Whole-Genome Survey Analyses of Five Goby Species Provide Insights into Their Genetic Evolution and Invasion-Related Genes
Abstract
:1. Introduction
2. Results
2.1. Whole-Genome Sequencing
2.2. K-mer Analysis
2.3. Genome Assembly and GC Content
2.4. Microsatellite Profile of Five Gobiidae Fish Genomes
2.5. Genome Annotation
2.6. Mitochondrial Genome Assembly and Phylogenetic Analysis
2.7. Demographic History
3. Discussion
3.1. Genome Sequencing and Characteristics
3.2. Profile of Repeat Sequences in 5 Gobiidae Fish
3.3. Genome Annotation
3.4. Overview of Mitochondrial Genome and Phylogenetic Relationship
3.5. Demographic Analysis
4. Materials and Methods
4.1. Ethics Statement
4.2. Sample Preparation and Genome Sequencing
4.3. Analysis of K-mer and GC Content
4.4. Microsatellite Identification
4.5. Search of Single-Copy Homologous Genes and Functional Annotation
4.6. Mitochondrial DNA Assembly and Phylogenetic Research
4.7. Demography History Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Raw Base (Gb) | Effective Rate (%) | Error Rate (%) | Q20 (%) | Q30 (%) | GC Content (%) |
---|---|---|---|---|---|---|
A. flavimanus | 52.48 | 99.51 | 0.04 | 96.31 | 91.18 | 41.04 |
A. stigmothonus | 54.54 | 99.54 | 0.04 | 96.78 | 92.22 | 40.80 |
F. gymnauchen | 53.77 | 99.18 | 0.05 | 96.83 | 91.19 | 40.05 |
C. microcephalus | 53.55 | 96.87 | 0.03 | 96.43 | 91.42 | 41.69 |
T. barbatus | 52.22 | 98.52 | 0.03 | 96.58 | 91.61 | 39.91 |
Species | K-mer Number | Genome Size (Mb) | Heterozygous Ratio (%) | Repeat Ratio (%) |
---|---|---|---|---|
A. flavimanus | 38,806,743,595 | 978.96 | 0.21 | 50.94 |
A. stigmothonus | 39,715,938,956 | 998.27 | 0.24 | 50.52 |
F. gymnauchen | 44,941,714,426 | 1601.98 | 1.56 | 59.83 |
C. microcephalus | 47,124,301,675 | 812.88 | 0.64 | 52.89 |
T. barbatus | 45,948,893,647 | 808.55 | 0.56 | 46.90 |
Species | Assembly Level | Total Length (bp) | Total Number | Max Length (bp) | N50 Length (bp) | N90 Length (bp) |
---|---|---|---|---|---|---|
A. flavimanus | Contig | 750,612,336 | 766,615 | 72,830 | 3318 | 382 |
Scaffold | 764,365,216 | 612,519 | 78,798 | 4596 | 542 | |
A. stigmothonus | Contig | 801,994,264 | 783,027 | 142,602 | 6066 | 301 |
Scaffold | 817,012,736 | 631,430 | 230,933 | 12,605 | 508 | |
F. gymnauchen | Contig | 1,538,128,271 | 7,370,457 | 75,210 | 2120 | 122 |
Scaffold | 1,558,061,154 | 6,001,135 | 90,310 | 3120 | 129 | |
C. microcephalus | Contig | 789,064,495 | 2,896,033 | 22,967 | 4431 | 150 |
Scaffold | 782,790,775 | 2,117,910 | 24,126 | 8719 | 335 | |
T. barbatus | Contig | 811,858,718 | 1,790,899 | 35,267 | 2116 | 245 |
Scaffold | 805,390,951 | 1,216,192 | 35,267 | 2990 | 307 |
A. flavimanus | A. stigmothonus | F. gymnauchen | C. microcephalus | T. barbatus | |
---|---|---|---|---|---|
Total amount of sequences assessed | 612,519 | 631,430 | 6,510,510 | 2,117,910 | 1,216,192 |
Total size of assessed sequences (bp) | 764,365,216 | 817,012,736 | 1,653,145,701 | 806,337,820 | 817,882,156 |
Total identified SSRs | 340,592 | 351,606 | 362,191 | 494,515 | 349,412 |
Number of sequences containing SSRs | 163,241 | 106,981 | 337,951 | 371,928 | 226,596 |
Number of sequences with multiple SSRs | 72,809 | 55,926 | 21,999 | 81,266 | 72,335 |
Number of SSRs involved in compound synthesis | 57,550 | 62,289 | 15,217 | 73,846 | 41,068 |
Genus | Species | Sampling Time | Sampling Site | Sample Quantity Obtained | Sample Quantity Used |
---|---|---|---|---|---|
Acanthogobius | Acanthogobius flavimanus | 26 November 2018 | Qingdao, Yellow Sea of China | 24 | 1 |
Acanthogobius stigmothonus | 2 September 2020 | Beihai, South China Sea | 18 | 1 | |
Favonigobius | Favonigobius gymnauchen | 20 November 2019 | Qingdao, Yellow Sea of China | 1 | 1 |
Ctenotrypauchen | Ctenotrypauchen microcephalus | 12 April 2022 | Rizhao, Yellow Sea of China | 12 | 1 |
Tridentiger | Tridentiger barbatus | 20 November 2021 | Yantai, Bohai Sea of China | 20 | 1 |
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Ma, S.; Zhao, X.; Song, N. Whole-Genome Survey Analyses of Five Goby Species Provide Insights into Their Genetic Evolution and Invasion-Related Genes. Int. J. Mol. Sci. 2024, 25, 3293. https://doi.org/10.3390/ijms25063293
Ma S, Zhao X, Song N. Whole-Genome Survey Analyses of Five Goby Species Provide Insights into Their Genetic Evolution and Invasion-Related Genes. International Journal of Molecular Sciences. 2024; 25(6):3293. https://doi.org/10.3390/ijms25063293
Chicago/Turabian StyleMa, Siyu, Xiang Zhao, and Na Song. 2024. "Whole-Genome Survey Analyses of Five Goby Species Provide Insights into Their Genetic Evolution and Invasion-Related Genes" International Journal of Molecular Sciences 25, no. 6: 3293. https://doi.org/10.3390/ijms25063293