Question

Chromosomal length prunus dulcis

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5.5 years ago

felipead66 ▴ 120

Is it possible to find the chromosomal length of prunus dulcis?

https://www.rosaceae.org/organism/Prunus/dulcis

I want to use it to build circus plots.

chromosomes length non-model • 1.3k views

ADD COMMENT • link updated 5.5 years ago by AK ★ 2.2k • written 5.5 years ago by felipead66 ▴ 120

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See if you find the reference genome (it is here), download it and then get length of the chromosomes e.g. using Get chromosome sizes from fasta file

ADD REPLY • link 5.5 years ago by ATpoint 85k

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Thank you for your reply,

I followed the instructions in the link and I would not trust it since I get around 10000 (!) chromosomes. So there must be something else, I do not know what went wrong.

ADD REPLY • link 5.5 years ago by felipead66 ▴ 120

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The rest (with ID such as pdulcis26_s0345) are the unplaced/unanchored scaffolds during assembly.

ADD REPLY • link 5.5 years ago by AK ★ 2.2k

score 1 · Answer 1 · 2019-05-27

Hi felipead66,

Given the chromosome number 2n=16 from here, you can calculate the length from the assembly:

$ curl -s "ftp://ftp.bioinfo.wsu.edu/www.rosaceae.org/Prunus_dulcis/pdulcis_v2.0/assembly/pdulcis26.chromosomes.fasta.gz" | zcat - | seqkit fx2tab --name --length | head -n8
Pd01            43996934
Pd02            26138581
Pd03            24073526
Pd04            24375383
Pd05            18233718
Pd06            29596931
Pd07            21340587
Pd08            20428636