centromere position

[junhaiqi]

Hello, I am very interested in your work. Is there a good way to get the location of the centromere region in the reference genome?

[lurebgi]

Below I paste the centromere positions which should be based on GCA_016699485.1
chr1 76500000 77000000
chr2 52100000 52300000
chr3 2650000 2850000
chr4 18700000 18900000
chr5 3250000 3350000
chr6 0 460000
chr7 7300000 7500000
chr8 10600000 10800000
chr9 0 100000
chr10 500000 900000
chr11 2900000 3100000
chr12 1 230000
chr13 700000 1000000
chr14 15800000 16159740
chr16 100000 450000
chr17 400000 900000
chr18 300000 600000
chr19 450000 900000
chr20 700000 900000
chr21 6800000 6956554
chr22 5250000 5472503
chr23 50000 400000
chr24 7300000 7891846
chr26 6000000 6534586
chr28 800000 900000
chr29 6150000 6729691
chr30 2950000 3408877
chr31 5300000 5465527
chr32 100000 300000
chr34 3680000 3780000
chr35 2700000 2885947
chr36 3150000 3305939

[junhaiqi]

Thank you.

[junhaiqi]

Further, I still have some questions. Where does this location information come from? Why is there only centromere position information for 36 chromosomes?

[lurebgi]

This is based CENP-A ChIP-seq data. For some small chromosomes we did not detect CENP-A peaks.

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On Feb 16, 2024, 4:59 PM +0800, qjh ***@***.***>, wrote: Further, I still have some questions. Where does this location information come from? Why is there only centromere position information for 36 chromosomes? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[junhaiqi]

This is based CENP-A ChIP-seq data. For some small chromosomes we did not detect CENP-A peaks.
…
On Feb 16, 2024, 4:59 PM +0800, qjh @.>, wrote: Further, I still have some questions. Where does this location information come from? Why is there only centromere position information for 36 chromosomes? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.>

Thanks

[junhaiqi]

Sorry, I still have some questions and hope to get your answers. Based on all the centromere positions you gave, we extracted the corresponding centromere sequences on the reference sequence. We found that these sequences do not seem to possess an important characteristic of highly tandemly repeated sequences: the same k-mer appears multiple times in the sequence. I want to confirm that these positions have a high level of confidence so that I can infer whether I am doing the right thing. Additionally, can you provide the sequence of the 41-bp repeat unit in the centromeric region of the reference genome?

[lurebgi]

Hi, You can use the https://github.com/yangao07/TideHunter to identify the unit of tandem repeats. For macrochromosomes the unit is also published by Shang et al 2010 Genome Research, you can cross check with the sequences under NCBI AB556430–AB556736. For the 41-bp unit: https://www.ncbi.nlm.nih.gov/nuccore/X51431.1

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On Feb 25, 2024, 3:33 PM +0800, qjh ***@***.***>, wrote: Sorry, I still have some questions and hope to get your answers. Based on all the centromere positions you gave, we extracted the corresponding centromere sequences on the reference sequence. We found that these sequences do not seem to possess an important characteristic of highly tandemly repeated sequences: the same k-mer appears multiple times in the sequence. I want to confirm that these positions have a high level of confidence so that I can infer whether I am doing the right thing. Additionally, can you provide the sequence of the 41-bp repeat unit in the centromeric region of the reference genome? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[junhaiqi]

Hi, You can use the https://github.com/yangao07/TideHunter to identify the unit of tandem repeats. For macrochromosomes the unit is also published by Shang et al 2010 Genome Research, you can cross check with the sequences under NCBI AB556430–AB556736. For the 41-bp unit: https://www.ncbi.nlm.nih.gov/nuccore/X51431.1
…
On Feb 25, 2024, 3:33 PM +0800, qjh @.>, wrote: Sorry, I still have some questions and hope to get your answers. Based on all the centromere positions you gave, we extracted the corresponding centromere sequences on the reference sequence. We found that these sequences do not seem to possess an important characteristic of highly tandemly repeated sequences: the same k-mer appears multiple times in the sequence. I want to confirm that these positions have a high level of confidence so that I can infer whether I am doing the right thing. Additionally, can you provide the sequence of the 41-bp repeat unit in the centromeric region of the reference genome? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.>

Thank you very much for your sincere answer.