A First Genome Survey and Genomic SSR Marker Analysis of Trematomus loennbergii Regan, 1913
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection and DNA Extraction
2.2. Library Construction and Sequencing
2.3. K-mer Analysis, Genome Assembly, and Microsatellite Analysis
3. Results and Discussion
3.1. Sequencing Data Statistics
3.2. K-mer Analysis and Genome Size Prediction
3.3. De Novo Assembly
3.4. Identification of Microsatellite Motifs
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
References
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Raw Data (bp) | Q20 (%) | Q30 (%) | GC Content (%) |
---|---|---|---|
53,486,656,166 | 96.3 | 91.3 | 41.3 |
17-mer | 19-mer | 25-mer | |
---|---|---|---|
Genome size (bp) | 774,371,521 | 786,515,471 | 815,042,992 |
Heterozygosity (%) | 0.485 | 0.532 | 0.536 |
Duplication ratio (%) | 0.798 | 0.744 | 0.724 |
MaSuRCA | |
---|---|
Number of contigs | 613,288 |
Total size of contigs | 820,644,295 |
Longest contig | 59,484 |
Number of contigs > 1000 nt | 192,849 (31.4%) |
Number of contigs > 10,000 nt | 7790 (1.3%) |
N50 contig length | 148,364 |
L50 contig count | 1526 |
GC content (%) | 40.65 |
Repeat Motif | Number of Repeats | Total | |||||||
---|---|---|---|---|---|---|---|---|---|
5 | 6 | 7 | 8 | 9 | 10 | 11–20 | >21 | ||
Di-nucleotide (1,970,270) | |||||||||
AC/GT | 562,651 | 252,660 | 135,367 | 89,123 | 61,221 | 45,302 | 170,290 | 77,929 | 1,394,543 |
AG/CT | 188,161 | 64,236 | 32,609 | 16,413 | 9982 | 6453 | 21,335 | 5587 | 344,776 |
AT/AT | 109,496 | 45,063 | 25,231 | 14,169 | 8234 | 6053 | 20,675 | 1362 | 230,283 |
CG/CG | 521 | 104 | 22 | 21 | 668 | ||||
Tri-nucleotide (236,541) | |||||||||
AAT/ATT | 29,084 | 12,994 | 7386 | 4347 | 2774 | 2076 | 3986 | 131 | 62,778 |
AGG/CCT | 24,138 | 11,861 | 7937 | 5006 | 3504 | 1903 | 4472 | 212 | 59,033 |
AGC/GCT | 14,871 | 6253 | 3373 | 1734 | 917 | 444 | 1211 | 81 | 28,884 |
AAC/GTT | 13,646 | 6495 | 4094 | 2152 | 720 | 469 | 650 | 9 | 28,235 |
AAG/CTT | 11,036 | 5730 | 2754 | 1535 | 815 | 616 | 1108 | 282 | 23,876 |
ATC/GAT | 8035 | 3684 | 2516 | 1456 | 954 | 415 | 1576 | 360 | 18,996 |
ACC/GGT | 3656 | 1960 | 1036 | 511 | 145 | 96 | 75 | 7479 | |
ACT/AGT | 2218 | 822 | 403 | 292 | 145 | 134 | 519 | 172 | 4705 |
CCG/CGG | 1099 | 228 | 92 | 54 | 53 | 1526 | |||
ACG/CGT | 643 | 248 | 87 | 15 | 6 | 30 | 1029 | ||
Tetra-nucleotide (43,907) | |||||||||
ACAG/CTGT | 1581 | 958 | 627 | 702 | 732 | 458 | 1192 | 21 | 6271 |
AGAT/ATCT | 1360 | 940 | 606 | 399 | 366 | 319 | 1397 | 297 | 5684 |
ACGC/GCGT | 1249 | 1089 | 656 | 364 | 279 | 175 | 263 | 4075 | |
