Next generation sequencing and de novo transcriptomics to study gene evolution

Table 3 De novo transcriptome assembly quality statistics

Gene	*H. annuus*	*A. montana*	*Z. haageana*	*Z. haageana*	*H. helianthoides*	*H. helianthoides*
	ws60, paired	ws60, paired	autows, non-paired	ws60, paired	autows, non-paired	ws60, paired
LEA	90%	80%	97%	79%	53%	73%
	165,041	23	25,957	5,584	162,273	176,283
OLE	100%	100%	57%	95%	100%	45%
	14,242	23,511	108,400	12,436	114,811	145,334
AP	78%	100%	63%	89%	97%	97%
	1,666	405	237	43	5,704	5,704
PR	100%	100%	89%	100%	79%	100%
	4,922	6,183	6	13	44,849	36,182
CP-1	51%	72%	100%	98%	100%	94%
	122	44	70	66	363	355
PK	73%	63%	83%	97%	75%	99%
	63	48	59	40	175	229
PawS1a	100%	-	100%	100%	70%	70%
	532		3,862	3,362	1,827	1,827
PawS1b	84%	-	79%	100%	32%	40%
	221		809	927	88	86
PawS1c	-	-	29%	58%	32%	41%
			15	58	798	782
PawS1d	-	-	70%	41%	-	-
			19,930	7,916
PawS1e	-	-	33%	36%	-	-
			2,236	7,394
PawS1f	-	-	33%	42%	-	-
			2,142	2,518
PawS1g	-	-	44%	-	-	-
			7,071
PawS1h	-	-	-	37%	-	-
				129
PawS1i	-	-	30%	-	-	-
			550
PawS1j	-	-	-	40%	-	-
				30
PawS1k	-	-	22%	52%	-	-
			4	8690
PawL1a	98%	100%	100%	-	100%	100%
	25	400	4		4,711	4,711
PawL1b	-	-	40%	87%	-	-
			4,125	4,736

All four species were assembled with word size (ws) 60, paired method. In addition, Z. haageana and H. helianthoides transcriptomes were assembled with the automatic word size (autows, 23), non-paired method. The first line shows the percentage coverage of the identified transcripts when compared to the expected full length protein query. The second line shows the average coverage by mapping trimmed, filtered reads on identified full/partial transcripts. Average coverage means sum of the bases of the aligned part of all the reads divided by the length of the reference sequence.