Table 2 |
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|
Summary of LTR and non-LTR retrotransposons and DNA transposons identified by TEpipe in the T. castaneum genome assembly |
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| Class |
TE library* (kb) |
Number of families |
Percentage of genome† |
TE length range (bp) |
Average length (bp) |
Copy number (range) |
Average copy number |
GC content range (%) |
Average GC content (%) |
|
|
|||||||||
| Non-LTR |
238.1 |
69 |
2.0 |
786-6,820 |
3,363 |
1-2,556 |
161 |
27.15-57.94 |
38.14 |
| LTR |
290.2 |
48 |
1.7 |
3,292-11,097 |
6,019 |
1-1,634 |
202 |
30.61-53.21 |
39.31 |
| DNA transposons |
78.6 |
45 |
2.2 |
456-4,878 |
1,746 |
1-8,949 |
420 |
30.90-46.08 |
37.22 |
|
|
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|
*Non-LTR, LTR and DNA transposon TE libraries were produced by TEpipe, which is based on sequence similarity searches using conserved domains from reverse transcriptase and transposase. †To calculate the abundance of TEs in the Tribolium genome assembly, RepeatMasker was run using our TEpipe libraries. |
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|
Wang et al. Genome Biology 2008 9:R61 doi:10.1186/gb-2008-9-3-r61 |
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