This guide shows the files to plot idiograms of measured karyotypes and optionally marks.

1 Load package

visit gitlab for installation instructions https://gitlab.com/ferroao/idiogramFISH

2 Get your chromosome size data

Initially you have to open your chromosome data as a data.frame.

loading saved data:

Initially, if you use RStudio, use menu “Session”, “Set working directory” for choosing your desired folder or:

Open your chromosome data data.frame importing it from a .csv (read.csv) or .xls file (readxl).

Editing a data.frame:

For fixing column names use:

3 Get marks general data

This data.frame is optional.

Open or make your mark data as a data.frame. This data.frame has the marks present in all karyotypes without position info. If style column is not present it will be filled with square during plotting.

markName markColor style
5S red dots
45S green square
DAPI blue square
CMA yellow square
B mark black square

For fixing column names use:

4 Get marks positions data

Open or write your mark positions as a data.frame. This data.frame has the marks present in all karyotypes with position info. This data.frame has also the centromeric marks present in all karyotypes.

OTU chrName markName chrRegion markSize markDistCen
Species one 1 45S p NA NA
Species one 1 5S q 0.5 0.5
Species one B B mark w NA NA
Species one 2 45S p 1.0 1.0
Species one 3 DAPI q 1.0 1.0
Species one 1 DAPI cen NA NA
Species one 3 CMA cen NA NA

For fixing column names use something like:

5 Add some text to the right

For ver. > 1.7

For adding just the OTU name (from column OTU of data.frame of chr. size) to the right, use OTUasNote=TRUE

6 Plotting

You can plot without marks (use only 1st data.frame), but we will use all 4 data.frames created. By default the function will calculate indices (Romero-Zarco, 1986; Watanabe et al., 1999) and morphological categories of Guerra (1986) and Levan (1964). Use parameters chrIndex and morpho of the function plotIdiograms to modify that. See ?plotIdiograms.

Vertices when centromereSize=0 are rounded:

For ver. > 1.0.0 there is no need to add dfMarkColor and you can also use the parameter mycolors (optional too), to establish marks’ colors. Colors are assigned depending on the order of marks, i.e.:

7 Example with several species (OTUs)

To illustrate this, we will load some data.frames from the package

  • Chromosome sizes
OTU chrName shortArmSize longArmSize
1 Species 1 1 1.5 2.0
2 Species 1 2 2.0 2.5
3 Species 1 3 1.0 1.5
4 Species 2 1 3.0 4.0
5 Species 2 2 4.0 5.0
6 Species 2 3 2.0 3.0
7 Species 2 X 1.0 2.0
8 Species 2 4 3.0 4.0
9 Species 3 1 3.2 4.0
10 Species 3 2 4.5 5.0
11 Species 3 3 2.0 3.0
12 Species 3 4 1.5 2.0
13 Species 3 5 4.8 6.0
14 Species 3 6 6.1 7.0
15 Species 4 1 1.5 2.0
16 Species 4 2 2.0 2.5
17 Species 4 3 1.0 1.5
18 Species 5 1 3.0 4.0
19 Species 5 2 4.0 5.0
20 Species 5 3 2.0 3.0
21 Species 5 X 1.0 2.0
22 Species 5 4 3.0 4.0
23 Species 6 1 3.2 4.0
24 Species 6 2 4.5 5.0
25 Species 6 3 2.0 3.0
26 Species 6 4 1.5 2.0
27 Species 6 5 4.8 6.0
28 Species 6 6 6.1 7.0
231 Species 7 1 3.9 4.0
241 Species 7 2 3.8 4.0
  • Mark characteristics, does not require OTU
  • optional for ver. > 1.0.0
markName markColor style
5S red dots
45S green square
DAPI blue square
CMA yellow square
  • Mark position
OTU chrName markName chrRegion markDistCen markSize
Species 1 1 5S p 0.5 1
Species 1 1 45S q 0.5 1
Species 1 2 45S p 1.0 1
Species 1 3 DAPI q 1.0 1
Species 3 3 5S p 1.0 1
Species 3 3 DAPI q 1.0 1
Species 3 4 45S p NA NA
Species 3 4 DAPI q 1.0 1
Species 3 5 CMA q 2.0 1
Species 3 6 5S q 0.5 1
Species 2 1 DAPI cen NA NA
Species 2 4 CMA cen NA NA

