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Table 3 NIRVS and transposable elements (TEs)

From: Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus

 

TE occupancy (%)

TE groupa

AaegL3b

NIRVSc

Region 1d

Region 2e

LTR retrotransposons

12.34

23.06 (25.88)

31.35

30.56

LTR/Pao_Bel

4.42

6.9 (6.49)

16.33

4.15

LTR/Ty1_copia

5.34

1.46 (1.90)

0.04

2.22

LTR/Ty3_gypsy

2.58

14.7 (17.50)

14.98

24.18

non-LTR retrotransposons

12.81

3.91 (5.54)

0

3.43

SINEs

1.14

0.16 (0.22)

0

0

DNA transposons

6.96

3.29 (3.49)

3.38

2.72

MITEs

12.81

8.03 (7.34)

0.26

2.34

Helitrons

1.2

2.01 (2.32)

0

2.04

Penelope

0.42

0.2 (0.28)

0.26

0.8

  1. TE occupancy in the entire Ae. aegypti genome (AaegL3), in regions harboring NIRVS (NIRVS), in region1 and in region 2
  2. aFor consistency with previous publications and for unambiguous classification, only TEs annotated in TEfam were used. TE occupancy was defined as the number of bases in the genomic sequence that match TEs
  3. bThe genome assembly described in [71] is slightly different from AaegL3 (Aedes-aegypti-Liverpool_SCAFFOLDS_AaegL3.fa), which is used in this analysis. For better comparison with viral integration sites, a new RepeatMasker analysis was performed using the AaegL3 assembly under default parameters
  4. cThe NIRVS sites plus 5 kb or 10 kb (in brackets) of sequence flanking each side were retrieved for the analysis. These results may under-estimate the actual TE occupancy because NIRVS sequences are included in the analyses
  5. dSupercontig 1.286 between positions 1,316,885 bp and 1,429,979 bp (plus 5 kb flanking each side)
  6. eSupercontig 1.1 between positions 1,160,748 bp and 1,472,976 bp (plus 5 kb flanking each side)
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BMC Genomics

ISSN: 1471-2164

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