Measurement of Chromosomal Arms and FISH Reveal Complex Genome Architecture and Standardized Karyotype of Model Fish, Genus <i>Carassius</i>

• Main Authors: Martin Knytl, Nicola Reinaldo Fornaini
• Format: Article
• Language: English
• Published: MDPI AG 2021-09-01
• Series: Cells
• Subjects: chromosome; karyogram; in situ hybridization; <i>i</i> value; <i>q</i>/<i>p</i> arm ratio; <i>Carassius auratus</i>
• Online Access: https://www.mdpi.com/2073-4409/10/9/2343

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 xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mi>q</mi><mo>+</mo><mi>p</mi></mrow></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" 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 xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mi>q</mi><mo>+</mo><mi>p</mi></mrow></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" 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 xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mi>Q</mi><mn>1</mn></msub></semantics></math></inline-formula>) up to the third quartile (<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" 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 xmlns="http://www.w3.org/1998/Math/MathML" 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 xmlns="http://www.w3.org/1998/Math/MathML" 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 xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mi>s</mi><mi>m</mi></mrow></semantics></math></inline-formula>), 2 subtelocentric (<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" 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 xmlns="http://www.w3.org/1998/Math/MathML" 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 xmlns="http://www.w3.org/1998/Math/MathML" 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 xmlns="http://www.w3.org/1998/Math/MathML" 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.