Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System
Abstract
:1. Introduction
2. Material and Methods
2.1. Plant Material
2.2. RNA Sequencing
2.3. De Novo Transcriptome Assembly
2.4. Functional Annotation and Gene Ontology Enrichment Analysis
2.5. Inferring Sex-Linked Contigs
2.6. Correcting Mapping Bias
2.7. Estimating the Age of Sex Chromosomes
2.8. Estimating Gene Loss
2.9. Analysis of Expression Level Differences between X and Y Alleles
2.9.1. Allelic Expression Measurement
2.9.2. Analysis of Dosage Compensation in X-Hemizygous Contigs
2.10. Identifying Contigs with Sex-Biased Expression
2.11. Statistics
3. Results
3.1. Sex-Linked Genes Identified by SEX-DETector
3.2. Age of the C. grandis XY System
3.3. Patterns of Y Degeneration
3.4. Patterns of Dosage Compensation
3.5. Genomic Distribution of Sex-Biased Genes
4. Discussion
4.1. Coccinia grandis XY are of Intermediate Age, Similarly to other Highly Heteromorphic Plant Systems
4.2. Coccinia grandis Y Chromosome Degeneration is Moderate, with an Unusually Reduced Y Expression
4.3. Coccinia grandis Exhibit Sex Chromosome Dosage Compensation, a Phenomenon Observed in Several Plant Systems
4.4. Coccinia grandis Sex Chromosomes are Enriched in Sex-Biased Genes
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Full Transcriptome | Longest ORF per Isoform | |
---|---|---|
Total contigs | 128,904 | 82,699 |
Total assembled bases (bp) | 103,275,123 | 27,290,670 |
Median contig length | 552 | 836 |
Average contig length | 801.18 | 836.83 |
Maximum contig length | 16,296 | 16,296 |
Minimum contig length | 297 | 297 |
N50 | 1029 | 1086 |
Total contigs longer than 1kb | 30,795 | 21,587 |
GC content (%) | 42.96 | 42.96 |
SEX-DETector with BWA Mapping | SEX-DETector with GSNAP SNP-Tolerant Mapping | |
Contigs in final assembly | 82,699 | 82,699 |
Contigs with enough coverage to be studied | 82,689 | 70,298 |
Contigs with enough informative SNPs to compute a segregation probability | 4320 | 3801 |
Contigs assigned to an autosomal segregation type | 2889 | 3706 |
Contigs assigned to a X-Y segregation type | 1239 | 1196 |
Contigs assigned to a X-hemizygous segregation type | 192 | 168 |
Molecular Clocks | Age Estimates of the Sex Chromosomes, with dS max = 0.17 | Age Estimates of the Sex Chromosomes, with dS max = 0.13 |
---|---|---|
From [70], calibrated with an assumed divergence time of Barbarea and Cardamine of 6.0 My | 11.3 | 8.7 |
From [71], generation time = 1 year, assumed for Arabidopsis thaliana | 12.1 | 9.3 |
From [71], generation time = 1.5 year | 18.2 | 13.9 |
From [72], calibrated with six Brassicales fossils | 34.7 | 26.5 |
From [71], generation time = 5.5 year | 66.8 | 51.1 |
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Fruchard, C.; Badouin, H.; Latrasse, D.; Devani, R.S.; Muyle, A.; Rhoné, B.; Renner, S.S.; Banerjee, A.K.; Bendahmane, A.; Marais, G.A.B. Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System. Genes 2020, 11, 787. https://doi.org/10.3390/genes11070787
Fruchard C, Badouin H, Latrasse D, Devani RS, Muyle A, Rhoné B, Renner SS, Banerjee AK, Bendahmane A, Marais GAB. Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System. Genes. 2020; 11(7):787. https://doi.org/10.3390/genes11070787
Chicago/Turabian StyleFruchard, Cécile, Hélène Badouin, David Latrasse, Ravi S. Devani, Aline Muyle, Bénédicte Rhoné, Susanne S. Renner, Anjan K. Banerjee, Abdelhafid Bendahmane, and Gabriel A. B. Marais. 2020. "Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System" Genes 11, no. 7: 787. https://doi.org/10.3390/genes11070787
APA StyleFruchard, C., Badouin, H., Latrasse, D., Devani, R. S., Muyle, A., Rhoné, B., Renner, S. S., Banerjee, A. K., Bendahmane, A., & Marais, G. A. B. (2020). Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System. Genes, 11(7), 787. https://doi.org/10.3390/genes11070787