Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens

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 types^a	lncRNA in 12 samples		Fecundity^d				Virulence					Populations
lncRNA types^a	Number of lncRNA	Percentage (%)	LFP^b adult 2 d	HFP^b adult 2 d	LFP 5^th instar larva	HFP 5^th instar larva	Mudgo^c fat body	TN1^c fat body	Mudgo salivary gland	TN1 salivary gland	TN1 antenna	I87i^c population	C89i^c 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

ISSN: 1471-2164