Chr9 of Rice(NIP) 4M do not have TE ?

[GooLey1025]

###
Chr8    EDTA    helitron        28596870        28597251        2596    +       .       ID=TE_homo_201873;Name=TE_00002121;classification=DNAnona/Helitron;sequence_ontology=S
O:0000544;identity=0.918;method=homology
###
Chr9    EDTA    Gypsy_LTR_retrotransposon       4060206 4061265 1607    -       .       ID=TE_homo_201874;Name=TE_00000666_LTR;classification=LTR/Gypsy;sequence_ontology=SO:0
002265;identity=0.734;method=homology
###
Chr9    EDTA    LTR_retrotransposon     4061262 4062223 5828    -       .       ID=TE_homo_201875;Name=TE_00000310_INT;classification=LTR/unknown;sequence_ontology=SO:0000186
;identity=0.838;method=homology

This is Teanno.gff3 , I found that chromosome 9 of rice(Nip-T2T genome) , “There are no transposable elements (TE) in the first 4 megabases of the chr 9 of rice genome.” It’s odd that no similar large blank regions were found in other chromosomes.

This is my output.log :

[oushujun]

Hello,

First, EDTA is design for whole genomes because it needs intact TEs from the whole genome for filtering and library making. Running on fractions will detriment both points.

Second, you have two fasta errors on your first screenshot. You probably want to correct that first.

Best, Shujun

On Mon, Sep 23, 2024 at 12:00 AM GooLey1025 @.***> wrote:

Chr8 EDTA helitron 28596870 28597251 2596 + . ID=TE_homo_201873;Name=TE_00002121;classification=DNAnona/Helitron;sequence_ontology=S O:0000544;identity=0.918;method=homology

Chr9 EDTA Gypsy_LTR_retrotransposon 4060206 4061265 1607 - . ID=TE_homo_201874;Name=TE_00000666_LTR;classification=LTR/Gypsy;sequence_ontology=SO:0 002265;identity=0.734;method=homology

Chr9 EDTA LTR_retrotransposon 4061262 4062223 5828 - . ID=TE_homo_201875;Name=TE_00000310_INT;classification=LTR/unknown;sequence_ontology=SO:0000186 ;identity=0.838;method=homology

This is Teanno.gff3 , I found that chromosome 9 of rice(Nip-T2T genome) , “There are no transposable elements (TE) in the first 4 megabases of the chr 9 of rice genome.” It’s odd that no similar large blank regions were found in other chromosomes.

This is my output.log : default.png (view on web) https://github.com/user-attachments/assets/7b41bfa8-e25a-4a26-8c7c-edbf3d42ac81

default.png (view on web) https://github.com/user-attachments/assets/2adeeeae-c08a-4a1e-af7a-abcf1d518e51

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[GooLey1025]

Hello,Shu jun. Thanks for you reply. Above is the map from NIP_T2T web (http://www.ricesuperpir.com/web/nip). Seeing the chr9 , perhaps there is no TE distribution in first 4M in chr9 indeed. Our software output conincide with this !