Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes
Abstract
:1. Introduction
2. Results and Discussion
2.1. Improved C. goreaui Genome Assembly Reveals More Repeats and More Duplicated Genes
2.2. Topologically Associated Domains (TADs) and Unidirectional Gene Blocks
2.3. Evolutionary Origin of C. goreaui Genes
2.4. Genes Implicating a History of Horizontal Transfer
2.5. Genes Implicating Vertical Inheritance
3. Conclusions
4. Materials and Methods
4.1. Generation of Long-Read Genome and Transcriptome Data
4.2. De Novo Genome Assembly Combining Short- and Long-Read Sequence Data
4.3. Estimation of Genome Size Based on Sequencing Data
4.4. Annotation of Repeat Content
4.5. Ab Initio Prediction of Protein-Coding Genes
4.6. Functional Annotation of C. goreaui Genes
4.7. Analysis of Duplicated Genes
4.8. GO Enrichment Analysis
4.9. Analysis of Unidirectional Gene Blocks and TADs
4.10. Phylogenomic Analysis of C. goreaui Genes
4.11. Inference of the Dinoflagellate Species Tree
4.12. Inference of C. goreaui Gene Origins
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Metric | Earlier Assembly [15] | Revised Assembly (This Study) | |
---|---|---|---|
Assembly size (Gbp) | 1.0 | 1.2 | |
Number of scaffolds | 41,235 | 6843 | |
Genome scaffolds N50 (Kbp) | 91 | 354 | |
Genome GC-content (%) | 44.76 | 44.38 | |
Number of predicted genes | 39,006 | 45,322 | |
Percentage of BUSCO proteins recovered (alveolata_odb10) | 67.3 | 82.4 | |
Genes with transcript support (%) | 76.5 | 82.5 | |
Average gene length (bp) | 8428 | 15,745 | |
Average CDS length (bp) | 1625 | 2018 | |
Total gene length (Mbp) | 328.7 | 713.6 | |
Total CDS length (Mbp) | 63.4 | 91.5 | |
Average number of exons per gene | 12.4 | 17.2 | |
Average exon length (bp) | 130.4 | 120.4 | |
Genes with introns (%) | 95.9 | 95.9 | |
Number of introns per gene | 11.4 | 16.2 | |
Average intron length (bp) | 593.5 | 838.8 | |
Splice donor motif (%) | GT | 35.7 | 36.6 |
GC | 43.3 | 43.6 | |
GA | 20.8 | 19.8 | |
Splice acceptor with AGG motif (%) | 96.3 | 96.1 | |
Number of intergenic regions | 24,243 | 39,720 | |
Average length of intergenic regions (bp) | 9539 | 7388 |
Duplication Type | Earlier Assembly [15] | Revised Assembly (This Study) |
---|---|---|
Singleton | 13,456 (34.5%) | 10,203 (22.5%) |
Dispersed | 24,441 (62.6%) | 31,827 (70.2%) |
Proximal | 273 (0.7%) | 907 (2.0%) |
Tandem | 836 (2.1%) | 1998 (4.4%) |
Segmental | 0 (0.0%) | 387 (0.9%) |
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Chen, Y.; Shah, S.; Dougan, K.E.; van Oppen, M.J.H.; Bhattacharya, D.; Chan, C.X. Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes. Microorganisms 2022, 10, 1662. https://doi.org/10.3390/microorganisms10081662
Chen Y, Shah S, Dougan KE, van Oppen MJH, Bhattacharya D, Chan CX. Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes. Microorganisms. 2022; 10(8):1662. https://doi.org/10.3390/microorganisms10081662
Chicago/Turabian StyleChen, Yibi, Sarah Shah, Katherine E. Dougan, Madeleine J. H. van Oppen, Debashish Bhattacharya, and Cheong Xin Chan. 2022. "Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes" Microorganisms 10, no. 8: 1662. https://doi.org/10.3390/microorganisms10081662
APA StyleChen, Y., Shah, S., Dougan, K. E., van Oppen, M. J. H., Bhattacharya, D., & Chan, C. X. (2022). Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes. Microorganisms, 10(8), 1662. https://doi.org/10.3390/microorganisms10081662