Genome Improvement and Core Gene Set Refinement of Fugacium kawagutii
Abstract
:1. Introduction
2. Materials and Methods
2.1. Algal Culture and Trace Metal Treatments
2.2. RNA Extraction
2.3. Hi-C, Illumina RNA-Seq, and PacBio Sequencing
2.4. Genome Improvement and Gene Set Refinement
2.5. Core Gene Set Update
2.6. Validation of Reference Genes for Reverse Transcription Quantitative PCR (RT-qPCR)
3. Results and Discussion
3.1. Genome Improvement and Gene Set Refinement
3.2. Characterization of Newly Identified Genes
3.3. Core Gene Set Refinement
3.4. Validation of Reference Genes for Gene Expression Studies
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Appendix A
References
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Species | Assembled Genome Size (M) | % Genome Assembled | Gene No. | Scaffold N50 (kbp) | Gene Average Length (+ Intron) | Gene Supported by EST *(%) | Reference |
---|---|---|---|---|---|---|---|
B. minutum | 616 | 41.07 | 41,925 | 126.2 | 11,959 | 77.20 | [8] |
S. microadriacticum | 808 | 73.45/57.71 | 49,109 | 573.5 | 12,898 | 76.30 | [11] |
C. goreaui | 1030 | 85.55 | 35,913 | 98.9 | 6967 | 67.02 | [10] |
Symbiodinium spp. | 767 | NA | 69,018 | 133.4 | 8834 | 67.50 | [12] |
Cladocopium spp. | 705 | NA | 65,850 | 248.9 | 8192 | 62.50 | [12] |
F. kawagutii | 935 | 79.24 | 36,850 | 381 | 3788 | 72.82 | [9] |
1050 | 88.98 | 26,609 | 268.8 | 6507 | 64.40 | [10] | |
937 | 79.41 | 45,192 | 13,533.5 | 7242 | 90.09 | This study |
Project | Methodology | Growth Condition | Clean Read Data | Mapping Rate (Genome, Geneset) | ||
---|---|---|---|---|---|---|
V1 * | V2 ** | V3 *** | ||||
Transcriptome1 # | BGI RNA-seq (DGE) (SE 50) | Normal Low Cu, Zn, Fe, Mn, Ni | 329 M | 75%, 33% | 69%, 33% | 69%, 54% |
Transcriptome2 # | Illumina NGS (PE150) | Mix of 1# | 10 Gbp | 88%, 25% | 87%, 29% | 87%, 50% |
Transcriptome3 # | Pacbio Sequel (full-length) | Mix of 1# | 15 Gbp | 99%, NA | 99%, NA | 99%, NA |
BUSCO | V1 | V2 | V3 |
---|---|---|---|
Complete | 68 | 126 | 141 |
Complete and single-copy | 56 | 112 | 130 |
Complete and duplicated | 12 | 14 | 11 |
Fragmented | 57 | 67 | 92 |
Missing | 304 | 236 | 196 |
Total detected (%) | 29% | 45% | 55% |
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Li, T.; Yu, L.; Song, B.; Song, Y.; Li, L.; Lin, X.; Lin, S. Genome Improvement and Core Gene Set Refinement of Fugacium kawagutii. Microorganisms 2020, 8, 102. https://doi.org/10.3390/microorganisms8010102
Li T, Yu L, Song B, Song Y, Li L, Lin X, Lin S. Genome Improvement and Core Gene Set Refinement of Fugacium kawagutii. Microorganisms. 2020; 8(1):102. https://doi.org/10.3390/microorganisms8010102
Chicago/Turabian StyleLi, Tangcheng, Liying Yu, Bo Song, Yue Song, Ling Li, Xin Lin, and Senjie Lin. 2020. "Genome Improvement and Core Gene Set Refinement of Fugacium kawagutii" Microorganisms 8, no. 1: 102. https://doi.org/10.3390/microorganisms8010102
APA StyleLi, T., Yu, L., Song, B., Song, Y., Li, L., Lin, X., & Lin, S. (2020). Genome Improvement and Core Gene Set Refinement of Fugacium kawagutii. Microorganisms, 8(1), 102. https://doi.org/10.3390/microorganisms8010102