Table 1.

The numbers of lncRNAs in individual RNA-seq datasets of different N. lugens strains/populations and in the comprehensive RNA-seq dataset

lncRNA typesa	lncRNA in 12 samples		Fecundityd				Virulence					Populations
	Number of lncRNA	Percentage (%)	LFPb adult 2 d	HFPb adult 2 d	LFP 5th instar larva	HFP 5th instar larva	Mudgoc fat body	TN1c fat body	Mudgo salivary gland	TN1 salivary gland	TN1 antenna	I87ic population	C89ic population	Wild population
Intergenic1	853	34.97	344	534	440	536	694	682	739	727	569	603	560	496
Intronic2	80	3.28	30	42	38	41	57	56	70	67	55	57	49	53
Intronic overlap3 (−)	5	0.21	1	3	0	1	4	4	5	5	2	4	4	3
Exonic overlap4 (+)	385	15.79	151	250	215	247	311	310	323	332	305	287	271	255
Exonic overlap5 (−)	211	8.65	78	137	117	147	175	176	188	187	153	147	145	139
Splice junction overlap6	264	10.28	103	172	150	175	218	221	227	226	199	197	190	188
Unclassified7	641	26.28	241	424	364	416	528	526	559	537	515	511	502	484
total	2,439	100	948	1,562	1,324	1,563	1,987	1,975	2,111	2,081	1,798	1,806	1,721	1,618

^aLncRNA types: 1) Intergenic transcript, 2) falling entirely within a reference intron, 3) overlaps with a reference intron on the opposite strand, 4) overlaps with a reference exon, 5) overlaps with a reference exon on the opposite strand, 6) At least one splice junction is shared with a reference transcript, 7) Unclassified

^b LFP low fecundity population, HFP high fecundity population

^c TN1: avirulent Taichung Native 1 host strain, Mudgo: virulent (carrying the resistance gene bph1) host strain, I87i Izumo87 strain, C89i: Chikugo89 strain

^dBased on the analysis of the 12 RNA-seq datasets together using the computational pipeline developed