RNA-Seq profile of flavescence dorée phytoplasma in grapevine

BMC Genomics

Table 3 The top 20 highly expressed FD genes during V. vinifera infection

locus ID	Description	RPK (mean)
Contig12	Group II catalytic intron	2749.2
Ctg0426_0019664_0020134_f2_flado_0426_0012	Imp	889.1
Ctg0234_0028748_0029098_f2_flado_0234_0025	Hypothetical protein with cold-shock binding domain	548.8
Ctg0482_0000001_0000355_r3_flado_0482_0001	Hypothetical protein with 1 TMD + SP	460.8
rplP-flado_0067_0029	50S ribosomal subunit protein L16	95.6
tuf-flado_6343_0022	Elongation factor EF-Tu	95.6
Contig6	Bacterial Rnase P class B	80.3
Ctg7221_0018383_0018643_r1_flado_7221_0014	Hypothetical protein with 1 TMD + SP	54.7
Ctg5304_0020454_0020660_f3_flado_5304_0019	Hypothetical protein with 1 TMD	48.6
vmpA-flado_0482_0026	Variable membrane protein A	48.3
Ctg7221_0002401_0002754_f1_flado_7221_0002	Hypothetical protein with 1 TMD + SP	47.9
rpsU-flado_5304_0006	30S ribosomal subunit protein S21	46.0
rplV-flado_0067_0031	50S ribosomal subunit protein L22	43.9
rpsK-flado_0067_0011	30S ribosomal subunit protein S11	41.8
Ctg0314_0004067_0004231_f2_flado_0314_0005	Hypothetical protein	41.7
groL-flado_0426_0003	Chaperonin GroEL	40.3
rplN-flado_0067_0026	50S ribosomal subunit protein L14	37.1
rpsM-flado_0067_0012	30S ribosomal subunit protein S13	37.1
fusA-flado_6343_0021	Elongation factor EF-G	34.5
rplB-flado_0067_0033	50S ribosomal subunit protein L2	33.4

Transcription levels are expressed as the mean of RPK (reads per kilobase of transcript) values obtained in the two expression libraries. The first column (locus ID) reported the IDs of the annotated FD92 genes, with the only exception of contig12, which was obtained in this study. A brief gene description and the mean of reads per kilobase of transcript (RPK) are also reported. TMD = transmembrane domain predicted by TMHMM; SP = signal peptide predicted by SignalP-HMM v. 3.

ISSN: 1471-2164