Go Component "Centromeric Region" Associated With Different Parts Of Chrs Of Arabidopsis, Why?

Question

[Biomonika (Noolean)]

Hi,

I am looking for Arabidopsis thaliana centromeric positions. I have found annotation table of chromosome 1, TAIR 10:

ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_chromosome_files/NCBI_Chr1.tbl

What I do not understand is, that when I search for "centromeric region", I see this annotation on different parts of chromosome (really distant places, I mean). Why is it so? Are centromeric-like regions observed multiple times on chromosome?

I have also found nice visualisation of genes and repetitive sequences along chromosomes of Arabidopsis, so one could try to infer where the centromeres approximately should be. However, more precise information is missing in browsers (or I just did not find it:)

Thanks for help.

Answer 1

[Tanya Berardini]

Hi,

Some TAIR users have asked us the same question before. I'm sending you a copy of the reply from my colleague David. Hope this helps!

Best

Tanya Berardini TAIR Curator

---

Dear Torsten,

You can find additional information regarding the Centromeres in 'Analysis of the genome sequence of the flowering plant Arabidopsis thaliana', Nature 408, 796-815. You can access a pdf file of this paper here:

http://www.nature.com/nature/journal/v408/n6814/pdf/408796a0.pdf

see figure 6 for a depiction of the centromeric regions

Determining where these regions begin and end depends somewhat on how they are defined in addition many of the regions are not fully sequenced due to the presence of a lot of repetitive DNA that was difficult or impossible to sequence using the technology available at the time.

For the location of the unsequenced centromeres and NORs you can check out the Assembly_GFF directory

ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR9_genome_release/TAIR9_gff3/Assembly_GFF (the assembly has not changed in TAIR10, hence the coordinates of TAIR9 are still valid for the current annotation)

You can also see these regions in our GBrowse viewer by searching for the assembly unit name e.g. CEN1, in addition by checking the GAPs track option this will highlight all regions where the sequence is unknown (marked with Ns). The centromere and NOR gaps have been arbitrarily set to 1000 nt (there are 1000 N's in the chromosome sequence). However this is NOT the estimated size of the gaps.

All the best david

Answer 2

[Larry_Parnell]

Cool question - takes me back a few years...

Arabidopsis has some regions of chromosomes, 4 in particular, that encode heterochromatic knobs, a centromere-like structure. I found the one on the short arm of chromosome 4. Look at our paper in Cell and you'll learn much about their primary structure and annotation.

[Biomonika (Noolean)]

Thank you very much, I will take a look on that.

Answer 3

[SES]

As Larry said, there are knobs (i.e., "neocentromeres") on the chromosomes of some plant species, and maize has numerous knobs. Barbara McClintock was also interested in these peculiar features of maize chromosomes, and she characterized them in numerous maize lines and teosinte populations. This is still an area of active research that is related to selfish elements and meiotic drive (these knobs do not follow Mendelian segregation). There is a good overview of these features of maize chromosomes in the Handbook of Maize.

I mentioned the examples from maize because this topic has been studied for more than 50 years in this species. Unlike maize, Arabidopsis has tiny chromosomes and is not really a model for cytogenetics. I'm certain you can find some good primary literature for Arabidposis, and here is one review that covers this topic more broadly in plants.

[Biomonika (Noolean)]

Thanks. Now I understand why there are such regions:) However, I would still like to identify real centromeres, like on this figure with yellow dots http://www.biomedcentral.com/content/supplementary/1471-2148-10-41-s3.png

well, not identify, just positions in TAIR 9 or TAIR 10 would be more than great. In the annotation I mentioned they are somehow lost in those neocentromeric regions..

[SES]

Noolean, the active centromeres (the "real" centromeres you are interested in) are defined epigenetically by the presence of histone variant CENH3. You might want to look for this info in TAIR or try to find some more information based on cytological studies: http://www.plantcell.org/content/18/10/2443.full

Answer 4

[nurithec]

from the GFF file:

Chr1    TAIR    BAC_cloned_genomic_insert   15086046    15087045    .   +   .   ID=AssemblyUnit_CEN1;Name=CEN1
Chr2    TAIR    BAC_cloned_genomic_insert   3607930 3608929 .   +   .   ID=AssemblyUnit_CEN2;Name=CEN2
Chr3    TAIR    BAC_cloned_genomic_insert   13799418    13800417    .   +   .   "ID=AssemblyUnit_""CEN3, PT.2OF3"";Name=""CEN3, PT.2OF3"""
Chr3    TAIR    BAC_cloned_genomic_insert   14208953    14209952    .   +   .   "ID=AssemblyUnit_""CEN3, PT.3OF3"";Name=""CEN3, PT.3OF3"""
Chr4    TAIR    BAC_cloned_genomic_insert   3956022 3957021 .   +   .   ID=AssemblyUnit_CEN4;Name=CEN4
Chr5    TAIR    BAC_cloned_genomic_insert   11725025    11726024    .   +   .   ID=AssemblyUnit_CEN5;Name=CEN5