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eweitz / ideogram

Chromosome visualization for the web
https://eweitz.github.io/ideogram
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Dog centromeres and Y chromosome; multi-row layout #196

Closed eweitz closed 4 years ago

eweitz commented 4 years ago

This adds manually-annotated centromere data for dog chromosomes, and dog chromosome Y. It also fixes issues with multi-row layout, restoring ideograms for dog, cow, and leishmania parasite.

Centromere data for dog chromosomes 1-38 and X was inferred from Figure 6 in Lindblad-Toh et al., 2005 (PMID: 16341006). Chromosomes 1-38 are telocentric -- the centromere is towards the extreme start of the chromosome. Chromosome X has a centromere positioned around 50 Mb, per the figure.

Dog_centromeres_figure_6c_Lindblad-Toh_2005_PMID_16341006

Dog chromosome Y data is approximate and derives from Li et al., 2013 (PMID: 23788650). "The evolutionary history of grey wolf Y chromosomes" from 2019 (PMID: 30788868) notes:

The canine Y chromosome has an estimated size of ≈20 Mb (Li et al., 2013). The p arm, which represents about half the chromosome, constitutes the heterochromatic nucleolus organizer region (NOR). On the q arm, the PAR is 6.6 Mb while the rest is divided into a single‐copy and an ampliconic segment respectively (Li et al., 2013).

Here is what the genome for dog (Canis lupus familiaris) now looks like in Ideogram: dog_genome_ideogram

coveralls commented 4 years ago

Coverage Status

Coverage increased (+0.005%) to 90.454% when pulling fa26ba49da0c0d49aeb979143ed275d2c56622c0 on dog-centromeres into 63a927baab2d2388c00d51fdcdafb71608da5f6e on master.