Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR
Table 2
Local BLAST analysis based on a database of previously assembled R. trigyna transcriptome unigenes.
DD-ID
Length (bp)
Ug-ID
Length (bp)
C-RPKM
T-RPKM
Fold change
Functional description
DD2
757
Ug812
774
136.7
268.7
+2.0
ATFP6
DD3
705
Ug49359
678
49.2
803.9
+16.3
LEA
DD4
469
Ug6492
656
3.1
8.6
+2.8
Phytocalpain
DD5
155
Ug14666
900
13.6
41.3
+3.0
ATP synthase subunit a
DD7
580
Ug29649
909
5.8
194.7
+33.4
Putative nuclease HARBI1
DD8
517
Ug65098
686
9.6
78.4
+8.1
No BLAST hit
DD11
168
Ug5022
1095
43.9
118.8
+2.7
Calcium-binding protein CML42
DD14
212
Ug47465
289
452.2
1697.8
+3.8
SRC2
DD16
952
Ug3621
1287
21.7
499.9
+23.0
OPR3
DD18
273
Ug56616
1037
0.6
12.0
+20
Cytochrome P450
DD19
503
Ug13783
1889
33.1
142.1
+4.3
Sulfate transporter
DD20
469
Ug814
1208
7.8
31.1
+4.0
Protein kinase-like protein
DD22
208
Ug15235
641
37.3
504.6
+13.5
Abscisic stress ripening protein
DD25
208
Ug49313
614
103.6
650.1
+6.3
Quercetin 3-O-methyltransferase 1
DD27
284
Ug17593
660
31.6
463.6
+14.7
PRP27
DD30
451
Ug1371
905
105.5
428.8
+4.1
Cold-regulated protein
DD32
311
Ug37946
1041
19.6
269.3
+13.8
Osmotic stress-induced zinc-finger protein
DD33
223
Ug1734
1246
2.2
31.0
+14.2
EXO70H7
DD: differential displayed fragment obtained by DDRT-PCR; Ug: previously assembled R. trigyna transcriptome unigene [8]; RPKM: reads per kilobase of exon model per million mapped reads in the whole transcriptome of R. trigyna; C-RPKM: transcript abundance in the control transcriptome; T-RPKM: transcript abundance in the salt-stressed transcriptome; “+”: salt-induced gene. Functional descriptions were obtained by aligning the 18 unigenes against the plant protein dataset of nr, Swiss-Prot/Uniprot protein database, Clusters of Orthologous Groups databases, Gene Ontology database, and Kyoto Encyclopedia of Genes and Genomes database, respectively [8].
