Efficient subtraction of insect rRNA prior to transcriptome analysis of Wolbachia-Drosophila lateral gene transfer

Table 1 Wolbachia genes represented in reads and arising from nuwts

				Pairs of Reads		Unpaired Reads
5′-end	3′-end	Locus	Name	Total RNA	Ribo-Zero-subtracted	Total RNA	Ribo-Zero-subtracted
8305	10323	WRi_000090	type IV secretion system protein VirD4	0	2*	0	0
20819	29332	WRi_000230	DNA-directed RNA polymerase, beta subunit	0	1	0	0
37758	35593	WRi_000280	ankyrin repeat domain protein	0	1	0	0
71725	72540	WRi_000680	hypothetical protein	1	0	0	0
188532	191277	WRi_r01850	23S ribosomal RNA	0	0	1‡	0
458087	457221	WRi_004260	4-diphosphocytidyl-2 C-methyl-D-erythritol kinase	0	1	0	0
663596	664402	WRi_006160	hypothetical protein	1	0	0	0
687296	685893	WRi_006360	transcription termination factor Rho	0	1	0	0
804498	806600	WRi_007420	hypothetical protein	3*	0	0	0
832611	833609	WRi_007700	tryptophanyl-tRNA synthetase	0	1	0	0
938372	936990	WRi_008690	transposase	2*^,†	0
1044899	1045516	WRi_009720	lipoyltransferase	0	0	1	0
1139870	1138959	WRi_010540	transcriptional regulator, putative	0	1†	0	0
1289969	1291473	WRi_r11990	16S ribosomal RNA	0	0	1‡	2‡
1334777	1336324	WRi_012430	penicillin-binding protein	1	0	0	0
1336345	1337274	WRi_012440	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	1	0	0	0
1436571	1435714	WRi_013460	4-hydroxybenzoate octaprenyltransferase	0	1	0	0

^*These are duplicate paired end reads; upon manually removing duplicates this reduces to one. However, these reads were not removed when analyzed with the duplicate analysis tool Picard.
^†These reads are not unique with respect to the reference genome.
^‡These reads likely arise from non-Wolbachia bacterial contaminants on the eggs.

ISSN: 1756-0500