Introduction

This repository contains three historical versions of curated maize TE libraries derived from the Maize TE Consortium (MTEC). I combined the three together and further clean the combined library with the following commands and curations. If you are looking for a comprehensive and high-quality maize TE library, look no further, this is the one (usually named like "maizeTE02052020" in the root directory).

Files

• maizeTE10102014 was download from the MTEC official website (http://maizesequence.org). The website is gone, but I managed to get a mirror of the first page. Please refer to the file history/Maizedatabase_mirror.pdf for more information about the MTEC project.
• TE_12-Feb-2015_15-35.fa was shared by Nicolas Blavet from https://github.com/mcstitzer/maize_v4_TE_annotation/issues/9.
• Wessler-Bennetzen_2.fasta was used to annotate the initial B73 genome (Schnable et al. 2009), which was shared by Kapeel Chougule. I believe this is an earlier version of the MTEC library.
• nonTE.repeat.fa contains 5 non-TE repeats (knob180, knob TR-1, rDNA spacer, subtelomere 4-12-1, and CentC) in maize, which was shared by Jianing Liu.

Combine the three MTEC libraries + nonTE repeats

1. Reformat sequence IDs

for i in history/Wessler-Bennetzen_2.fasta history/maizeTE10102014 history/TE_12-Feb-2015_15-35.fa; do perl -nle 's/\s+$//g; $_=(split)[0]; s/\-/_/g; print $_' $i > $i.mod; done

2. Combine sequences with unique IDs

perl bin/output_by_list.pl 1 <(cat history/*.mod) 1 <(cat history/*.mod|grep \>|sort -u) -FA > history/maizeTE11212019.ori

3. Split the library into consensus and others

perl bin/output_by_list.pl 1 history/maizeTE11212019.ori 1 <(grep consen history/maizeTE11212019.ori) -FA > history/maizeTE11212019.ori.consensus

perl bin/output_by_list.pl 1 history/maizeTE11212019.ori 1 <(grep consen history/maizeTE11212019.ori) -FA -ex > history/maizeTE11212019.ori.others

4. Remove TEs in others that are represented by consensus TEs

RepeatMasker -pa 36 -div 40 -lib history/maizeTE11212019.ori.consensus -cutoff 225 history/maizeTE11212019.ori.others

perl bin/make_masked.pl -rmout history/maizeTE11212019.ori.others.out -genome history/maizeTE11212019.ori.others -maxdiv 20 -minscore 200 -minlen 80 -t 30

perl bin/cleanup_tandem.pl -nc 1000 -nr 0.5 -minlen 80 -cleanN 1 -cleanT 1 -trf 0 -f history/maizeTE11212019.ori.others.new.masked > history/maizeTE11212019.ori.others.new.masked.cln

cat history/maizeTE11212019.ori.consensus history/maizeTE11212019.ori.others.new.masked.cln > history/maizeTE11212019.ori2

5. Remove redundant sequences

perl bin/cleanup_nested.pl -in history/maizeTE11212019.ori2 -cov 0.98 -minlen 80 -miniden 95 -iter 2 -t 36

6. Remove nonTE repeats and tandem repeats

RepeatMasker -pa 36 -div 40 -no_is -norna -nolow -lib history/nonTE.repeat.fa -cutoff 225 history/maizeTE11212019.ori2.cln

perl bin/cleanup_tandem.pl -nc 1000 -nr 0.5 -minlen 80 -cleanN 1 -cleanT 1 -trf 1 -f history/maizeTE11212019.ori2.cln.masked > history/maizeTE11212019.ori2.cln2

cat history/nonTE.repeat.fa history/maizeTE11212019.ori2.cln2 > history/maizeTE11212019.ori3

Improve the combined library

1. Reclassify unknown TEs

python2 TEsorter.py history/maizeTE11212019.ori3 -p 36

2. Find misclassified entries

The file history/maizeTE11212019.ori3.rexdb.cls.tsv contains new classifications of the library. Most of them are consistent with the old classification. What really improved are the LTR/unknown classification.

perl -nle '($info, $cla)=(split)[0,2]; my $oldcla=$1 if $info=~/^([A-Z]+)_/; $cla=~s/EnSpm_CACTA/DTC/; $cla=~s/hAT/DTA/; $cla=~s/PIF_Harbinger/DTH/; $cla=~s/MuDR_Mutator/DTM/; $cla=~s/Tc1_Mariner/DTT/; $cla=~s/Gypsy/RLG/; $cla=~s/Copia/RLC/; print "$oldcla\t$cla\t$info" if $cla ne $oldcla' history/maizeTE11212019.ori3.rexdb.cls.tsv |less

3. Some LTRs appear to have the same name but different classifications (RLG/RLC/RLX)

grep RL history/maizeTE11212019.ori3|perl -nle 's/RL._//; print $_'|sort|uniq -c |sort -k1,1|tac|less blastn -query list.fa -subject list.fa -outfmt=6 > list.fa.out

4. Manually check misclassified sequences (list.fa).

These entries are put in the history/removal.list and removed:

