Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in Rhododendron simsii (Ericaceae)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. RNA Extraction
2.3. Library Construction and SMRT Sequencing
2.4. Error Correction and Quality Filtering
2.5. Functional Annotation of Transcripts
2.6. Identification of TFs, lncRNAs and SSR
2.7. Development of SSR Markers
2.8. qRT-PCR Analysis
3. Results and Analysis
3.1. Single Molecule Real Time Sequencing (SMRT)
3.2. Open Reading Frame and Alternative Splicing Event Prediction
3.3. Long Non-Coding RNA Identification
3.4. Transcription Factor Prediction
3.5. Functional Annotation of Transcripts
3.6. GO Classified Transcripts
3.7. COG Function Classification
3.8. KEGG Annotated Transcripts
3.9. Expression Analysis in qRT PCR
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Primer ID | Gene ID | Forward Primer | Reverse Primer |
---|---|---|---|
RhCHS | F01_transcript/61502 | GCTTACCGTCGAGACCGTGG | AACAATGGGCCTCACCAGCC |
RhCHI | F01_transcript/68926 | GCCGCGTTGGAGCAAATTGT | CCCCCTGGTTCCACCCAAAT |
RhF3H | F01_transcript/64242 | CTCACTCTCGGCCTCAAGCG | TGCCTCAGGGGCTGGATTCT |
RhDFR | F01_transcript/64345 | GGCTTCATCGGCTCATGGCT | TCCGCTTTGGGCAACTCCAG |
RhANS | F01_transcript/40426 | CTCCTTCTCCTCCACCGGCT | GGGGGTTGTTCCAGGTGGTG |
RhF3’H | F01_transcript/54870 | CGATCCCCACCACTCCATC | AAGAACTGTGCGGCAACCGA |
RhF3’5’H | F01_transcript/50526 | TGCTGACTACGGCCCGAGAT | GGTATCACCACTGCCTCGCC |
RhMYB1 | F01_transcript/63169 | ACTCGAGCTGTAGCCCACCA | CGTTCGGAAGACGAGCCTCC |
RhMYB2 | F01_transcript/66405 | GGCAACTGGAGGTCTCTGCC | CCGGCAGCCTTCCTGCTATG |
RhbHLH1 | F01_transcript/65059 | CCCTTTCGGCTATGCTGCGA | CCCTTTCGGCTATGCTGCGA |
RhbHLH2 | F01_transcript/50357 | CTTGGTTGCTTCGGCCTCCA | ACCTCACTCCCTCTCGCCTC |
Samples | cDNA Size | CCS Number | Read Bases of CCS | Mean Read Length of CCS | Mean Number of Passes |
---|---|---|---|---|---|
F01 | 1–6 k | 833,137 | 2,298,485,998 | 2758 | 19 |
Annotated Databases | Isoform Number |
---|---|
COG | 16,102 |
GO | 18,565 |
KEGG | 17,450 |
KOG | 25,787 |
Pfam | 34,156 |
Eggnog | 29,498 |
Swiss-Prot | 38,933 |
Nr | 39,411 |
All | 39,521 |
Databases | Unigene Number | 300~1000 bp | ≥1000 bp | ||
---|---|---|---|---|---|
Number | Percentage | Number | Percentage | ||
NR | 39,411 | 2171 | 5.51% | 37,230 | 94.47% |
GO | 18,565 | 1521 | 8.19% | 17,040 | 91.79% |
COG | 16,102 | 800 | 4.97% | 15,300 | 95.02% |
eggNOG | 38,933 | 2115 | 5.43% | 36,811 | 94.55% |
KEGG | 17,450 | 1109 | 6.36% | 16,336 | 93.62% |
KOG | 25,787 | 1249 | 4.84% | 24,534 | 95.14% |
Pfam | 34,156 | 1699 | 4.97% | 32,454 | 95.02% |
Swiss-Prot | 29,498 | 1521 | 5.16% | 27,971 | 94.82% |
All | 39,521 | 2201 | 5.57% | 37,310 | 94.41% |
No. | Name of Pathway | Pathway ID | No of Transcripts (%) | |
---|---|---|---|---|
1. | Carbon metabolism | ko01200 | 605 | (3.47%) |
2. | Protein processing in endoplasmic reticulum | ko04141 | 608 | (3.48%) |
3. | Biosynthesis of amino acid | ko01230 | 525 | (3.01%) |
4. | Spliceosome | ko03040 | 700 | (4.01%) |
5. | Ribosome | ko03010 | 491 | (2.81%) |
6. | RNA transport | ko03013 | 558 | (3.20%) |
7. | Starch and sucrose metabolism | ko00500 | 377 | (2.16%) |
8. | Plant hormone signal transduction | ko04075 | 470 | (2.69%) |
9. | Oxidative phosphorylation | ko00190 | 280 | (1.60%) |
10. | Glycolysis/gluconeogenesis | ko00010 | 322 | (1.85%) |
11. | Plant pathogen interaction | ko04626 | 324 | (1.86%) |
12. | mRNA surveillance pathway | ko03015 | 469 | (2.69%) |
13. | Ubiquitin mediated proteolysis | ko04120 | 321 | (1.84%) |
14. | Amino sugar and nucleotide sugar metabolism | ko00520 | 271 | (1.55%) |
15. | Endocytosis | ko04144 | 251 | (1.44%) |
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Liu, Q.; Liaquat, F.; He, Y.; Munis, M.F.H.; Zhang, C. Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in Rhododendron simsii (Ericaceae). Plants 2021, 10, 649. https://doi.org/10.3390/plants10040649
Liu Q, Liaquat F, He Y, Munis MFH, Zhang C. Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in Rhododendron simsii (Ericaceae). Plants. 2021; 10(4):649. https://doi.org/10.3390/plants10040649
Chicago/Turabian StyleLiu, Qunlu, Fiza Liaquat, Yefeng He, Muhammad Farooq Hussain Munis, and Chunying Zhang. 2021. "Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in Rhododendron simsii (Ericaceae)" Plants 10, no. 4: 649. https://doi.org/10.3390/plants10040649