Table 2.

Annotation summaries for Roche-based and Illumina-based transcriptomes

			Roche GS-FLX Titanium					Illumina GA/HiSeq
No.	Abbrev.	Plant	Unigenes	Overall annotated	High-level annotated	GO annotated	EC number allocated	Unigenes	Overall annotated	High-level annotated	GO annotated	EC number allocated
1	AME	Argemone mexicana	25,499	22,121	17,979	21,974	3086	75,101	60,836	45,404	60,254	7653
2	BTH	Berberis thunbergii	41,672	33,548	23,243	33,080	4197	88,302	61,576	41,927	60,561	7289
3	CMA	Chelidonium majus	23,678	19,635	13,977	19,460	2368	45,005	42,057	33,449	41,956	6092
4	CMU	Cissampelos mucronata	35,166	27,451	19,865	27,139	3147	69,822	32,209	22,943	31,597	3314
5	CTR	Cocculus trilobus	34,783	26,678	18,701	26,338	3197	84,793	33,055	21,961	30,542	432
6	CCH	Corydalis chelanthifolia	22,511	19,161	14,633	19,024	2433	51,797	48,423	42,784	48,139	7738
7	ECA	Eschscholzia californica	32,150	28,430	21,403	28,194	4221	42,167	38,332	32,677	38,063	6545
8	GFL	Glaucium flavum	26,520	20,945	15,645	20,725	2719	31,100	31,100	19,669	31,100	3231
9	HCA	Hydrastis canadensis	23,809	20,443	15,491	20,230	2511	33,335	33,335	20,898	33,335	3637
10	JDI	Jeffersonia diphylla	38,773	24,583	16,777	24,199	2581	86,832	31,712	22,574	30,842	3118
11	MAQ	Mahonia aquifolium	36,429	30,209	20,624	29,805	3581	98,375	53,093	33,434	47,040	521
12	MCA	Menispermum canadense	36,399	31,715	24,565	31,482	4495	87,141	70,524	52,713	69,877	8924
13	NDA	Nandina domestica	45,387	33,501	24,308	33,010	4186	70,425	53,109	38,428	52,531	6553
14	NSA	Nigella sativa	50,508	36,231	25,560	35,591	4526	67,591	41,260	29,127	40,316	4807
15	PBR	Papaver bracteatum	46,224	33,168	24,381	32,767	4988	70,428	56,463	37,334	53,039	6793
16	SCA	Sanguinaria canadensis	25,652	20,493	15,938	20,301	2621	53,019	47,247	40,122	46,890	7715
17	SDI	Stylophorum diphyllum	43,568	34,954	26,144	34,614	5115	50,125	40,797	30,157	40,324	5276
18	TFL	Thalictrum flavum	21,146	17,609	12,121	17,431	2294	41,982	33,120	23,900	32,711	4123
19	TCO	Tinospora cordifolia	34,518	28,044	21,199	27,795	3444	81,927	35,851	24,174	34,712	3386
20	XSI	Xanthoriza simplicissima	42,969	33,657	22,165	33,187	3740	48,447	39,281	27,434	38,831	4642
		Average	34,368	27,128	19,736	26,817	3472	63,886	44,169	32,055	43,133	5089