Repetitive element annotation and construction of Circos
picture
The extended de-novo TE Annotator
(EDTA)(Ou et al., 2019) was
used to annotate the DNATE and LTR type sequences of the genome. TRF
(tandem repeats finder)
(Benson, 1999) was used to
identify the centromere sequence with 20000 points as the threshold.
Finally, the repeat sequences were annotated with
MAKER(Cantarel et al.,
2008). MCScanX(Y. Wang et al., 2012) was used to find the collinearity
from the comparison results and generate link files. Four tracks were
constructed from the outer to the inner of Circos(Krzywinski et al.,
2009), showing gene density, LTR density, DNATE density and TE density
respectively, and the collinearity within the genome was shown in the
inner circle.