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Table 1 Top 25 TE-derived small RNAs associated with BmAgo2

From: RIP-seq of BmAgo2-associated small RNAs reveal various types of small non-coding RNAs in the silkworm, Bombyx mori

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)

  1. *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.
  2. **Total reads of TE-derived small RNAs are shown in parenthesis.
  3. §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].