Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection and Genome Sequencing
2.2. Data Analysis, Genome Assembly, and Microsatellite Detection
3. Results and Discussion
3.1. Genome Sequencing Data Analysis and Genome Survey
3.2. Genome Assembly and Microsatellite Detection
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Raw Data (bp) | Total Reads | Q20 (%) | Q30 (%) | GC Content (%) |
---|---|---|---|---|
60,426,455,804 | 400,175,204 | 96.1 | 91.0 | 49.9 |
MaSuRCA | |
---|---|
Number of scaffolds | 695,247 |
Total size of scaffolds | 897,784,561 |
Longest scaffold | 51,375 |
Number of scaffolds > 1 K nt | 222,128 (31.9%) |
Number of scaffolds > 10 K nt | 6622 (1.0%) |
N50 scaffold length | 2401 |
L50 scaffold count | 87,813 |
GC contents (%) | 41.72 |
Primer No. | Motif | PCR Product Size (bp) | Forward Primer (5′ → 3′) | Tm (°C) | Reverse Primer (5′ → 3′) | Tm (°C) |
---|---|---|---|---|---|---|
1 | AT 9 | 105 | AACTGCACAGAACAGGGTCA | 59.823 | AAGCCTCGGTATGCAGAGTG | 59.454 |
2 | AC 14 | 120 | GTGAAGAACTTGGTGCTGCC | 59.897 | CAGGTACGCTAAGCCAGGAG | 59.688 |
3 | AC 7 | 128 | AAGTGGGCTGGTGAACTTGT | 59.187 | TCCCGTGATGTCTTACCGAC | 59.741 |
4 | AC 8 | 133 | TAAACCCAGGAGCGTAAGGC | 59.824 | GCCTCTTGCTCCGACACATA | 59.749 |
5 | AC 7 | 138 | CCCTGAATGGCTTCCAACAC | 59.964 | ACGAGCCTTAATGCACACCA | 59.109 |
6 | AC 11 | 141 | AGCATGTGTTCTTGCCAGGA | 59.307 | CACAGGTGGAGGCTACCTTT | 59.889 |
7 | AC 10 | 149 | TGTGTTAAGAGCCGTGCTGT | 59.821 | CCTCGCTGCCTTTGAGGTAT | 59.894 |
8 | AC 17 | 159 | CACCAGGCAGCTCGTTACTA | 59.061 | GTGTTTACGAACAGCGGGTT | 59.469 |
9 | AC 12 | 161 | ACAGCCGGTTGACTGAAACT | 59.179 | ATCTCCAGTTCTCTGCGTCC | 59.82 |
10 | AT 9 | 163 | CATGAGCAATGTTCCGTCGG | 59.046 | CCTGTTGGAGACACAAAGCC | 59.625 |
11 | AC 11 | 166 | CCACAGATGTTGACTTGGCG | 59.746 | GGCCCGTAACACCCTGTATT | 59.481 |
12 | AC 22 | 171 | AGGCATTTAACCTCGGCACA | 59.451 | GGCTCCTATTTCACCCAGCT | 59.962 |
13 | AC 12 | 190 | GAAAGCAGGCACTCAGATGC | 59.753 | TCATTCCAGCACACTCTCCG | 59.549 |
14 | AC 14 | 192 | GTGCATCTTTCTACCGCTGC | 59.537 | CTGCTCGACCCTGATGACAT | 59.625 |
15 | AC 9 | 194 | CGGGTAAACGCTATGGAGGT | 59.751 | CGGACTCCATACTGTTGGCA | 59.537 |
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Kim, J.; Lee, S.-J.; Jo, E.; Choi, E.; Cho, M.; Choi, S.; Kim, J.-H.; Park, H. Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti. Animals 2022, 12, 2598. https://doi.org/10.3390/ani12192598
Kim J, Lee S-J, Jo E, Choi E, Cho M, Choi S, Kim J-H, Park H. Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti. Animals. 2022; 12(19):2598. https://doi.org/10.3390/ani12192598
Chicago/Turabian StyleKim, Jinmu, Seung-Jae Lee, Euna Jo, Eunkyung Choi, Minjoo Cho, Soyun Choi, Jeong-Hoon Kim, and Hyun Park. 2022. "Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti" Animals 12, no. 19: 2598. https://doi.org/10.3390/ani12192598
APA StyleKim, J., Lee, S.-J., Jo, E., Choi, E., Cho, M., Choi, S., Kim, J.-H., & Park, H. (2022). Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti. Animals, 12(19), 2598. https://doi.org/10.3390/ani12192598