AGGG/CCCT | 2503 | 1045 | 243 | 113 | 22 | 30 | 3956 | ||
AAAC/GTTT | 1755 | 830 | 359 | 181 | 73 | 78 | 89 | 3365 | |
ATCC/GGAT | 945 | 676 | 357 | 51 | 195 | 120 | 502 | 15 | 2861 |
AATC/GATT | 1121 | 616 | 370 | 124 | 100 | 75 | 68 | 2474 | |
AAAG/CTTT | 1214 | 317 | 162 | 175 | 76 | 72 | 117 | 2133 | |
AAAT/ATTT | 1508 | 301 | 97 | 24 | 6 | 24 | 53 | 2013 | |
ACTC/GAGT | 399 | 303 | 325 | 95 | 125 | 243 | 349 | 80 | 1919 |
ACAT/ATGT | 583 | 314 | 62 | 178 | 117 | 27 | 339 | 33 | 1653 |
AAGG/CCTT | 761 | 317 | 186 | 27 | 15 | 60 | 200 | 15 | 1581 |
Others (17) | 2934 | 1297 | 548 | 387 | 205 | 90 | 420 | 41 | 5922 |
Penta-nucleotide (7733) | |||||||||
AGAGG/CCTCT | 481 | 275 | 250 | 83 | 109 | 156 | 756 | 2110 | |
AAGAT/ATCTT | 397 | 228 | 36 | 29 | 23 | 713 | |||
AAGGC/GCCTT | 253 | 79 | 48 | 12 | 35 | 42 | 469 | ||
AATGT/ACATT | 339 | 87 | 12 | 438 | |||||
AAGCT/AGCTT | 180 | 132 | 39 | 27 | 378 | ||||
AGCAT/ATGCT | 92 | 96 | 15 | 42 | 30 | 21 | 296 | ||
AAATC/GATTT | 234 | 30 | 15 | 279 | |||||
AAAGG/CCTTT | 117 | 18 | 29 | 1 | 54 | 219 | |||
Others (49) | 1795 | 421 | 214 | 122 | 121 | 60 | 89 | 2831 | |
Hexa-nucleotide (6196) | |||||||||
AACCCT/AGGGTT | 664 | 468 | 202 | 128 | 75 | 57 | 105 | 1699 | |
ACACGC/GCGTGT | 377 | 167 | 171 | 102 | 176 | 114 | 12 | 1119 | |
ACACTC/GAGTGT | 78 | 72 | 85 | 187 | 96 | 518 | |||
ACACAT/ATGTGT | 18 | 24 | 37 | 54 | 70 | 80 | 43 | 326 | |
AAGAGG/CCTCTT | 125 | 49 | 174 | ||||||
AATCAG/CTGATT | 102 | 45 | 147 | ||||||
ACTCTG/CAGAGT | 86 | 23 | 18 | 18 | 145 | ||||
Others (73) | 1092 | 416 | 299 | 70 | 60 | 43 | 88 | 2068 | |
Total | 993,598 | 423,971 | 228,963 | 140,477 | 92,382 | 66,295 | 232,325 | 86,636 | 2,264,647 |
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Choi, E.; Kim, S.H.; Lee, S.J.; Jo, E.; Kim, J.; Kim, J.-H.; Parker, S.J.; Chi, Y.-M.; Park, H. A First Genome Survey and Genomic SSR Marker Analysis of Trematomus loennbergii Regan, 1913. Animals 2021, 11, 3186. https://doi.org/10.3390/ani11113186
Choi E, Kim SH, Lee SJ, Jo E, Kim J, Kim J-H, Parker SJ, Chi Y-M, Park H. A First Genome Survey and Genomic SSR Marker Analysis of Trematomus loennbergii Regan, 1913. Animals. 2021; 11(11):3186. https://doi.org/10.3390/ani11113186
Chicago/Turabian StyleChoi, Eunkyung, Sun Hee Kim, Seung Jae Lee, Euna Jo, Jinmu Kim, Jeong-Hoon Kim, Steven J. Parker, Young-Min Chi, and Hyun Park. 2021. "A First Genome Survey and Genomic SSR Marker Analysis of Trematomus loennbergii Regan, 1913" Animals 11, no. 11: 3186. https://doi.org/10.3390/ani11113186