Table 2.
Number, length, frequency, and density of SSRs by type (mono- to hexanucleotide repeats) in the investigated weevil genomes.
| Repeat Type | Parameter | R. ferrugineus (F) | R. ferrugineus (M) | R. ferrugineus (L) | S. oryzae | H. hampei | D. ponderosae (F) | D. ponderosae (M) | P. strobi | E. kamerunicus | I. nitidus | L. oregonensis | L. bonariensis |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mono- | Number of SSRs | 6393 | 5748 | 4906 | 22,484 | 3924 | 1415 | 1395 | 48,345 | 939 | 12,459 | 286,859 | 57,721 |
| Total length (bp) | 98,929 | 79,577 | 69,520 | 429,331 | 70,509 | 18,625 | 18,802 | 725,181 | 11,752 | 178,828 | 4,316,826 | 809,526 | |
| Average length (bp) | 15.47 | 13.84 | 14.17 | 19.09 | 17.97 | 13.16 | 13.48 | 15.00 | 12.52 | 14.35 | 15.05 | 14.02 | |
| Frequency (SSR/Mb) | 5.70 | 7.35 | 8.32 | 29.18 | 24.14 | 6.32 | 6.21 | 23.87 | 3.48 | 36.11 | 221.81 | 51.89 | |
| Density (bp/Mb) | 88.22 | 101.75 | 117.95 | 557.16 | 433.71 | 83.24 | 83.64 | 358.11 | 43.58 | 518.33 | 3337.89 | 727.70 | |
| Di- | Number of SSRs | 34,681 | 27,781 | 47,993 | 196,96 | 3077 | 944 | 1128 | 18,612 | 517 | 19,728 | 190,064 | 46,373 |
| Total length (bp) | 1,084,748 | 748,002 | 1,823,936 | 1,157,184 | 335,416 | 15,834 | 19,970 | 360,806 | 7412 | 493,798 | 13,130,600 | 2,463,404 | |
| Average length (bp) | 31.28 | 26.92 | 38.00 | 58.75 | 109.00 | 16.77 | 17.70 | 19.39 | 14.34 | 25.03 | 69.09 | 53.12 | |
| Frequency (SSR/Mb) | 30.93 | 35.52 | 81.43 | 25.56 | 18.93 | 4.22 | 5.02 | 9.19 | 1.92 | 57.18 | 146.96 | 41.69 | |
| Density (bp/Mb) | 967.35 | 956.40 | 3094.55 | 1501.73 | 2063.20 | 70.77 | 88.84 | 178.17 | 27.49 | 1431.28 | 10,152.94 | 2214.42 | |
| Tri- | Number of SSRs | 8517 | 8897 | 7407 | 15,786 | 4028 | 2558 | 2663 | 45,395 | 1050 | 10,357 | 23,752 | 16,301 |
| Total length (bp) | 142,764 | 149,838 | 126,207 | 284,631 | 79,143 | 44,475 | 46,941 | 1,137,378 | 15,882 | 196,965 | 457,914 | 304,446 | |
| Average length (bp) | 16.76 | 16.84 | 17.04 | 18.03 | 19.64821 | 17.39 | 17.63 | 25.06 | 15.13 | 19.02 | 19.28 | 18.68 | |
| Frequency (SSR/Mb) | 7.60 | 11.38 | 12.57 | 20.49 | 24.78 | 11.43 | 11.85 | 22.42 | 3.89 | 30.02 | 18.37 | 14.65 | |
| Density (bp/Mb) | 127.31 | 191.58 | 214.13 | 369.38 | 486.82 | 198.78 | 208.82 | 561.66 | 58.90 | 570.90 | 354.07 | 273.67 | |
| Tetra- | Number of SSRs | 5368 | 6700 | 5515 | 19,698 | 1627 | 1310 | 1323 | 32,698 | 1510 | 3915 | 21,085 | 29,736 |
| Total length (bp) | 94,688 | 116,572 | 97,284 | 422,340 | 30,380 | 22,688 | 22,752 | 621,160 | 24,604 | 95,912 | 406,368 | 654,160 | |
| Average length (bp) | 17.64 | 17.40 | 17.64 | 21.44 | 18.67 | 17.32 | 17.20 | 18.99 | 16.29 | 24.50 | 19.27 | 21.99 | |
| Frequency (SSR/Mb) | 4.79 | 8.57 | 9.36 | 25.56 | 10.01 | 5.86 | 5.89 | 16.15 | 5.60 | 11.35 | 16.30 | 26.73 | |
| Density (bp/Mb) | 84.44 | 149.05 | 165.06 | 548.09 | 186.87 | 101.40 | 101.21 | 306.74 | 91.25 | 278.00 | 314.21 | 588.04 | |
| Penta- | Number of SSRs | 1318 | 1324 | 1151 | 5375 | 382 | 230 | 239 | 6630 | 348 | 1289 | 5786 | 5784 |
| Total length (bp) | 30,555 | 28,995 | 25,330 | 135,845 | 13,175 | 4900 | 5145 | 147,940 | 6960 | 70,845 | 136,620 | 158,590 | |
| Average length (bp) | 23.18 | 21.90 | 22.01 | 25.27 | 34.49 | 21.30 | 21.52 | 22.31 | 20.00 | 54.96 | 23.61 | 27.42 | |
| Frequency (SSR/Mb) | 1.18 | 1.69 | 1.95 | 6.98 | 2.35 | 1.03 | 1.06 | 3.27 | 1.29 | 3.74 | 4.47 | 5.20 | |
| Density (bp/Mb) | 27.25 | 37.07 | 42.98 | 176.29 | 81.04 | 21.90 | 22.89 | 73.06 | 25.81 | 205.35 | 105.64 | 142.56 | |
| Hexa- | Number of SSRs | 898 | 273 | 289 | 1352 | 54 | 48 | 55 | 2831 | 33 | 624 | 6577 | 801 |
| Total length (bp) | 29,538 | 7872 | 8718 | 103,614 | 1398 | 1248 | 1356 | 79,230 | 792 | 42,576 | 183,012 | 33,432 | |
| Average length (bp) | 32.89 | 28.84 | 30.17 | 76.64 | 25.89 | 26.00 | 24.65 | 27.99 | 24.00 | 68.23 | 27.83 | 41.74 | |
| Frequency (SSR/Mb) | 0.80 | 0.35 | 0.49 | 1.75 | 0.33 | 0.21 | 0.24 | 1.40 | 0.12 | 1.81 | 5.09 | 0.72 | |
| Density (bp/Mb) | 26.34 | 10.07 | 14.79 | 134.47 | 8.60 | 5.58 | 6.03 | 39.13 | 2.94 | 123.41 | 141.51 | 30.05 |