Extensive Adaptive Variation in Gene Expression within and between Closely Related Horseshoe Bats (Chiroptera, Rhinolophus) Revealed by Three Organs
<p>Venn diagram showing the numbers of intersecting differentially expressed genes (DEGs) under natural selection among the three organs in (<b>a</b>) the inter-specific and (<b>b</b>) inter-subspecific comparison. The labels ‘cochlea’, ‘brain’, and ‘liver’ indicate the cochlea, brain, and liver samples in each comparison, respectively. The size of diagram is proportional to quantity. Colors have no meaning.</p> "> Figure 2
<p>The ratio of differentially expressed genes (DEGs) whose expression likely evolved under natural selection, including directional selection, stabilizing selection, and balancing selection, in the inter-specific and inter-subspecific comparisons for three organs.</p> "> Figure 3
<p>Significantly enriched gene ontology (GO) terms obtained using differentially expressed genes (DEGs) whose expression likely evolved under natural selection in the inter-specific comparison for three organs. Left and right indicate terms related to cellular components and biological processes, respectively. The bar colors represent different organs. ‘*’ indicates the terms also enriched in the inter-subspecific comparison.</p> "> Figure 4
<p>The ratio of trait-related differentially expressed genes (DEGs) whose expression likely evolved under natural selection, including directional selection and stabilizing selection, in the inter-specific and inter-subspecific comparisons for three organs.</p> ">
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection and Data Acquisition
2.2. Expression Variation between Taxa and among Individuals within Taxon
2.3. Identifying Expression Variation Forced by Natural Selection, Especially Related to Phenotypic Divergence
2.4. Functional Enrichment Analysis
3. Results
3.1. Differences in Gene Expression within and between Taxa
3.2. Expression Variation Extensively Governed by Natural Selection
3.3. Functional Patterns of Adaptive Expression Variation
3.4. Adaptive Expression Variation Related to Phenotypes
4. Discussion
4.1. Extensive Adaptive Variation in Inter-Specific and Inter-Subspecific Gene Expression
4.2. Organ-Specificity of Expression Variation Governed by Natural Selection
4.3. Functional Patterns of Adaptive Expression Variation at Two Different Classification Categories
4.4. Trait-Related Expression Variation Forced by Natural Selection
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Comparison | Organ | Number of DEGs | |||
---|---|---|---|---|---|
Directional Selection | Stabilizing Selection | Balancing Selection | In Total | ||
Inter-specific comparison | brain | 371 | 144 | 1 | 516 |
cochlea | 542 | 171 | 7 | 720 | |
liver | 473 | 160 | 1 | 634 | |
Inter-subspecific comparison | brain | 249 | 120 | 2 | 371 |
cochlea | 326 | 68 | 7 | 401 | |
liver | 962 | 366 | 0 | 1328 |
Comparison | Organ | Number of DEGs Related to RF/FA | |||
---|---|---|---|---|---|
Directional Selection | Stabilizing Selection | Balancing Selection | In Total | ||
Inter-specific comparison | brain | 91/139 | 13/27 | 0/0 | 104/166 |
cochlea | 240/233 | 45/45 | 0/0 | 285/278 | |
liver | 117/107 | 22/19 | 0/0 | 139/126 | |
Inter-subspecific comparison | brain | 47/47 | 10/10 | 0/0 | 57/57 |
cochlea | 86/86 | 11/11 | 0/0 | 97/97 | |
liver | 125/170 | 13/17 | 0/0 | 138/187 |
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Li, J.; Sun, K.; Dai, W.; Leng, H.; Li, A.; Feng, J. Extensive Adaptive Variation in Gene Expression within and between Closely Related Horseshoe Bats (Chiroptera, Rhinolophus) Revealed by Three Organs. Animals 2022, 12, 3432. https://doi.org/10.3390/ani12233432
Li J, Sun K, Dai W, Leng H, Li A, Feng J. Extensive Adaptive Variation in Gene Expression within and between Closely Related Horseshoe Bats (Chiroptera, Rhinolophus) Revealed by Three Organs. Animals. 2022; 12(23):3432. https://doi.org/10.3390/ani12233432
Chicago/Turabian StyleLi, Jun, Keping Sun, Wentao Dai, Haixia Leng, Aoqiang Li, and Jiang Feng. 2022. "Extensive Adaptive Variation in Gene Expression within and between Closely Related Horseshoe Bats (Chiroptera, Rhinolophus) Revealed by Three Organs" Animals 12, no. 23: 3432. https://doi.org/10.3390/ani12233432