Table 1.
Top 25 TE-derived small RNAs associated with BmAgo2
|
Name of TEs |
TE types |
Length |
piRNAs |
Other small RNAs |
||
|---|---|---|---|---|---|---|
| Sense | Antisense | Sense | Antisense | |||
| Gypsy-9_BM(Aquila)-I |
LTR/ Gypsy |
7716 |
621(2803) |
692(5297) |
12022(57722)** |
11149(52894) |
| bm1866 |
LTR/Pao |
6465 |
576(1668) |
613(1988) |
6921(27652) |
7048(28122) |
| bm1645 |
LINE/R1 |
13595 |
42(54) |
633 (4794) |
1690(3400) |
11906(220080) |
| bm1456 |
LTR/Pao |
8702 |
570(2359) |
671(2944) |
4135(22334) |
3842(20498) |
|
L09635 |
LTR/Pao |
4791 |
376(1123) |
408(1644) |
4043(23398) |
4177(18148) |
|
AB480244.1(BMC1) * |
LINE/Jockey |
25948 |
474(1757) |
359(821) |
3598(26788) |
2713(8313) |
|
AB480245.1(Tama) * |
non-LTR |
34087 |
322(631) |
329(1492) |
1832(6701) |
1966(4254) |
| Yamato |
LTR/Pao |
6400 |
207(608) |
299(1628) |
1705(6094) |
2087(9633) |
|
AB480243.1(Taguchi) * |
LINE/R1 |
32792 |
255(738) |
302(841) |
1587(7621) |
1570(5069) |
| BmpiggyBac-MER85 |
ClassII§:TIR/piggyBac |
3504 |
305(1379) |
258(938) |
1684(9442) |
1456(6983) |
| bm228 |
LTR/Unknown |
8077 |
205(473) |
261(786) |
1423(3304) |
1760(5449) |
| Bmori_326.1597 |
LINE/Unknown |
576 |
142(760) |
148(800) |
1218(6510) |
2022(17937) |
| Gypsy-20_BM-I |
LTR/ Gypsy |
4469 |
436(1125) |
261(3602) |
1974(7179) |
807(4194) |
|
AB480240.1(Bm1) * |
SINE/SINE |
14359 |
337(1093) |
257(1114) |
1366(3521) |
1466(5126) |
| Moriya-I |
LTR/ Bel |
6871 |
196(412) |
220 (947) |
1180(3113) |
1350(5170) |
|
AB480234.1(Bm1) * |
SINE/SINE |
18645 |
169(386) |
183(659) |
1095(5477) |
1246(4397) |
| Kabuki |
LTR/Unknown |
5342 |
221(668) |
240(2406) |
1134(2787) |
1002(2610) |
| SART1 |
LINE/R1 |
6702 |
77(197) |
123(260) |
807(1468) |
1575(4629) |
|
AB480242.1(BMC1) * |
LINE/Jockey |
20035 |
223(1024) |
176(450) |
1125(4006) |
856(3017) |
| bm1222 |
Unknown/Unknown |
1468 |
126(220) |
160 (495) |
1221(3003) |
814(2988) |
| bm154 |
LINE/R1 |
9083 |
104(304) |
73(171) |
1224(4407) |
884(1988) |
|
AB480235.1(Kendo) * |
LINE/CR1 |
32287 |
196(473) |
143(368) |
858(3345) |
622(1317) |
| bm447 |
LTR/Pao |
7110 |
104(140) |
152 (384) |
333(724) |
1197(5351) |
| BMC1 |
LINE/Jockey |
5091 |
85(152) |
120(344) |
765(1623) |
815(2924) |
| bm1770 | LTR/Pao | 6669 | 96(159) | 162(756) | 301(646) | 1089(5433) |
*These contigs from the W chromosome contained TEs and generated a large amount of small RNAs around the TEs, which might be related with the transcription of the TEs.
**Total reads of TE-derived small RNAs are shown in parenthesis.
§TEs have been divided into two classes based on their transposition intermediate. Class I TEs use an RNA-mediated mode of transposition and are further divided into two subclasses, including LTR and non-LTR retrotransposons. Non-LTR retrotransposons are also called LINEs (long interspersed nuclear elements) and SINEs (short interspersed nuclear elements). Class II TEs use a DNA-mediated mode of "cut and paste" transposition. In Bombyx mori, many TEs have been identified, such as bm447, bm1770, bm1645 and SART1 [69].