Table 2

Genes with changed antisense transcription
(A)
ATCC 1015 ID CBS ID putative gene function T0-T1 fold change ↓ T1 AS/T0 AS AS/S at T1
TID_54223 An18g05740 GTP binding protein 7.96 41.60 5.26
TID_54624 An04g01450 glycolate oxidase 37.69 23.20 3.43
TID_53523 An15g06700 dihydroxy-acid dehydratase 3.98 23.00 0.74*
TID_210938 An14g01050 serine/threonine protein kinase 6.64 19.50 0.46*
TID_57034 An04g03290 acyl-CoA dehydrogenase - β oxidation 2.68 15.50 0.35*
TID_173684 An02g09690 lipase 16.30 15.29 5.04
TID_50444 An04g03950 serine/threonine protein kinase 4.12 13.75 0.75*
TID_197387 An02g06430 transketolase 194.28 11.86 3.91
An15g02810 phosphatidylinositol phosphate phosphatase 14.05 11.15 36.43
TID_210245 An15g04770 calmodulin-binding glutamate decarboxylase 27.10 7.82 6.26
TID_39560 An07g10430 hypothetical protein involved in stress 6.84 6.95 0.92*
An01g03400 transcription factor/amino acid metabolism 5.73 6.92 1.30
TID_203198 An12g00030 L-iditol 2-dehydrogenase 12.89 1.76 2.34
(B)
ATCC 1015 ID CBS ID putative gene function T0-T1 fold change ↑ T0 AS/T1 AS AS/S at T0
TID_57297 An17g02080 hypothetical protein - metal ion transporter 4.36 264.00 0.84*
TID_44497 An03g05020 carnitine/acylcarnitine translocase 1.75 42.38 7.44
TID_187258 An18g03060 leucine carboxyl methyltransferase 14.27 16.86 6.14
TID_52216 An02g04860 cytochrome-b5 reductase 12.36 16.29 5.48
TID_207532 An02g14860 ornithine decarboxylase - polyamine biosynthesis 1.13 12.79 0.92*
TID_182952 An15g01810 hypothetical protein/amino acid metabolism 20.26 9.90 9.99
TID_173423 An02g14950 ATP-dependent RNA helicase 12.04 8.94 0.87*
TID_119526 An06g01130 kinesin heavy chain 3.34 5.68 2.68
TID_46289 An01g13630 oxidoreductase 2.05 3.76 2.21
TID_36448 An01g11750 tyrosine kinase 2.66 3.34 4.43
TID_187212 An18g01610 RNA polymerase II suppressor protein 3.90 2.97 5.42
TID_39426 An11g09660 ethanolaminephosphotransferase 39.61 0.95 11.51
TID_214246 An04g06840 P-type ATPase -Ca2+/phospholipid transport 24.34 −31.00 2.43

* AS/S Ratio is < 1 because part of AS reads do not fall within the ORF but in upstream or downstream regions of these genes therefore were not included in calculations using Ht-seq. Presence of antisense reads in these genes was detected visually using IGV, Integrative Genomic Viewer [49].

(A) Genes with predominant sense transcripts in dormant conidia (T0) that changes to predominant antisense transcription in germinating conidia (T1) showing also down-regulation of sense transcription at T0-T1. (B) Genes with predominant antisense transcription in dormant conidia (T0) that changes to predominant sense transcription in germinating conidia (T1), the same genes also increased their sense transcription at T0-T1. Fold-changes were made using sense and antisense RPKM values generated by RNA-seq.

Novodvorska et al.

Novodvorska et al. BMC Genomics 2013 14:246   doi:10.1186/1471-2164-14-246

Open Data