosa^e	SAG 7.73	1	mRNA	EC116339	− 13.4
	Chlamydomonas sphaeroides	NIES-2242	3	gDNA	BDDC01000297 (2 sequences)	− 14.0
					BDDC01000297 (2 sequences)	− 14.0
					BDDC01001831	− 13.4
	“Chloromonas” oogama	SAG 9.79	1	mRNA^d	IHOI scaffold 2001609	− 13.4
	Gonium pectorale	CCAC 0085	2	mRNA^d	KUJU scaffold 2000900	− 16.0
	Gonium pectorale	CCAC 0085	2	mRNA^d	KUJU scaffold 2000901	− 16.0
	Eudorina elegans	CCAC 0011	3	mRNA^d	RNAT scaffold 2001381	− 16.0
					RNAT scaffold 2001382	− 16.0
					RNAT scaffold 2001383	− 16.0
	Heterochlamydomonas inaequalis	SAG 4.75	1	mRNA^d	IRYH scaffold 2037065	− 17.3
	Lobomonas francei	SAG 45–1	3	mRNA^d	JKKI scaffold 2001057	− 15.4
					JKKI scaffold 2001059	− 15.4
					JKKI scaffold 2001061	− 15.7
	Neochlorosarcina sp.	CCAC 0208	1	mRNA^d	USIX scaffold 2005162	− 14.0
	Volvox aureus	CCAC 1028	3	mRNA^d	JWGT scaffold 2000603	− 13.4
					JWGT scaffold 2000604	− 13.4
					JWGT scaffold 2000606	− 13.4
		CCAC 2242	4	mRNA^d	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	mRNA^d	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 microstigmatum^f	SAG 11–43	1	mRNA^d	QRTH scaffold 2038871	− 24.1
Spermatozopsis^g	Spermatozopsis similis	CCAC 0013	2	mRNA^d	ENAU scaffold 2000800	− 28.8
Spermatozopsis^g	Spermatozopsis similis	CCAC 0013	2	mRNA^d	ENAU scaffold 2000801	− 28.8

^aNumbers of RBCS paralogs used for comparison of hydrophobicity scales of helices A and B (Fig. 3)
^bHydrophobicity of RBCS helices A and B. For details, see Methods
^cFor details, see Additional file 3: Table S2
^dOne thousand plant transcriptome data (https://db.cngb.org/onekp/) [48]
^eFormerly identified as Chlamydomonas incerta [49]
^fFormerly identified as Chloromonas perforata [50]
^gNot identified as strongly supported primary clade because of its uncertain phylogenetic position [14]

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