SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data

Table 3 Operon prediction (SLOPPR) results in four nematode and two tunicate species

Species	Genome	Bioproject	QC reads	SL reads	SL genes (%)	Reference operons	Predicted operons	Specificity \| sensitivity	Operonic genes	Intercistronic distance (bp)
Caenorhabditis elegans	GCF_000224145.3	PRJNA270896	621,744,295	937,587	52	1542	345	86% \| 19%	721	99
Caenorhabditis briggsae	CB3	PRJNA104933	21,265,790	209,005	27	1034	840	81% \| 66%	1847	342
		PRJNA231838	59,271,467	286,520	36	1034	752	81% \| 59%	1631	332
	CB4	PRJNA104933	21,265,790	235,001	38	48	921	5% \| 96%	2058	111
		PRJNA231838	59,271,467	289,834	41	48	750	5% \| 81%	1626	110
Pristionchus pacificus	Hybrid1	SRP039388	81,387,873	438,557	20	2219	190	61% \| 5%	382	981
		PRJNA338247	330,856,071	312,718	28	2219	205	50% \| 5%	414	872
Trichuris muris	PRJEB126.WBPS15	PRJEB1054	115,460,947	168,727	35	2	718	–^a	1492	418
Ciona intestinalis	KH	PRJNA376667	194,089,029	452,505	51	1328	1172	94% \| 83%	2563	1
Oikopleura dioica	GCA_000209535.1	PRJNA269316, PRJDB5668	250,361,592	5,860,107	9	1765	464	98% \| 26%	1017	31

Identifiers for reference genomes and paired-end RNA-Seq libraries are presented alongside numbers of quality-trimmed reads (QC), numbers of reads with a spliced leader (SL), percentage of genes receiving an SL, numbers of available reference operons, numbers of predicted operons, specificity (predicted operons matching reference operons), sensitivity (fraction of reference operons detected), numbers of operonic genes, and median intercistronic distance among operonic genes. Downstream operonic genes were required to have SL2:SL1 read ratio ≧ 2, and upstream operonic genes were not required to be SL trans-spliced. Since the two tunicates C. intestinalis and O. dioica do not use SL2-type trans-splicing, operonic genes were obtained by filtering SL trans-spliced genes by intercistronic distance (cut-offs: 84 bp for C. intestinalis and 60 bp for O. dioica; see main text)
^aNot calculated due to low sample size (n = 2)

ISSN: 1471-2105