Comparative Analysis of Alternative Splicing in Two Contrasting Apple Cultivars Defense against Alternaria alternata Apple Pathotype Infection
Abstract
:1. Introduction
2. Results
2.1. General Analysis of RNA-Seq Data
2.2. Detection and Classification of AS Events in Responding to A. alternata AP Infection in Apples
2.3. Identification and Analysis of DAS Events and Genes in Responding to A. alternata AP Infection
2.4. Validation of AS Events in Responding to A. alternata AP Infection
2.5. Comparative Analysis of the AS Genes in Responding to A. alternata AP Infection at AS and Transcriptional Levels
3. Discussion
3.1. AS Increased the Diversity of Transcripts in Apple
3.2. AS Is an Important Regulation Mechanism of Apple in Response to A. alternata AP Infection
3.3. Considerable Number of Genes Occurring AS Changes Were Related to Stress Response
3.4. AS Provoked Specific Regulatory Functions during A. alternata AP Defensive Response
4. Materials and Methods
4.1. Plant Materials and Fungal Inoculation
4.2. RNA Extraction, RNA-Seq Libraries Construction and Sequencing
4.3. Detection and Classification of AS Events
4.4. Validation of AS Events
4.5. Analysis of Differentially Expressed Genes and Differentially Spliced Genes
4.6. Analysis of Gene Structure and Protein Domains
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
AS | Alternative splicing |
DAS | Differential alternative splicing |
DSG | Differentially spliced gene |
DEG | Differentially expressed gene |
FPKM | Fragments per kilobase of transcript per million mapped reads |
J | Jonathan |
SD | Starking Delicious |
HPI | Hours post inoculation |
GO | Gene ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
SE | Skipped exon |
RI | Retained intron |
A3SS | Alternative 3′ splice sites |
A5SS | Alternative 5′ splice sites |
MXE | Mutually exclusive exon |
A. alternata AP | Alternaria alternata apple pathotype |
Bgt | Blumeria graminis f. sp. tritici |
Pst | Puccinia striiformis f. sp. Tritici |
M. oryzae | Magnaporthe oryzae |
Xoo | Xanthomonas oryzae pv oryzae |
SJs | Splicing junctions |
CDS | Coding sequence |
5′-UTR | 5′ Un-translated region |
3′-UTR | 3′ Un-translated region |
PTC | Premature stop codons |
ORF | Open reading frame |
NMD | Nonsense-mediated-decay |
JA | Jasmonic acid |
SA | Salicylic acid |
ABA | Abscisic acid |
PR | Pathogenesis-related |
SR | Serine/arginine-rich |
PDA | Potato dextrose agar |
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Zhou, T.; He, Y.; Zeng, X.; Cai, B.; Qu, S.; Wang, S. Comparative Analysis of Alternative Splicing in Two Contrasting Apple Cultivars Defense against Alternaria alternata Apple Pathotype Infection. Int. J. Mol. Sci. 2022, 23, 14202. https://doi.org/10.3390/ijms232214202
Zhou T, He Y, Zeng X, Cai B, Qu S, Wang S. Comparative Analysis of Alternative Splicing in Two Contrasting Apple Cultivars Defense against Alternaria alternata Apple Pathotype Infection. International Journal of Molecular Sciences. 2022; 23(22):14202. https://doi.org/10.3390/ijms232214202
Chicago/Turabian StyleZhou, Tingting, Youlei He, Xianqi Zeng, Binhua Cai, Shenchun Qu, and Sanhong Wang. 2022. "Comparative Analysis of Alternative Splicing in Two Contrasting Apple Cultivars Defense against Alternaria alternata Apple Pathotype Infection" International Journal of Molecular Sciences 23, no. 22: 14202. https://doi.org/10.3390/ijms232214202