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Table 2 Genes with changed antisense transcription

From: Transcriptional landscape of Aspergillus nigerat breaking of conidial dormancy revealed by RNA-sequencing

(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

  1. * 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].
  2. (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.