Positional RNA-Seq identifies candidate genes for phenotypic engineering of sexual traits

Table 1 Positional classification of the transcriptome of Macrostomum lignano and details on the candidate transcripts selected for validation

Class	n	%	Mean B-A	Mean C-B	Mean D-C	Candidates	B-A	C-B	D-C	ISH	RNAi
[0,0,0]	70064	93.7	−0.14	−0.09	0.09	RNA815_92.1	1.15	0.55	0.24	X	-
Non-diff.						RNA815_40.1	0.82	0.27	0.51	X	-
expressed						RNA815_2403.2	−1.08	−0.23	−0.32	X	X
						RNA815_2224.1	0.52	−0.02	0.24	-	-
[+,0,0]	3360	4.4	4.00	−0.18	−0.41	RNA815_7008	5.17	−0.03	−0.39	X	X
Testis region						RNA815_9973.1	5.02	−0.03	−0.41	X	X
						RNA815_6628.2	4.13	−0.27	−0.46	X	-
						RNA815_3228	4.50	−0.25	−0.67	X	-
						RNA815_10311.2	2.89	0.61	−0.14	X	-
						RNA815_9262	2.55	0.12	−0.24	X	-
[+,+,0]	127	<0.1	3.18	4.14	0.52	RNA815_16738	2.77	4.75	0.77	X	-
Ovary region						RNA815_1618.1	5.46	4.35	0.47	X	-
						RNA815_2640	3.62	4.40	0.67	X	X
						RNA815_7725.2	2.91	4.15	−0.01	X	-
						RNA815_7498	2.28	4.92	0.61	X	-
						RNA815_12337.1	2.32	6.04	−0.14	-	-
[0,+,0]	323	0.4	0.57	3.41	0.36	RNA815_4558	0.39	4.09	0.64	X	-
Ovary region						RNA815_6266	2.00	5.35	0.88	-	-
[0,0,+]	366	0.4	−0.02	−0.03	4.23	RNA815_22046	0	1.00	7.69	X	-
Tail region						RNA815_80.4	0	0	8.30	X	X
						RNA815_9549.4	0	0	8.93	X	-
Others	468	0.6				RNA815_5404.2	3.58	−0.18	3.97	X	-
						RNA815_13	0	4.85	4.87	X	-

The transcripts are classified on the basis of their differential expression profile between samples using a three digit code (the 'Class'). Higher than two-fold differences in log2-expression level were considered indicative of differential expression (see Methods). Each digit in the code refers to the comparison between two adjacent samples (i.e. [B vs. A, C vs. B, D vs. C]) with the following coding: positive differential expression (+), no differential expression (0) or negative differential expression (−). The classes correspond to the predicted expression in different organs and body regions. We also give the number (n) and percentage (%) of transcripts in each class and the class mean difference in log2-expression between samples (Mean B-A, Mean C-B, Mean D-C). Furthermore, we give the accession codes of the selected candidate transcripts belonging to different classes (Candidates), the transcript difference in log2-expression between samples (B-A, C-B, D-C), and the summary of the in situ hybridization (ISH) and RNA interference (RNAi) screens, namely expression or phenotype detected (X) or non-detected (−)

ISSN: 1742-9994