Background
Methods
Plant growth and virus inoculation
RNA extraction
RNA-Seq library construction and sequencing
Data analysis of RNA-Seq
Evaluation of differentially expressed genes
Quantitative real-time PCR validation
Gene name | Gene primer for qRT-PCR (5′ → 3′) |
---|---|
Csa1G009810 | Sa: ATTTGACCCGTTGGGATTAG |
Csa1G009810 | Ab: GTTGACGACGAGGCGAAGTA |
Csa3G099680 | Sa: GAGTTCCCTGGTGATTATGG |
Csa3G099680 | Ab: TCTAAGACTTCGGGTGTTATG |
Csa6G445760 | Sa: CCTCTTCGTGGAACCATTAC |
Csa6G445760 | Ab: AACAATAGAAGCCAATCCTG |
Csa3G645940 | Sa: CTACTACCTCCGACAACGC |
Csa3G645940 | Ab: CACAGAGGCAGATTTCTCAT |
Csa3G730800 | Sa: ATAATCACGCCAAGCCTCAG |
Csa3G730800 | Ab: CACCGACACCGAACAATCCT |
Csa3G836520 | Sa: GGCTTTCCAATAACAACACT |
Csa3G836520 | Ab: ACCATTCGCCATATCTTCTG |
Csa1G264550 | Sa: CCCCTTTGCTAAGGAACCTA |
Csa1G264550 | Ab: TGTATGGCATCCCACTGTAT |
Csa1G423100 | Sa: CCAACGGCCAAAGATTCTAC |
Csa1G423100 | Ab: ATTGCAGCGATCATACTCGA |
Csa2G179730 | Sa: AGGGAGGCGATAGTGGAATA |
Csa2G179730 | Ab: GGCGGATAGTAATGACAGAACA |
Csa2G295430 | Sa: ACGATGCGTGGGATGGGTAG |
Csa2G295430 | Ab: AGCGTGGCAGGTTCCAGAAG |
Csa6G217470 | Sa: CACCACCGCTGACACTGACT |
Csa6G217470 | Ab: GGACGATGCTCGACCAAAG |
Csa6G318690 | Sa: GAGCAGCCTCCAAGGATAAG |
Csa6G318690 | Ab: TACGGACGCCAAGTTGTTAT |
CsUBIF | Sa: CACCAAGCCCAAGAAGATC |
CsUBIR | Ab: TAAACCTAATCACCACCAGC |
Results
Overview of transcriptome sequencing
Library | CCYV-infected | Mock-inoculated | ||||
---|---|---|---|---|---|---|
CCYV-1 | CCYV-2 | CCYV-3 | CK-1 | CK-2 | CK-3 | |
Total clean reads | 34158314 | 39138040 | 29823892 | 32161272 | 36948220 | 33314552 |
High quality clean reads | 33769294 (98.86%) | 38661136 (98.78%) | 29444160 (98.73%) | 31754492 (98.74%) | 36473130 (98.71%) | 32946276 (98.89%) |
Unique mapped reads | 31165849 (92.37%) | 35530271 (91.97%) | 26854505 (91.28%) | 29004918 (91.46%) | 33297555 (91.40%) | 30220259 (91.85%) |
Number of mapped gene | 17842 (76.75%) | 18016 (77.49%) | 17803 (76.58%) | 17729 (76.26%) | 17732 (76.27%) | 17717 (76.21%) |