Integrative Analysis of Iso-Seq and RNA-Seq Identifies Key Genes Related to Fatty Acid Biosynthesis and High-Altitude Stress Adaptation in Paeonia delavayi
Abstract
1. Introduction
2. Materials and Methods
2.1. Plant Materials and Measurement of Traits
2.2. RNA Extraction and Assessment
2.3. PacBio Iso-Seq Library Construction, Sequencing, and Annotation
2.4. RNA-Seq Analysis
2.5. Gene Expression Validation Using qPCR
3. Results
3.1. The Difference in Traits Between Different Altitudes
3.2. PacBio ISO-Seq Analysis
3.3. Function Annotation of Full-Length Transcripts
3.4. RNA-Seq Analysis of P. delavayi Seeds
3.5. Identification of DEGs
3.6. Enrichment Analysis of DEGs
3.7. Analysis of DEGs at Varying Altitudes and Different Developmental Stages of Seeds
3.8. Key Genes Associated with Fatty Acid Biosynthesis
3.9. Validation of RNA-Seq by 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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Altitude | 2400 m | 3400 m |
---|---|---|
Height (cm) | 121.00 ± 5.30 a | 133.67 ± 12.66 a |
No. of bearing branches | 6.00 ± 1.00 b | 9.67 ± 1.15 a |
No. of pods | 9.67 ± 0.58 a | 10.33 ± 0.58 a |
No. of carpels | 4.33 ± 1.53 a | 5.00 ± 1.00 a |
No. of seeds | 7.00 ± 1.00 a | 7.33 ± 1.53 a |
No. of seeds per pod | 30.00 ± 1.00 b | 35.00 ± 1.00 a |
Setting rate/% | 67.72 ± 2.87 a | 72.45 ± 3.62 a |
Abortion rate/% | 32.28 ± 2.87 a | 27.55 ± 3.62 a |
Seed length (cm) | 1.33 ± 0.036 b | 1.48 ± 0.09 a |
Seed width (cm) | 1.22 ± 0.04 a | 1.26 ± 0.02 a |
Seed thickness(cm) | 1.06 ± 0.04 a | 1.15 ± 0.05 a |
Weight of per seed (g) | 1.02 ± 0.05 b | 1.37 ± 0.04 a |
Weight of seeds (g) | 215.00 ± 4.58 b | 346.67 ± 6.66 a |
Library | Total Bases (Gbp) | Subreads Number | CCS Reads Number | Full-Length Non-Chimeric Reads |
---|---|---|---|---|
m1_mix | 46.28 | 27,846,502 | 522,779 | 33,805 |
m2_mix | 63.82 | 36,685,495 | 624,399 | 42,187 |
m3_mix | 41.75 | 26,623,625 | 463,744 | 25,347 |
m4_mix | 39.78 | 24,704,351 | 451,654 | 28,679 |
m5_mix | 38.17 | 24,116,939 | 433,280 | 24,677 |
m6_mix | 55.83 | 31,617,941 | 542,445 | 31,559 |
Total | 285.63 | 171,594,853 | 3,038,301 | 186,254 |
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He, Q.; Yuan, W.; Wang, R.; Yang, W.; He, G.; Cao, J.; Li, Y.; Ye, L.; Li, Z.; Hou, Z. Integrative Analysis of Iso-Seq and RNA-Seq Identifies Key Genes Related to Fatty Acid Biosynthesis and High-Altitude Stress Adaptation in Paeonia delavayi. Genes 2025, 16, 919. https://doi.org/10.3390/genes16080919
He Q, Yuan W, Wang R, Yang W, He G, Cao J, Li Y, Ye L, Li Z, Hou Z. Integrative Analysis of Iso-Seq and RNA-Seq Identifies Key Genes Related to Fatty Acid Biosynthesis and High-Altitude Stress Adaptation in Paeonia delavayi. Genes. 2025; 16(8):919. https://doi.org/10.3390/genes16080919
Chicago/Turabian StyleHe, Qiongji, Wenjue Yuan, Rui Wang, Wengao Yang, Guiqing He, Jinglong Cao, Yan Li, Lei Ye, Zhaoguang Li, and Zhijiang Hou. 2025. "Integrative Analysis of Iso-Seq and RNA-Seq Identifies Key Genes Related to Fatty Acid Biosynthesis and High-Altitude Stress Adaptation in Paeonia delavayi" Genes 16, no. 8: 919. https://doi.org/10.3390/genes16080919
APA StyleHe, Q., Yuan, W., Wang, R., Yang, W., He, G., Cao, J., Li, Y., Ye, L., Li, Z., & Hou, Z. (2025). Integrative Analysis of Iso-Seq and RNA-Seq Identifies Key Genes Related to Fatty Acid Biosynthesis and High-Altitude Stress Adaptation in Paeonia delavayi. Genes, 16(8), 919. https://doi.org/10.3390/genes16080919