Seq_ID	Removal reason
RLC_chr3_D_28761151	rDNA-contained
DTM_Zm08959_AC199876_1	LTRcoding-contained
DTM_Zm22805IC_AC207689_1	LINE-contained
RIX_nugimu_AC203843_0	Duplicted_with_RIL_nugimu_AC203843_0
RLX_fageri_AC204875_8470	misclassified_as_LINE
DTA_ZM00171_consensus	misclassified_as_CACTA
DTA_ZM00205_consensus	misclassified_as_CACTA
DTA_ZM00284_consensus	misclassified_as_CACTA
RLX_teki_AC202867-7492	rDNA-contained
RLG_ajajog_AC191578_3186	A_RLG_nested_in_RLC_ajajog_AC191578_3186
RLC_iwim_AC203300_7761	misclassified_RLG_duplicated
RLC_kupu_AC216069_13264	misclassified_RLG_duplicated
RLX_pute_AC197188_5467	duplicated_RLC_pute_AC197188_5467
RLX_votaed_AC215881_13209	duplicated_RLC_votaed_AC215881_13209
RLC_votaed_AC215881_13209	5-6_LTR_nested_together
RLX_bobeg_AC193485_3670	5_LTR_nested_together

perl bin/output_by_list.pl 1 history/maizeTE11212019.ori3 1 history/removal.list -FA -ex > history/maizeTE11212019.ori3.cln

5. PPP_PPO_AC185414 is changed to DTH_PPO_AC185414 manually

6. Update LTR classifications

perl -nle '($info, $cla)=(split)[0,2]; my $oldcla=$1 if $info=~/^([A-Z]+)_/; $cla=~s/EnSpm_CACTA/DTC/; $cla=~s/hAT/DTA/; $cla=~s/PIF_Harbinger/DTH/; $cla=~s/MuDR_Mutator/DTM/; $cla=~s/Tc1_Mariner/DTT/; $cla=~s/Gypsy/RLG/; $cla=~s/Copia/RLC/; next unless /LTR/; my $info_new=$info; $info_new=~s/$oldcla/$cla/; print "$info|$info_new" if $cla ne $oldcla' history/maizeTE11212019.ori3.rexdb.cls.tsv > history/maizeTE11212019.ori3.rexdb.cls.tsv.LTR

for i in cat history/maizeTE11212019.ori3.rexdb.cls.tsv.LTR; do perl -i -slane 'my ($old, $new)=(split /\|/, $info); s/$old/$new/; print $_' -- -info=$i history/maizeTE11212019.ori3.cln; done

7. Convert sequence names to RepeatMasker format

perl -nle 'my $id=(split)[0]; $id=~s/RLC_(.*)/$1#LTR\/Copia/; $id=~s/RLG_(.*)/$1#LTR\/Gypsy/; $id=~s/RLX_(.*)/$1#LTR\/unknown/; $id=~s/DHH_(.*)/$1#DNA\/Helitron/; $id=~s/DTA_(.*)/$1#DNA\/DTA/; $id=~s/DTC_(.*)/$1#DNA\/DTC/; $id=~s/DTH_(.*)/$1#DNA\/DTH/; $id=~s/DTM_(.*)/$1#DNA\/DTM/; $id=~s/DTT_(.*)/$1#DNA\/DTT/; $id=~s/(RIT_.*)/$1#LINE\/RTE/; $id=~s/(RIL_.*)/$1#LINE\/L1/; $id=~s/(RIX_.*)/$1#LINE\/unknown/; $id=~s/(ZM_CACTA_noncoding.*)/$1#MITE\/DTC/; $id=~s/(ZM_Stowaway.*)/$1#DNA\/DTT/; $id=~s/(ZM_Tourist.*)/$1#DNA\/DTH/; $id=~s/(ZM_hAT_noncoding.*)/$1#MITE\/DTA/; $id=~s/(RST_.*)/$1#SINE\/tRNA/; print $id' history/maizeTE11212019.ori3.cln > history/maizeTE11222019.ori

8. Rename short TIR (<= 600bp) to MITE

perl bin/rename_MITE.pl history/maizeTE11222019.ori > history/maizeTE11222019.ori.rename

Remove gene sequences

1. Mask gene cds

RepeatMasker -pa 36 -q -no_is -norna -nolow -div 40 -lib history/Zea_mays.AGPv4.cds.all.noTE.fa.mod.cln -cutoff 500 history/maizeTE11222019.ori.rename

perl bin/cleanup_tandem.pl -misschar n -Nscreen 1 -nc 1000 -nr 0.3 -minlen 80 -maxlen 5000000 -cleanN 1 -cleanT 1 -trf 0 -f history/maizeTE11222019.ori.rename.masked > history/maizeTE11222019.ori.rename.nogene

2. Finalize

Manually add the sequence CL569186.1#subtelomere/4-12-1 back to history/maizeTE11222019.ori.rename.nogene

cp history/maizeTE11222019.ori.rename.nogene maizeTE11222019

Updates

01/30/2020

Added four CRM sequences (CRM1-4) contributed by Na Wang from Gernot and Presting (2008).

02/03/2020

Added 3-letter names before all consensus seq IDs. IDs like "ZM00034_consensus" were inherited from the 2014 version MTEC, so kept it unchanged.

perl -nle 's/>(.*)#(.*)\/(.*)/>$3_$1#$2\/$3/; print $_' maizeTE01302020 > maizeTE02032020

02/05/2020

Fix namings

perl -nle 's/>(.*)#(.*)\/(.*)/>$3_$1#$2\/$3/ if /consensus/; s/>(.*)/>$1#LTR\/CRM/ if /CRM/; print $_' history/maizeTE01302020 > maizeTE02052020