Updated Aug 15th, 2023
For Citation:
Mahmoudi, S., Mirzaghaderi, G. (2023). Tools for Drawing Informative Idiograms. In: Heitkam, T., Garcia, S. (eds) Plant Cytogenetics and Cytogenomics. Methods in Molecular Biology, vol 2672. Humana, New York, NY.
https://doi.org/10.1007/978-1-0716-3226-0_31
KaryoMeasure can be easily calibrated so that all following calculations would be in micrometer (µm).
The ability to calculate mean and standard deviation of chromosomal parameters of each homologous group.
After tracing chromosomes, this software is capable to draw ideogram of both diploid and allopolyploid species into a single image file
KaryoMeasure calculates a wide variety of karyotype parameters and asymmetry indices.
KaryoMeasure software is used for calculation of chromosomal and karyotypic parameters and to build idiograms. For this, a project is created at first, in which chromosome pictures are uploaded for karyotype analysis or idiogram generation via ‘Image’ button in menu bar. By this way, the pictures and upcoming activities on the pictures are automatically saved to the project so it is possible to continue analysis later after closing and reopening the project. Chromosomal and karyotypic parameters represented in Table 1, are extracted by KaryoMeasure. The nomenclature used for the description of type or morphology of monocentric chromosomes is that proposed by Levan et al. (1964) in which the chromosome type is defined based on mean of arm ratio (Table 2). Stebbin’s asymmetry index is according to Table 3.
Table 1. Chromosomal parameters and karyotypic asymmetry indices along with their formula that are extracted by KaryoMeasure software.
|
Reference |
Formula |
Chromosomal parameter or asymmetry index |
|---|---|---|
|
Chromosomal parameters |
||
|
|
AR = L/S |
Arm ratio |
|
|
CL = L + S |
Chromosome length |
|
|
S/L |
r-value |
|
|
RL% = (CL/∑CL)×100 |
Relative length of chromosome |
|
|
CI = S/CL |
Centromeric index |
|
(Levan et al., 1964) |
Defined Terms in Table 2 |
Chromosome type |
|
|
F% = (S/∑CL)×100 |
Form percentage of chromosome |
|
Karyotypic parameters or asymmetry indices |
||
|
|
HCL = ∑CL |
Total chromosome length of the haploid complement |
|
(Huziwara, 1962) |
TF% = (∑S/∑CL)×100 |
Total form percentage |
|
(Stebbins, 1971) |
A–C, 1-4 (Table 3) |
Stebbins asymmetry index |
|
(Arano, 1963) |
AsK% = (∑L/∑CL)×100 |
Arano index of karyotype asymmetry |
|
(Romero-Zarco, 1986) |
A1 = 1-[ /n] |
Intrachromosomal asymmetry index |
|
(Romero-Zarco, 1986) |
A2 = sCL/xCL |
Interchromosomal asymmetry index |
|
|
S% = (CLmin/CLmax)×100 |
Symmetry index |
|
|
xCI = ∑CI/n |
Mean centromeric index |
|
(Watanabe et al., 1999) |
|
Degree of karyotype asymmetry |
|
|
xCA = A×100 |
Mean Centromeric Asymmetry |
|
(Paszko, 2006) |
CVCL = (sCL/xCL)×100 = A2×100 |
Coefficient of variation of chromosome length |
|
(Paszko, 2006) |
CVCI = (sCI/xCI)×100 |
Coefficient of variation of centromeric index |
|
(Paszko, 2006) |
AI = (CVCL×CVCI)/100 |
Asymmetry Index |
L: Length of long arm, S: Length of short arm, i: homologous group number, s: standard deviation, x: mean, n: haploid chromosome number of an individual or a taxon.
Table 2. Nomenclature of chromosomes based on Levan et al. 1964.
|
CI × 100 |
Arm ratio |
Centromeric position |
Term |
|---|---|---|---|
|
50 |
1 |
Median point |
M |
|
50-39.5 |
1-1.7 |
Median region |
m |
|
39.5-25 |
1.7-3 |
Submedian region |
sm |
|
25-12.5 |
3-7 |
Subterminal region |
st |
|
12.5-0 |
7-∞ |
Terminal region |
t |
|
0 |
∞ |
Terminal point |
T |
Table 3. The classification of karyotypes in relation to their degree of asymmetry according to Stebbins (1971).
|
Ratio |
Proportion of chromosomes with arm ratio < 2 |
|||
|---|---|---|---|---|
|
1.00 (1) |
0.99–0.51 (2) |
0.50–0.01 (3) |
0.00 (4) |
|
|
< 2 (A) 2 – 4 (B) > 4 (C) |
1A 1B 1C |
2A 2B 2C |
3A 3B 3C |
4A 4B 4C |
The chromosomal and karyotypic parameters are extracted after click-wise tracing of the chromosomes in KaryoMeasure. After that, all the parameters are automatically stored in a text file in the output folder of the project. The output text file include karyotypic parameters, chromosomal parameters and raw data which can be opened in Excel software as well. KaryoMeasure calculates mean and standard deviation of chromosomal parameters for all chromosomes of the same homologous group. These homologous chromosomes may be from one image or may belong to different images already opened in the project.
Bug reports may be submitted by email at the above address.