8 GISH of monocentric chromosomes

You need the data.frame of chr. sizes, and a d.f. of marks

Chr. sizes:

parentalAndHybChrSize
OTU chrName shortArmSize longArmSize
Parental 1 1 3.2 4
Parental 1 4 1.5 2
Parental 1 5 4.8 6
Parental 1 6 6.1 7
Parental 2 1 3.2 4
Parental 2 2 4.5 5
Parental 2 3 2.0 3
Allopolyploid 1 3.2 4
Allopolyploid 2 4.5 5
Allopolyploid 3 2.0 3
Allopolyploid 4 1.5 2
Allopolyploid 5 4.8 6
Allopolyploid 6 6.1 7

Marks’ positions data

dfAlloParentMarks
OTU chrName markName chrRegion
Allopolyploid 1 Parental 1 p
Allopolyploid 1 Parental 2 q
Allopolyploid 1 Parental 2 cen
Allopolyploid 2 Parental 2 w
Allopolyploid 3 Parental 2 w
Allopolyploid 4 Parental 1 w
Allopolyploid 5 Parental 1 w
Allopolyploid 6 Parental 1 w
Parental 1 6 Parental 1 w
Parental 1 5 Parental 1 w
Parental 1 1 Parental 1 w
Parental 1 4 Parental 1 w
Parental 2 2 Parental 2 w
Parental 2 1 Parental 2 w
Parental 2 3 Parental 2 w

9 Plot data in micrometers and bases

For version > 1.9.1 info in number of bases can be combined in the same plot with info. in micrometers.

Let’s explore those data.frames

OTU chrName shortArmSize longArmSize chrSize
1 Species 1 1 1.5 2.0 NA
2 Species 1 2 2.0 2.5 NA
3 Species 1 3 1.0 1.5 NA
15 Species 1 genome 1 NA NA 3500000
16 Species 1 genome 2 NA NA 4500000
17 Species 1 genome 3 NA NA 2500000
OTU chrName markName chrRegion markDistCen markSize markPos
1 Species 1 1 5S p 0.5 1 NA
2 Species 1 1 45S q 0.5 1 NA
3 Species 1 2 45S p 1.0 1 NA
4 Species 1 3 DAPI q 1.0 1 NA
13 Species 1 genome 1 5S NA NA 1000000 2500000
14 Species 1 genome 1 45S NA NA 1000000 500000
15 Species 1 genome 2 45S NA NA 1000000 3500000
16 Species 1 genome 3 DAPI NA NA 1000000 0

References

Guerra M. 1986. Reviewing the chromosome nomenclature of Levan et al. Brazilian Journal of Genetics, 9(4): 741–743

Levan A, Fredga K, Sandberg AA. 1964. Nomenclature for centromeric position on chromosomes Hereditas, 52(2): 201–220. https://doi.org/10.1111/j.1601-5223.1964.tb01953.x. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1601-5223.1964.tb01953.x

Romero-Zarco C. 1986. A new method for estimating karyotype asymmetry Taxon, 35(3): 526–530. https://onlinelibrary.wiley.com/doi/abs/10.2307/1221906

Watanabe K, Yahara T, Denda T, Kosuge K. 1999. Chromosomal evolution in the genus Brachyscome (Asteraceae, Astereae): statistical tests regarding correlation between changes in karyotype and habit using phylogenetic information Journal of Plant Research, 112: 145–161. http://link.springer.com/article/10.1007/PL00013869