Chromosome-Level Genome Assembly and Genomic Analysis of the Hybrid Grouper ShanHu (Epinephelus fuscoguttatus ♀ × Epinephelus polyphekadion ♂)
Abstract
1. Introduction
2. Results
2.1. Genome Assembly and Quality Assessment
2.2. Pseudochromosome Construction
2.3. Genome Annotation
2.4. Phylogenetic Analysis of Economically Epinephelus
2.5. Comparative Analyses of the Genome Structure
3. Discussion
4. Materials and Methods
4.1. Sample Collection, Library Construction, and Sequencing
4.2. Genome Size Estimation, Assembly, and Quality Assessment
4.3. Pseudochromosome Construction
4.4. Genome Prediction and Annotation
4.5. Phylogenetic Analysis
4.6. Comparative Genomic Analyses
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
Appendix A
Sequeues ID | Cluster Number | Sequeues Length (bp) |
---|---|---|
Chr1 | 1 | 44,551,120 |
Chr2 | 2 | 37,351,789 |
Chr3 | 1 | 53,015,742 |
Chr4 | 1 | 47,211,449 |
Chr5 | 1 | 48,719,712 |
Chr6 | 1 | 53,326,279 |
Chr7 | 1 | 48,243,466 |
Chr8 | 1 | 46,120,958 |
Chr9 | 1 | 45,365,500 |
Chr10 | 1 | 48,494,318 |
Chr11 | 1 | 43,829,164 |
Chr12 | 1 | 43,297,142 |
Chr13 | 1 | 47,782,323 |
Chr14 | 1 | 24,826,122 |
Chr15 | 1 | 48,046,878 |
Chr16 | 1 | 52,374,887 |
Chr17 | 1 | 41,935,179 |
Chr18 | 1 | 58,196,232 |
Chr19 | 1 | 45,048,601 |
Chr20 | 1 | 45,100,459 |
Chr21 | 2 | 46,795,679 |
Chr22 | 2 | 39,857,385 |
Chr23 | 25 | 41,020,352 |
Chr24 | 100 | 32,676,861 |
Appendix B
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Type | E fuscoguttatus | E. polyphekadion | ShanHu |
---|---|---|---|
Total length of Contigs (bases) | 1,082,718,103 | 1,099,728,802 | 1,176,882,344 |
Number of Contigs | 396 | 164 | 171 |
Max length Contig (bases) | 52,327,456 | 53,203,867 | 58,196,232 |
Contig N50 (bases) | 37,367,964 | 40,804,240 | 45,365,500 |
Contig N90 (bases) | 9,232,285 | 12,950,428 | 15,571,449 |
Total length of Scaffolds (bases) | 1,082,726,703 | 1,099,733,602 | 1,176,892,644 |
Number of Scaffolds | 310 | 116 | 68 |
Scaffold N50 (bases) | 44,785,048 | 47,393,752 | 46,120,958 |
Scaffold N90 (bases) | 39,728,480 | 39,964,760 | 24,826,122 |
Type | Gene Set | Number | Average Transcript Length (bp) | Average CDS Length (bp) | Average Exons Per Gene | Average Exon Length (bp) | Average Intron Length (bp) |
---|---|---|---|---|---|---|---|
De novo | Augustus | 39,878 | 10,427.62 | 1197.88 | 6.60 | 181.45 | 1647.61 |
SNAP | 41,336 | 39,332.49 | 1185.35 | 8.12 | 145.91 | 5355.06 | |
Homolog | E.fuscoguttatus | 25,123 | 17,952.51 | 1712.51 | 9.69 | 176.79 | 1869.54 |
E.lanceolatus | 24,336 | 17,919.25 | 1698.19 | 9.68 | 175.49 | 1869.42 | |
E.moara | 24,927 | 17,676.76 | 1694.95 | 9.63 | 176.05 | 1852.45 | |
T. rubripes | 21,740 | 17,560.21 | 1688.49 | 9.49 | 177.94 | 1869.64 | |
G. aculeatus | 22,296 | 17,691.72 | 1702.10 | 9.56 | 178.12 | 1868.87 | |
D.rerio | 22,09 | 15,746.66 | 1541.84 | 8.50 | 181.39 | 1893.95 | |
RNA-seq | Transcripts | 106,29 | 4100.74 | 898.00 | 2.50 | 151.12 | 1749.27 |
PASA | 21,723 | 7242.56 | 715.03 | 4.73 | 177.73 | 1876.96 | |
EVM | EVM | 35,887 | 13,394.27 | 1320.96 | 7.43 | 177.73 | 1876.96 |
Pasaupdate | pasaupdate | 35,739 | 13,629.09 | 1326.57 | 7.47 | 177.64 | 1902.11 |
Final set | Final | 26,102 | 17,514.95 | 1626.80 | 9.43 | 172.60 | 1885.81 |
Type | Number | Length (bp) | Percentage (%) |
---|---|---|---|
SINEs | 11,410 | 905,388 | 0.08 |
LINEs | 328,957 | 91,778,626 | 7.80 |
LTRs | 563,312 | 103,517,634 | 8.80 |
DNA | 1,733,660 | 316,822,578 | 26.92 |
Unknown | 106,739 | 16,787,622 | 1.43 |
Total | 552,112,951 | 46.91 |
Type | Copy (w) | Total Length (bp) | % in Genome | |
---|---|---|---|---|
miRNA | 3438 | 471,917 | 0.040% | |
tRNA | 2415 | 180,826 | 0.015% | |
rRNA | rRNA | 4187 | 1,069,967 | 0.091% |
18s | 445 | 279,049 | 0.024% | |
28s | 1058 | 474,992 | 0.040% | |
5.8s | 145 | 22,458 | 0.002% | |
5s | 2539 | 293,468 | 0.025% | |
snRNA | SnRNA | 836 | 121,144 | 0.010% |
CD-box | 171 | 19,670 | 0.002% | |
HACA-box | 95 | 14,842 | 0.001% | |
splicing | 504 | 74,708 | 0.006% | |
scaRNA | 65 | 11,867 | 0.001% |
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Liu, Y.; Mao, Y. Chromosome-Level Genome Assembly and Genomic Analysis of the Hybrid Grouper ShanHu (Epinephelus fuscoguttatus ♀ × Epinephelus polyphekadion ♂). Int. J. Mol. Sci. 2025, 26, 5036. https://doi.org/10.3390/ijms26115036
Liu Y, Mao Y. Chromosome-Level Genome Assembly and Genomic Analysis of the Hybrid Grouper ShanHu (Epinephelus fuscoguttatus ♀ × Epinephelus polyphekadion ♂). International Journal of Molecular Sciences. 2025; 26(11):5036. https://doi.org/10.3390/ijms26115036
Chicago/Turabian StyleLiu, Yiqun, and Yunxiang Mao. 2025. "Chromosome-Level Genome Assembly and Genomic Analysis of the Hybrid Grouper ShanHu (Epinephelus fuscoguttatus ♀ × Epinephelus polyphekadion ♂)" International Journal of Molecular Sciences 26, no. 11: 5036. https://doi.org/10.3390/ijms26115036
APA StyleLiu, Y., & Mao, Y. (2025). Chromosome-Level Genome Assembly and Genomic Analysis of the Hybrid Grouper ShanHu (Epinephelus fuscoguttatus ♀ × Epinephelus polyphekadion ♂). International Journal of Molecular Sciences, 26(11), 5036. https://doi.org/10.3390/ijms26115036