RNA-Seq profile of flavescence dorée phytoplasma in grapevine

BMC Genomics

Table 4 Transcripts selected for validation by qRT-PCR

locus ID	Abbreviation	Description	RPK (mean)	EI (mean)
Contig12	contig12	Group II intron	2749.2	10.9
Ctg0426_0019664_0020134_f2_flado_0426_0012	Imp	Imp	889.1	3.5
Ctg0234_0028748_0029098_f2_flado_0234_0025	comp83	Hypothetical protein with cold-shock binding domain	548.8	2.1
Ctg7221_0018383_0018643_r1_flado_7221_0014	comp100	Hypothetical protein	54.7	1.1
Ctg0314_0004067_0004231_f2_flado_0314_0005	comp115	Hypothetical protein with 1 TMD + SP	41.7	1.4
Ctg0482_0033346_0033975_f1_flado_0482_0023	spoVG	septation protein	32	0.5
ysdC-flado_4539_0017	ysdC	β-glucanase	29.2	0.5
Ctg0338_0006451_0007086_f1_flado_0338_0005	comp126	Hypothetical protein with 1 TMD + SP	23.3	0
vmpB-flado_0031_0011	vmpB	Variable membrane protein B	13.1	0.1
tldD-flado_0426_0020	tldD	Metalloprotease	12.2	0.2
ftsY-flado_0482_0016	fstY	Signal recognition particle receptor	9.1	0.1
Ctg0314_0007223_0007996_f2_flado_0314_0008	PAM266	Hypothetical protein (similar to PAM266)	8	0.1
CbiO2-flado_0067_0008	CoABC	Cobalt transporter ATP-binding subunit	5	0.2
Ctg5304_0021069_0021488_f3_flado_5304_0021	osm	OsmC-like protein	4.8	0.1
rpoD-flado_4539_0007	rpoD	RNA polymerase sigma factor	0	0.5

Selected genes are listed according to the IDs of the FD92 annotated genes (locus ID), with the only exception of contig12, which was obtained in this study. The abbreviation used in this work, a brief gene description, the mean of reads per kilobase of transcript (RPK) and the mean of the expression indices (EI, N° of transcript per FD cell) are reported.

ISSN: 1471-2164