The number of LTRS is very strange.

[zhiyongli1995]

Hi Shujun,
I am studying a maize genome, when I check the .tbl file obtained using LTR_retriever, I find that the LRT number is very strange, Gypsy should not have such a low ratio, the normal is about 45%, tell me which step is wrong, please!

LTR elements: 1858586 1817455189 bp 81.84 %
BEL/Pao 0 0 bp 0.00 %
Ty1/Copia 307740 280680382 bp 12.64 %
Gypsy/DIRS1 483033 481607327 bp 21.69 %

Incidentally, the LAI program took me a long time in the step of "Estimate the identity of LTR sequences in the genome: standard mode", it has been seven days and it is still running.

My code is showed bellow, the program ran without error:

source /home/root/miniconda3/etc/profile.d/conda.sh #conda 
conda activate LTR_retriever 

genome=yumi.genome.fasta
## To obtain raw input files with LTRharvest and LTR_FINDER_parallel 
# LTRharvest
date 
echo "gt"
/data/biotools/gt-1.6.2-Linux_x86_64-64bit-complete/bin/gt suffixerator -db $genome -indexname $genome -tis -suf -lcp -des -ssp -sds -dna
/data/biotools/gt-1.6.2-Linux_x86_64-64bit-complete/bin/gt ltrharvest -index $genome -minlenltr 100 -maxlenltr 7000 -mintsd 4 -maxtsd 6 -motif TGCA -motifmis 1 -similar 85 -vic 10 -seed 20 
date
echo "finder"
# LTR_FINDER_parallel
/data/biotools/LTR_FINDER_parallel-1.1/LTR_FINDER_parallel -seq $genome -threads 72 -harvest_out -size 1000000 -time 300
cat $genome.harvest.scn $genome.finder.combine.scn > $genome.rawLTR.scn
date
echo "LTR"
# LTR_retriever
/data/biotools/LTR_retriever/LTR_retriever -genome $genome -inharvest $genome.rawLTR.scn -threads 72 
date
echo "LAI"
/data/biotools/LTR_retriever/LAI -t 72 -genome $genome -intact $genome.pass.list -all $genome.out 

conda deactivate 

[zhiyongli1995]

Finally, the LAI program has done. The logs were showed bellow:

2024年 12月 11日 星期三 02:06:05 CST
LAI

######################################
### LTR Assembly Index (LAI) beta3.2 ###
######################################

Developer: Shujun Ou

Please cite:

Ou S., Chen J. and Jiang N. (2018). Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. gky730: https://doi.org/10.1093/nar/gky730

Parameters: -t 72 -genome yumi.genome.fasta -intact yumi.genome.fasta.pass.list -all yumi.genome.fasta.out


2024年 12月 11日 星期三 02:06:05 CST    Dependency checking: Passed!
2024年 12月 11日 星期三 02:06:05 CST    Calculation of LAI will be based on the whole genome.
                                Please use the -mono parameter if your genome is a recent ployploid, otherwise high identity between LTR homeologues will overcorrect raw LAI scores and result in low LAI.
2024年 12月 11日 星期三 02:06:05 CST    Estimate the identity of LTR sequences in the genome: standard mode
2024年 12月 19日 星期四 04:11:46 CST    The identity of LTR sequences: 95.4406775735217%
2024年 12月 19日 星期四 04:11:46 CST    Calculate LAI:

                                                Done!

2024年 12月 19日 星期四 04:12:40 CST    Result file: yumi.genome.fasta.out.LAI

                                You may use either raw_LAI or LAI for intraspecific comparison
                                but please use ONLY LAI for interspecific comparison

[oushujun]

did you compare it to other maize genomes annotated with the same process?

[zhiyongli1995]

I did the same test on B73v5 genome, it seems got a similar result, is this normal? The total LTR is 80%, it means almost 43% LTR type is unknow?
B73v5 result :
LTR elements: 2101240 1764071281 bp 80.84 %
BEL/Pao 0 0 bp 0.00 %
Ty1/Copia 371159 305880475 bp 14.02 %
Gypsy/DIRS1 581636 509125363 bp 23.33 %
Retroviral 0 0 bp 0.00 %