Table 1.

Characteristics of chrysophyte plastid genomes analyzed in this study.

General characteristics	Pedospumella sp. Jangsampo120217C5	Poteriospumella lacustris Yongseonkyo072317C3	Spumella sp. Baeckdong012018B8	“Spumella” sp. NIES-1846	Ochromonas sp. CCMP1393	Synura petersenii S114.C7, CZ	Synura sphagnicola CNUKRJ2	Synura uvella CNUKR	Mallomonas splendens CCMP1872	Neotessella volvocina CCMP1871
Nutrition	Heterotroph	Heterotroph	Heterotroph	Heterotroph	Mixotroph	Phototroph	Phototroph	Phototroph	Phototroph	Phototroph
Type of plastid	Leucoplast	Leucoplast	Leucoplast	Leucoplast	Plastid	Plastid	Plastid	Plastid	Plastid	Plastid
Key characteristics for genus classification	Small, colorless, naked single cell, independent clade in nuclear SSU rDNA phylogeny	Small, colorless, naked single cell, independent clade in nuclear SSU rDNA phylogeny	Small, colorless, naked single cell, independent clade in nuclear SSU rDNA phylogeny	Small, colorless, naked cell, independent clade in nuclear SSU rDNA phylogeny	naked single cell	colonized cells covered with silica scale on each cell	colonized cells covered with silica scale on each cell	colonized cells covered with silica scale on each cell	single cell covered with silica scale	colonized cells covered with silica scale on colony
Size (bp)	58,577	62,910	55,641	53,209	126,746	133,059	129,699	133,257	146,918	130,705
Inverted repeat (IR)	8,531	8,078	8,283	5,603	22,906	23,151	22,505	23,691	31,611	24,064
Small single-copy region	153	2,144	1,548	1,297	805	1,135	1,191	2,939	711	2,432
Large single-copy region	41,362	44,610	37,527	40,706	80,129	85,622	83,498	82,936	82,985	80,145
G+C (%)	35	32.2	38.9	21.5	30.9	37.89	38.76	38.19	42.39	37.54
Total gene (include RNAs)	97	99	97	82	183	182	181	189	187	186
No. of protein-coding genes	60	63	59	45	144	144	144	151	150	149
tRNAs	33	32	34	33	33	34	33	34	33	33
rRNA operons	2	2	2	2	2	2	2	2	2	2
Introns	–	–	–	–	–	trnL	trnL	trnL	trnL	trnP, trnS
Unknown ORFs	1	2	3	3	7	8	3	9	11	9
Pseudogene	–	–	–	–	–	–	–	trnR	trnR	trnE
Partial copied gene	dnaK	secA	rps14	-	-	–	dnaK	–	-	dnaK
Specific encoded genes	petF	petF	petF	petF	–	dnaB/cemA	dnaB/cemA	dnaB/cemA	dnaB/cemA	cemA
Missing gene	psa-, psb-, pet-, acpP, acsF, cbbX, ccs1, ccsA, chlI, ftrB, ftrH, groEL, ilvB, ilvH, rbcL, rbcS, rpl24, secA , secG, secY, syfB, tatC,	psa-, psb-, pet-, acsF, cbbX, ccs1, ccsA, chlI, groEL, ftrB, ftrH, ilvB, ilvH, rbcL, rbcS, secG, syfB, tatC, tsf,	psa-, psb-, pet-, acsF, acpP, cbbX, ccs1, ccsA, chlI, dnaK , ftrB, ftrH, groEL, ilvB, ilvH, rbcL, rbcS, rpl24, secA , secG, secY, syfB, tatC, tsf, tufA	psa-, psb-, pet-, acsF, acpP, cbbX, chlI, ccs1, ccsA, clpN, dnaK , ftrB, ftrH, groEL, ilvB, ilvH, rbcL, rbcS, rpl18, rpl23, rpl24, rpl29, rpl31, rpl34, rpl35, rpl36, rps18, rps20, secA , secG, secY, syfB, tatC, tsf	–	syfB	syfB	–	–	–
GenBank accession	MN935477	MN935478	MN935479	AP019363	KJ877675	MH795128	MH795129	NC_040134	NC_040135	MH795132

Bold type indicates gene loss in specific lineages among non-photosynthetic chrysophytes.