Whole Genome Sequence of the Newly Prescribed Subspecies Oreochromis spilurus saudii: A Valuable Genetic Resource for Aquaculture in Saudi Arabia
Abstract
:1. Introduction
2. Materials and Methods
2.1. Preparing and Sequencing Sample
2.2. Raw Sequence Data and Quality Control
2.3. Estimation of Genome Size and Assembly
2.4. Phylogenetic and Divergence Time Trees
2.5. High-Throughput Identification of Antimicrobial Peptides
3. Results
3.1. Genome Assembly and Annotation
3.2. Sequencing Depth Analysis and GC Content
3.3. Summary of Phylogeny Tree
3.4. Antimicrobial Peptides in Oreochromis Spilurus
3.5. Annotation of the Putative AMP Genes
3.6. Newly prescribed Subspecies Identification
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
BUSCO | Benchmarking Universal Single-copy Orthologs |
Gb | Gigabase |
Mb | Megabase |
Kb | Kilobase |
N50 | The genome (50%) is in fragments of this length |
WGS | Whole Genome Sequence |
AMP | Antimicrobial Peptide |
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Contents | O. spilurus |
---|---|
Genome assembly | |
Contig N50 size (Kb) | 11.85 |
Scaffold N50 size (Mb) | 0.22 |
Raw paired reads | 205,924,310 |
Assembled genome size (Gb) | 0.76 |
Genome annotation | - |
Predicted protein-coding peptides | 51,642 |
Predicted protein-coding genes | 10,641 |
Conserved vertebrate genes | 3144 |
Conserved annotated vertebrate genes with other species | 2046 |
Species | O. spilurus |
---|---|
BUSCO Complete | 173 |
Complete and Single-copy BUSCOs (S) | 171 |
Complete and Duplicated BUSCOs (D) | 2 |
Fragmented BUSCOs (F) | 86 |
Total BUSCO Groups Searched | 255 |
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Aljahdali, M.O.; Molla, M.H.R.; Filfilan, W.M. Whole Genome Sequence of the Newly Prescribed Subspecies Oreochromis spilurus saudii: A Valuable Genetic Resource for Aquaculture in Saudi Arabia. J. Mar. Sci. Eng. 2021, 9, 506. https://doi.org/10.3390/jmse9050506
Aljahdali MO, Molla MHR, Filfilan WM. Whole Genome Sequence of the Newly Prescribed Subspecies Oreochromis spilurus saudii: A Valuable Genetic Resource for Aquaculture in Saudi Arabia. Journal of Marine Science and Engineering. 2021; 9(5):506. https://doi.org/10.3390/jmse9050506
Chicago/Turabian StyleAljahdali, Mohammed Othman, Mohammad Habibur Rahman Molla, and Wessam Mansour Filfilan. 2021. "Whole Genome Sequence of the Newly Prescribed Subspecies Oreochromis spilurus saudii: A Valuable Genetic Resource for Aquaculture in Saudi Arabia" Journal of Marine Science and Engineering 9, no. 5: 506. https://doi.org/10.3390/jmse9050506