Integrated Morphological, Comparative Transcriptomic, and Metabolomic Analyses Reveal Mechanisms Underlying Seasonal Patterns of Variation in Spines of the Giant Spiny Frog (Quasipaa spinosa)
Abstract
:1. Introduction
2. Results
2.1. Morphological Differences in Quasipaa spinosa Skin across Different Periods
2.2. Correlation Analysis between Spine Polymorphism and Body Morphometric Indices
2.3. Analysis of the Skin Transcriptome in Quasipaa spinosa
2.3.1. Transcriptome Data Quality Control
2.3.2. Mining DEGs in Skin Transcriptomes
2.3.3. Functional Categorization of DEGs in the Skin Transcriptome
2.3.4. Analysis of Gene Expression Differences Related to Cell Proliferation and Keratin Synthesis among Comparison Groups
2.4. Validation of DEGs through qPCR
2.5. Comparative Metabolomic Analysis of Thoracic and Abdominal Skin in Quasipaa spinosa
2.5.1. Identification of Differentially Expressed Metabolites (DEMs)
2.5.2. DEM Functional Categorization through KEGG Enrichment Analysis
2.6. Integrated Analysis of DEGs and DEMs
3. Discussion
3.1. Biological Functions and Morphological Characteristics of Spines
3.2. Seasonal Variation in Spines Is Driven by a Complex Regulatory Network
3.3. Joint Analysis of DEGs and DEMs Underscores the Role of Citric Acid Metabolism in Maintaining Spine Morphology
4. Materials and Methods
4.1. Sample Collection and Experimental Design
4.2. Morphometric and Spine Parameters Measurement
4.3. HE Staining and Histology
4.4. RNA-Seq Library Construction and Sequencing
4.5. Validation of RNA-Seq Data by qRT-PCR
4.6. Metabolite Extraction and Analysis
4.7. Comprehensive Metabolome and Transcriptome Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
AMC | Pre-breeding period male thoracic skin |
AFC | Pre-breeding period female thoracic skin |
BMC | Breeding period male thoracic skin |
BFC | Breeding period female thoracic skin |
CMC | Late reproductive period male thoracic skin |
CFC | Late reproductive period female thoracic skin |
AMA | Pre-breeding period male abdominal skin |
BMA | Breeding period male abdominal skin |
CMA | Late reproductive period male abdominal skin |
BM | Body mass |
SVL | Snout–vent length |
FLAH | Forearm plus hand length |
CLA | Forearm circumference |
HL | Hand length |
LL | Hind limb length |
TL | Tibia length |
TW | Tibia width |
FL | Foot length |
SD | Spine density |
ASEH | Average spine elevation height |
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Primer Name | Primer Sequence (5′–3′) |
---|---|
QsCOL1A2-F | CTGGTTCATCTGGTGGTGGA |
QsCOL1A2-R | TCGGGGTGGCTGAGTCTTA |
QsKRT12-F | CAAGAGAAGCAATGGGGAAG |
QsKRT12-R | AAACCAGAACAAGGAGGGATG |
QsTNC-F | GTTTCGCCGTTGTCTCTAAGG |
QsTNC-R | AACTGTCAAGGAGGTTGCTCTG |
QsENO1-F | ACTCGGTCACGGAGCCAATCT |
QsENO1-R | AGCCAGTGCAGGAATCCAGGTA |
QsMYL10-F | AAGCGGACAGATTCAGCCAAGA |
QsMYL10-R | CGCTACTCCTGGTCCTTCTCCT |
QsTNN-F | TTGGTCCAGTTCCTCCTCCTCT |
QsTNN-R | TTCTCCGTCTTCCGTGGGTTTG |
QsKRT-F | TTGCCCACTGTGCTTATTCC |
QsKRT-R | TTCTCTTCCATTCGCTTCTGAT |
QsTHBS4-F | GCCCAAATCTACAACCACCC |
QsTHBS4-R | CAATGAACCTCCCATGACCAC |
QsTYRP1-F | GGCAGAAGTACTAACCACAACG |
QsTYRP1-R | GAGAAGAGCCACATCTAAACGC |
Qsβ-Actin-F | CTGCTGAGCGTGAGATT |
Qsβ-Actin-R | GGCTGGAAGAGGGTTT |
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Wan, G.; Jiang, Z.-Y.; Shi, N.; Xiong, Y.-G.; Zheng, R.-Q. Integrated Morphological, Comparative Transcriptomic, and Metabolomic Analyses Reveal Mechanisms Underlying Seasonal Patterns of Variation in Spines of the Giant Spiny Frog (Quasipaa spinosa). Int. J. Mol. Sci. 2024, 25, 9128. https://doi.org/10.3390/ijms25169128
Wan G, Jiang Z-Y, Shi N, Xiong Y-G, Zheng R-Q. Integrated Morphological, Comparative Transcriptomic, and Metabolomic Analyses Reveal Mechanisms Underlying Seasonal Patterns of Variation in Spines of the Giant Spiny Frog (Quasipaa spinosa). International Journal of Molecular Sciences. 2024; 25(16):9128. https://doi.org/10.3390/ijms25169128
Chicago/Turabian StyleWan, Gang, Ze-Yuan Jiang, Nuo Shi, Yi-Ge Xiong, and Rong-Quan Zheng. 2024. "Integrated Morphological, Comparative Transcriptomic, and Metabolomic Analyses Reveal Mechanisms Underlying Seasonal Patterns of Variation in Spines of the Giant Spiny Frog (Quasipaa spinosa)" International Journal of Molecular Sciences 25, no. 16: 9128. https://doi.org/10.3390/ijms25169128