Comparative Transcriptomic Analysis of Differentially Expressed Transcripts Associated with Flowering Time of Loquat (Eriobotya japonica Lindl.)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. Endogenous Phytohormone Determination by LC-MS
2.3. Total RNA Extraction and RNA-Seq
2.4. Quality Control and de Novo Assembly
2.5. Functional Annotation
2.6. Identification of Differentially Expressed Transcripts (DETs) Involved in Flowering Time
2.7. Gene Expression Analysis by qRT-PCR
2.8. Statistical Analysis
3. Results
3.1. Loquat Apical Bud Phytohormone Analyses
3.2. Sequence Analysis and Assembly
3.3. Sequence Annotation
3.4. Loquat DET Identification
3.5. Identification of DETs Involved in Flowering Time
3.6. Identification of DETs Involved in ABA Signalling
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Cultivar | Sampling Date | Raw Reads | Clean Reads | Q30 (%) | GC (%) |
---|---|---|---|---|---|
‘Baiyu’ | T0 | 48,991,094 | 46,581,732 | 93.30 | 47.44 |
T1 | 46,842,090 | 44,358,410 | 93.02 | 47.14 | |
T2 | 49,193,824 | 46,596,186 | 93.12 | 47.02 | |
T3 | 47,387,894 | 40,851,014 | 87.95 | 47.36 | |
T4 | 49,068,496 | 46,912,890 | 93.54 | 47.02 | |
T5 | 48,987,770 | 46,583,754 | 93.22 | 47.22 | |
T6 | 48,997,596 | 46,632,968 | 93.14 | 46.92 | |
‘Huoju’ | T0 | 49,150,924 | 47,013,524 | 93.70 | 46.93 |
T1 | 49,784,092 | 47,560,900 | 93.54 | 46.99 | |
T2 | 49,889,156 | 47,546,378 | 93.35 | 47.13 | |
T3 | 49,605,682 | 47,133,928 | 93.29 | 47.57 | |
T4 | 48,971,664 | 46,264,188 | 93.00 | 47.23 | |
T5 | 49,348,500 | 46,926,020 | 93.17 | 47.14 | |
T6 | 49,333,148 | 47,048,570 | 93.23 | 46.71 |
Term | ≥300 bp | ≥500 bp | ≥1000 bp | Total Number | Total Length (nt) | Average Length | N50 |
---|---|---|---|---|---|---|---|
Unigene | 78,599 | 55,189 | 28,292 | 162,080 | 87,192,678 | 1109.34 | 1625 |
Anno_Database | Annotated Number | 300 ≤ Length < 1000 | Length ≥ 1000 |
---|---|---|---|
NR | 45,107 (57.39%) | 20,034 (25.49%) | 25,073 (31.90%) |
Swissport | 31,795 (40.45%) | 11,273 (14.34%) | 20,522 (26.11%) |
KEGG | 15,890 (20.22%) | 6774 (8.62%) | 9116 (11.60%) |
KOG | 23,886 (30.39%) | 8853 (11.26%) | 15,033 (19.13) |
eggNOG | 38,848 (49.43%) | 15,125 (19.24%) | 23,723 (30.18%) |
GO | 28,705 (36.52%) | 10,314 (13.12%) | 18,391 (23.40%) |
Pfam | 57 (0.07%) | 50 (0.06%) | 7 (0.01%) |
Item | Upregulated | Downregulated | Total |
---|---|---|---|
Huoju_713-vs-Baiyu_713 | 1885 | 2224 | 4109 |
Huoju_719-vs-Baiyu_719 | 2628 | 1707 | 4335 |
Huoju_727-vs-Baiyu_727 | 2341 | 1986 | 4327 |
Huoju_803-vs-Baiyu_803 | 1339 | 1913 | 3252 |
Huoju_810-vs-Baiyu_810 | 2039 | 2121 | 4160 |
Huoju_817-vs-Baiyu_817 | 2420 | 1692 | 4112 |
Huoju_824-vs-Baiyu_824 | 2731 | 1816 | 4547 |
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An, H.; Jiang, S.; Zhang, J.; Xu, F.; Zhang, X. Comparative Transcriptomic Analysis of Differentially Expressed Transcripts Associated with Flowering Time of Loquat (Eriobotya japonica Lindl.). Horticulturae 2021, 7, 171. https://doi.org/10.3390/horticulturae7070171
An H, Jiang S, Zhang J, Xu F, Zhang X. Comparative Transcriptomic Analysis of Differentially Expressed Transcripts Associated with Flowering Time of Loquat (Eriobotya japonica Lindl.). Horticulturae. 2021; 7(7):171. https://doi.org/10.3390/horticulturae7070171
Chicago/Turabian StyleAn, Haishan, Shuang Jiang, Jiaying Zhang, Fangjie Xu, and Xueying Zhang. 2021. "Comparative Transcriptomic Analysis of Differentially Expressed Transcripts Associated with Flowering Time of Loquat (Eriobotya japonica Lindl.)" Horticulturae 7, no. 7: 171. https://doi.org/10.3390/horticulturae7070171