Table 1.

Summary of Sequencing, Cleanup, and Assembly of Tissue-Specific and Combined Transcriptomes

Species	Sequencinga		Trimmomatic				Trinity			CEGMA
Tissue	Yield (Mbases)	# PE Reads (2 × 100 bp)	F and R Recovered	F Only	R Only	Dropped	Isoforms	Genes	N50	Complete (%)
Anemonia sulcata
Tentacle	8,793	43,966,062	42,158,521	1,440,580	242,354	124,607	116,940	90,709	1,167	75
EC		40,114,944	32,725,211	3,534,322	2,282,523	1,572,888	54,365	39,503	1,262	77.02
Column	10,480	52,402,099	49,231,820	2,561,688	385,801	222,790	134,535	105,984	1,052	90.73
EC		47,615,852	36,988,265	4,813,831	3,185,361	2,628,395	55,868	41,679	1,242	81.42
Filament	14,657	73,285,750	69,599,682	3,027,316	411,698	247,054	167,752	140,339	789	88.31
EC		63,044,097	51,425,852	5,771,906	3,334,536	2,511,803	45,421	35,879	953	59.27
Combined	33,930	169,653,911	160,990,023	7,029,584	1,039,853	594,451	303,773	245,737	1,186	94.76
Heteractis crispa
Tentacle	8,054	40,269,872	38,950,621	1,071,964	170,250	77,037	186,284	142,194	1,227	93.55
EC		34,831,282	28,422,326	2,916,966	2,165,659	1,326,331	112,900	85,627	1,162	85.05
Column	11,629	58,142,549	55,456,896	2,220,420	318,314	146,919	—	—	—	—
EC		15,862,609	12,892,450	1,480,601	919,042	570,516	103,035	97,215	289	15.73
Filament	6,975	34,877,218	33,252,993	1,315,400	207,390	101,435	307,498	275,492	421	55.25
EC		23,826,103	19,561,405	1,915,171	1,502,125	847,402	67,733	56,039	711	43.95
Combined	26,658	133,289,639	127,660,510	4,607,784	695,954	325,391	655,116	581,957	545	94.34
Megalactis griffithsi
T. Lobe	7,201	33,993,938	31,743,659	2,008,599	147,255	94,425	208,940	146,020	1,119	88.71
EC		27,928,980	22,883,168	2,916,204	1,288,046	841,562	141,408	103,182	1,123	83.87
Column	8,303	36,006,836	33,419,868	2,330,576	162,784	93,608	572,734	547,297	268	19.76
EC		21,270,705	17,482,032	2,312,185	849,156	627,332	85,311	93,406	590	17.75
Filament	6,799	41,516,836	39,947,259	1,336,863	151,386	81,328	197,441	157,660	1,144	88.71
EC		35,093,477	29,602,445	2,759,483	1,633,100	1,098,449	93,566	76,840	1,157	87.50
Combined	22,303	111,517,610	105,110,786	5,676,038	461,425	269,361	1,200,511	1,073,369	392	97.18

Note.—F, Forward; R, Reverse.

^aValues represent the number of paired end reads (2 × 100 bp) at each step, EC indicates that the raw reads were subjected to the errorcorrect.pl script from the ALLPATHS-LG pipeline (Gnerre et al. 2011).