Genome assemblies metrics

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Species	Sex	Ploidy	Sequencing	Assembly size	Number of scaffolds	GC content	N content	N50	L50
Chondrus crispus  Sequencing: Sanger	Gametophyte (male)	Haploid	Sanger	100.12 Mbp	926	52.8%	8526%	237.01 Kbp	126
Cyanidiococcus yangmingshanensis  Sequencing: Illumina, PacBio	Unknown	Undetermined	Illumina, PacBio	11.51 Mbp	20	54.6%	0%	637.78 Kbp	7
Gracilaria gracilis  Sequencing: PacBio Good quality assembly	Male	Haploid	PacBio	72.49 Mbp	279	49.6%	0%	562.98 Kbp	38
Gracilaria vermiculophylla  Sequencing: Illumina, HiC Near chromosome scale assembly	Male	Haploid	Illumina, HiC	44.95 Mbp	4240	49.4%	7385%	2.56 Mbp	6
Gracilaria chilensis  Sequencing: PacBio Near chromosome scale assembly	Male	Haploid	PacBio	76.07 Mbp	138	48.9%	0%	1.56 Mbp	18
Gracilaria caudata  Sequencing: Illumina Draft genome	Male	Haploid	Illumina	30.28 Mbp	5535	49.9%	1282%	20.84 Kbp	396
Neoporphyra haitanensis  Sequencing: Illumina, PacBio	Female	Haploid	Illumina, PacBio	47.36 Mbp	143	0%	0.11%	7.44 Mbp	2
Porphyridium purpureum  Sequencing: Illumina, Nanopore	Unknown	Undetermined	Illumina, Nanopore	21.16 Mbp	52	55.9%	0%	1.77 Mbp	3

Structural annotations metrics

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Species	Sex	Protein-coding genes	Exons per gene (mean | median)	CDS length (mean | median)	CDS percentage	Monoexonic genes	Contigs with at least one gene (percentage of genome | percentage of bases)	lncRNAs
Chondrus crispus  Sequencing:	Gametophyte (male)	9807	1.29 | 1.0	1051.1 | 774.0	9.81%	8336	70.95% | 95.74%	Undetermined
Cyanidiococcus yangmingshanensis  Sequencing: Illumina, PacBio	Unknown	Undetermined	Undetermined	Undetermined	Undetermined	Undetermined	Undetermined	Undetermined
Gracilaria gracilis  Sequencing: PacBio   Good quality assembly	Male	9460	1.55 | 1.0	1324.22 | 1043.0	16.85%	6680	77.41% | 96.7%	Undetermined
Gracilaria vermiculophylla  Sequencing: Illumina, HiC   Near chromosome scale assembly	Male	6807	1.4 | 1.0	1351.84 | 1085.0	20.21%	5169	6.58% | 96.21%	Undetermined
Gracilaria chilensis  Sequencing: PacBio   Near chromosome scale assembly	Male	7943	1.37 | 1.0	1334.23 | 1082.0	13.45%	6079	53.62% | 95.51%	Undetermined
Gracilaria caudata  Sequencing: Illumina   Draft genome	Male	8737	1.53 | 1.0	1273.29 | 1043.0	36.35%	6231	34.2% | 86.77%	Undetermined
Neoporphyra haitanensis  Sequencing: Illumina, PacBio	Female	Undetermined	Undetermined	Undetermined	Undetermined	Undetermined	Undetermined	Undetermined
Porphyridium purpureum  Sequencing:	Unknown	Undetermined	Undetermined	Undetermined	Undetermined	Undetermined	Undetermined	Undetermined

BUSCO metrics

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Species	Sex	Single copy genes (genome)	Duplicated genes (genome)	Fragmented genes (genome)	Missing genes (genomes)	Single copy genes (proteome)	Duplicated genes (proteome)	Fragmented genes (proteome)	Missing genes (proteome)
Chondrus crispus  Sequencing:	Gametophyte (male)	224	8	24	47	224	8	24	47
Cyanidiococcus yangmingshanensis  Sequencing: Illumina, PacBio	Undetermined	51	0	12	34	Undetermined	Undetermined	Undetermined	Undetermined
Gracilaria gracilis  Sequencing: PacBio   Good quality assembly	Male	194	6	18	37	192	5	16	42
Gracilaria vermiculophylla  Sequencing: Illumina, HiC   Near chromosome scale assembly	Male	166	2	23	64	165	1	17	72
Gracilaria chilensis  Sequencing: PacBio   Near chromosome scale assembly	Male	194	3	20	38	187	5	16	47
Gracilaria caudata  Sequencing: Illumina   Draft genome	Male	189	7	22	37	182	4	22	47
Neoporphyra haitanensis  Sequencing: Illumina, PacBio	Female	53	1	11	33	Undetermined	Undetermined	Undetermined	Undetermined
Porphyridium purpureum  Sequencing:	Undetermined	54	0	8	36	Undetermined	Undetermined	Undetermined	Undetermined