De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray

Table 2 Overview of assembled transcriptomes in S. senegalensis and S. solea

	S. senegalensis				S. solea
	v3		v4		v1
	Transcripts	%	Transcripts	%	Transcripts	%
Transcripts	252,416	-	697,125	-	523,637	-
Artifacts²	nc	-	7,095	1.02	10,086	1.92
Valid transcripts	252,416	100.00	701,767	100.00	531,463	100.00
>500pb	37,593	14.90	156,083	22.24	165,860	31.22
>200pb	168,914	66.92	385,411	54.92	338,967	63.89
Longest transcript	6,050	-	40,163	-	30,526	-
Transcripts with ortholog¹	81,348	32.23	147,536	21.02	121,696	22.90
Different orthologous IDs	41,792	51.37	45,063	30.54	38,402	31.56
Complete ORFs	6,742	8.31	39,727	26.93	52,051	42.77
Different, complete ORFs	4,376	5.38	18,738	12.70	22,683	18.64
C-terminus	14,757	18.14	27,080	18.35	19,579	16.09
N-terminus	11,298	13.88	27,638	18.73	25,131	20.65
Internal	47,529	58.43	53,091	35.99	24,935	20.49
Putative ncRNAs	539	0.21	1,252	0.18	1,075	0.20
Transcripts without ortholog¹	171,067	67.56	545,491	77.73	408,692	76.90
Putative new transcripts	22,612	13.21	39,812	7.30	34,194	8.37
Non-redundant new transcripts	nc	–	14,451	2.65	15,603	3.55
Unknown	147,916	86.48	505,679	92.70	374,498	91.63
Reference transcriptome	nc	–	v4.1: 59,514	8.48	v1.1: 54,005	10.16

The values were calculated using FullLengtherNext software. The minimum number of transcripts that can be considered as a reference transcriptome is shown in bold.
¹Percentages for subclassifications of this category were calculated using this line as 100% reference.
²Artifacts refer mainly to misassemblies and chimeric contigs.
nc: Non-calculated.

ISSN: 1471-2164