Table 1 Reference transcriptome sources and assembly metrics

Species	Type	No. contigs	Complete & single copy	Complete and duplicated	Fragmented	Missing	N50	Percent annotated
Coral host transcriptome assembly metrics based on metazoan reference
C. natans	de novo	50,582	631	86	115	146	12,255	27%
M. cavernosa	genome-guided⁸²	38,865	709	75	91	103	8027	30%
O. annularis	genome-guided⁵⁶	34,741	719	99	95	65	7601	38%
P. astreoides	de novo	37,167	806	44	60	68	6457	36%
P. strigosa	de novo	23,116	603	104	79	192	4970	42%
Symbiodiniaceae transcriptome assembly metrics based on eukaryote reference
S. CassKB8	de novo	72,152	123	6	39	87	17,845	15%
B. minutum	de novo	51,199	172	6	19	58	11,053	20%
C. goreaui	de novo	65,838	110	66	18	61	18,032	18%
D. trenchii	de novo	82,273	173	13	15	54	17,347	13%

Reference transcriptomes for M. cavernosa, C. natans, and P. astreoides were sourced from Dimos et al.²⁶. Reference transcriptomes for S. CassKB8, B. minutum, C. goreaui and D. trenchii were sourced from Bayer et al.⁸³, Parkinson et al.⁸⁴, Davies et al.⁸⁵, and Bellantuono et al.⁸⁶, respectively. The “Percent annotated” column shows the percentage of protein-coding transcripts that were annotated with an evalue cutoff of 1.0e⁻⁶.

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