| Summary: | The widely distributed ray-finned fish genus <i>Carassius</i> is very well known due to its unique biological characteristics such as polyploidy, clonality, and/or interspecies hybridization. These biological characteristics have enabled <i>Carassius</i> species to be successfully widespread over relatively short period of evolutionary time. Therefore, this fish model deserves to be the center of attention in the research field. Some studies have already described the <i>Carassius</i> karyotype, but results are inconsistent in the number of morphological categories for individual chromosomes. We investigated three focal species: <i>Carassius auratus</i>, <i>C. carassius</i> and <i>C. gibelio</i> with the aim to describe their standardized diploid karyotypes, and to study their evolutionary relationships using cytogenetic tools. We measured length (<inline-formula><math display="inline"><semantics><mrow><mi>q</mi><mo>+</mo><mi>p</mi></mrow></semantics></math></inline-formula><inline-formula><math display="inline"><semantics><mrow><mi>l</mi><mi>e</mi><mi>n</mi><mi>g</mi><mi>t</mi><mi>h</mi></mrow></semantics></math></inline-formula>) of each chromosome and calculated centromeric index (<i>i</i> value). We found: (i) The relationship between <inline-formula><math display="inline"><semantics><mrow><mi>q</mi><mo>+</mo><mi>p</mi></mrow></semantics></math></inline-formula><inline-formula><math display="inline"><semantics><mrow><mi>l</mi><mi>e</mi><mi>n</mi><mi>g</mi><mi>t</mi><mi>h</mi></mrow></semantics></math></inline-formula> and <i>i</i> value showed higher similarity of <i>C. auratus</i> and <i>C. carassius</i>. (ii) The variability of <i>i</i> value within each chromosome expressed by means of the first quartile (<inline-formula><math display="inline"><semantics><msub><mi>Q</mi><mn>1</mn></msub></semantics></math></inline-formula>) up to the third quartile (<inline-formula><math display="inline"><semantics><msub><mi>Q</mi><mn>3</mn></msub></semantics></math></inline-formula>) showed higher similarity of <i>C. carassius</i> and <i>C. gibelio</i>. (iii) The fluorescent in situ hybridization (FISH) analysis revealed higher similarity of <i>C. auratus</i> and <i>C. gibelio</i>. (iv) Standardized karyotype formula described using <inline-formula><math display="inline"><semantics><mrow><mi>m</mi><mi>e</mi><mi>d</mi><mi>i</mi><mi>a</mi><mi>n</mi></mrow></semantics></math></inline-formula> value (<inline-formula><math display="inline"><semantics><msub><mi>Q</mi><mn>2</mn></msub></semantics></math></inline-formula>) showed differentiation among all investigated species: <i>C. auratus</i> had 24 metacentric (<i>m</i>), 40 submetacentric (<inline-formula><math display="inline"><semantics><mrow><mi>s</mi><mi>m</mi></mrow></semantics></math></inline-formula>), 2 subtelocentric (<inline-formula><math display="inline"><semantics><mrow><mi>s</mi><mi>t</mi></mrow></semantics></math></inline-formula>), 2 acrocentric (<i>a</i>) and 32 telocentric (<i>T</i>) chromosomes (<inline-formula><math display="inline"><semantics><mrow><mn>24</mn><mi>m</mi><mo>+</mo><mn>40</mn><mi>s</mi><mi>m</mi><mo>+</mo><mn>2</mn><mi>s</mi><mi>t</mi><mo>+</mo><mn>2</mn><mi>a</mi><mo>+</mo><mn>32</mn><mi>T</mi></mrow></semantics></math></inline-formula>); <i>C. carassius</i>: <inline-formula><math display="inline"><semantics><mrow><mn>16</mn><mi>m</mi><mo>+</mo><mn>34</mn><mi>s</mi><mi>m</mi><mo>+</mo><mn>8</mn><mi>s</mi><mi>t</mi><mo>+</mo><mn>42</mn><mi>T</mi></mrow></semantics></math></inline-formula>; and <i>C. gibelio</i>: <inline-formula><math display="inline"><semantics><mrow><mn>16</mn><mi>m</mi><mo>+</mo><mn>22</mn><mi>s</mi><mi>m</mi><mo>+</mo><mn>10</mn><mi>s</mi><mi>t</mi><mo>+</mo><mn>2</mn><mi>a</mi><mo>+</mo><mn>50</mn><mi>T</mi></mrow></semantics></math></inline-formula>. (v) We developed R scripts applicable for the description of standardized karyotype for any other species. The diverse results indicated unprecedented complex genomic and chromosomal architecture in the genus <i>Carassius</i> probably influenced by its unique biological characteristics which make the study of evolutionary relationships more difficult than it has been originally postulated.
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