Table 2.

Total number of reads used in the assembly of the O. faveolata metatranscriptome and those aligned against each of the holobiont components (‘O. faveolata’, ‘Symbiodinium spp.’ and ‘other-eukaryotes’). Percentages are of the total of the raw reads for each row.

	raw reads		aligned reads
month	colony condition and no.	total	O. faveolata	%	Symbiodinium spp.	%	other-eukaryotes	%	total	%
bleaching
November 2010	unbleached 1	25 263 324	18 397 266	72.8	3 458 682	13.7	1 760 588	7.0	23 616 536	93.5
	unbleached 2	22 167 068	17 899 877	80.7	2 400 183	10.8	838 853	3.8	21 138 913	95.4
	bleached 1	17 619 525	15 869 696	90.1	292 570	1.7	143 158	0.8	16 305 424	92.5
	bleached 2	17 321 791	15 740 825	90.9	1 098 670	6.3	161 552	0.9	15 902 377	91.8
post-bleaching
March 2011	unbleached 1	45 411 481	35 655 303	78.5	5 944 196	13.1	1 160 146	2.6	42 759 645	94.2
	unbleached 2	21 592 782	15 583 474	72.2	1 855 259	8.6	3 018 662	14.0	204 57395	94.7
	bleached 1	33 446 863	25 284 275	75.6	1 377 763	4.1	4 268 640	12.8	30 930 678	92.5
	bleached 2	64 535 106	50 983 253	79.0	4 804 314	7.4	5 339 275	8.3	56 322 528	87.3
October 2011	unbleached 1	31 158 747	22 055 972	70.8	949 427	3.0	6 541 857	21.0	29 547 256	94.8
	unbleached 2	50 476 948	40 373 490	80.0	6 881 860	13.6	1 144 076	2.3	48 399 426	95.9
	bleached 1	30 226 535	21 934 584	72.6	1 376 168	4.6	4 297 944	14.2	26 232 528	86.8
	bleached 2	28 292 342	18 843 835	66.6	1 207 627	4.3	4 005 816	14.2	18 843 835	66.6
	average	32 292 709	24 885 154	77.5	2 894 993	7.6	2 606 796	8.5	29 204 712	93.6