riceTElib

A collection of manually curated TE examplars in rice (Oryza sativa) provided by Ning Jiang and colleagues.
The latest library, ricex.x.x.liban, is placed in the root folder. x.x.x is the version number. Older versions were placed in the historic_versions folder. Sequences contained in the library are non-redundant examplars that can be used to annotate all related TEs in the rice genome.

Commannds used to update the library

Combine the SINE library with rice6.9.5.liban

mask lib with new SINEs

RepeatMasker -pa 36 -q -no_is -norna -nolow -div 40 -cutoff 225 -lib riceSINE_210517 rice6.9.5.liban

get non-SINE lib seqs

perl ~/bin/LTR_retriever/bin/output_by_list.pl 1 rice6.9.5.liban.masked 1 <(awk '{print $5}' rice6.9.5.liban.out) -FA -ex | \
	perl ~/bin/LTR_retriever/bin/output_by_list.pl 1 - 1 <(grep SINE rice6.9.5.liban) -FA -ex \
> rice6.9.5.liban.nosine

get SINE-related non-SINE lib seqs

perl ~/bin/LTR_retriever/bin/output_by_list.pl 1 rice6.9.5.liban.masked 1 <(awk '{print $5}' rice6.9.5.liban.out|grep -v SINE) -FA \
> rice6.9.5.liban.masked.sine

clean up SINE-masked lib seqs

perl ~/bin/LTR_retriever/bin/cleanup.pl -misschar n -Nscreen 0 -minlen 80 -cleanN 1 -trf 0 -f rice6.9.5.liban.masked.sine > rice6.9.5.liban.masked.sine.cln

combine clean seqs and format

cat rice6.9.5.liban.nosine rice6.9.5.liban.masked.sine.cln riceSINE_210517 | perl ~/bin/LTR_retriever/bin/fasta-reformat.pl - 50 > rice7.0.0.liban

check ID uniqueness

grep \> rice7.0.0.liban|sed 's/#.*//' |sort -u|wc -l
grep -c \> rice7.0.0.liban

Identify novel Helitron candidates

xxx

Citations

Different parts of this library were published in different studies:

The LTR library

Ou S. and Jiang N.✉ (2018). LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Plant Physiol. 176(2): 1410-1422

The DNA TE library

Ou S., Su W., Liao Y., Chougule K., Agda J. R. A., Hellinga A. J., Lugo C. S. B., Elliott T. A., Ware D., Peterson T., Jiang N.✉, Hirsch C. N.✉ and Hufford M. B.✉ (2019). Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline. Genome Biol. 20(1): 275

The SINE library

Li Y., Jiang N., and Sun Y.✉ (2021). AnnoSINE: a short interspersed nuclear elements annotation tool for plant genomes. Plant Physiol. 188(2): 955–970