Chromosomes of Iberian Leuciscinae (Cyprinidae) Revisited: Evidence of Genome Restructuring in Homoploid Hybrids Using Dual-Color FISH and CGH

Abstract

Iberian Leuciscinae have been used in many studies as models to explore topics such as hybridization, allopolyploidy, modes of reproduction, and evolution. This article focuses on the contribution of cytogenomics to foster research in this group of cyprinid fish. Conventional and molecular banding results were reviewed, facilitating comparative analysis between nase and chub taxa inhabiting Portuguese freshwaters. Hybridization is known to occur within both Chondrostoma s.l. and Squalius genera although polyploidy has only been reported in the latter; the reasons behind such differential genome flexibility remain unidentified. FISH tools allowed recognizing additional chromosome markers, confirming NOR polymorphism and distinguishing species and their hybrids. Recombination and genome instability were detected in homoploid and polyploid hybrid genomes supporting active NOR transposition. However, the multiplication of rDNAs in these species does not seem to be associated with Rex3 retroelement, though hybrids were not surveyed. CGH and GISH allowed reaffirming the hybrid origin of S. alburnoides and confirming that the conservative karyotype patterns within Iberian leuciscines are restricted to the macrostructure. Current data also support the usefulness of mapping repetitive DNAs, especially for nonmodel compact genomes with less variable karyotypes and sequence data resources unavailable, like in many cyprinid lineages.

Dynamics of tandemly repeated DNA sequences during evolution of diploid and tetraploid botiid loaches (Teleostei: Cobitoidea: Botiidae)

“…In most fishes [ 104 – 106 ], including other loach families [ 51 – 53 , 55 ] the ancestral diploid pattern appears to be one pair of NOR/45S rDNA sites and the emerging information suggest similar scenario for U2 snDNA. In 5S rDNA, however, the situation has been found to be too variable and complex to reconstruct the ancestral situation ([ 106 , 107 ]; for examples in loaches and cypriniform polyploids, see: [ 30 , 33 , 50 , 53 , 55 , 108 ]). Contrary to expectations, our present results show that the number of 45S rDNA signals range from two to six in diploid botiids, thereby exceeding frequently the expected number.…”

Using asexual vertebrates to study genome evolution and animal physiology: Banded (Fundulus diaphanus) x Common Killifish (F. heteroclitus) hybrid lineages as a model system

“…In the following section, we review what is known about Fundulus diaphanus x F. heteroclitus asexual lineages, present some preliminary results from our laboratories, and discuss future research goals. We do not focus extensively on other asexual fishes, so we refer interested readers to reviews by Arai and Fujimoto (2013), Avise (2008, 2012, 2015), Lampert (2009), Lampert and Schartl (2008), Lamatsch and Stöck (2009), and Vrijenhoek (1994), as well as some of the recent research on asexual Poeciliidae (Alberici da Barbiano, Gompert, Aspbury, Gabor, & Nice, 2013; Gabor, Barbiano, & Aspbury, 2013; Schedina, Groth, Schlupp, & Tiedemann, 2018; Schlupp, Riesch, & Tobler, 2007; Stöck, Lampert, Möller, Schlupp, & Schartl, 2010; Warren et al, 2018), Hexagrammidae (e.g., Munehara, Horita, Kimura‐Kawaguchi, & Yamazaki, 2016; Suzuki, Miyake, Arai, & Munehara, 2019), Cyprinidae [ Carassius (Gui & Zhou, 2010; Jiang et al, 2013; Li et al, 2018), Chrosomus (Lafond et al., 2019; Leung & Angers, 2018; Leung et al, 2016, 2018; Mee, 2014; Mee, Brauner, & Taylor, 2011; Mee & Taylor, 2012; Vergilino, Leung, & Angers, 2016), S qualius alburnoides (Collares‐Pereira & Coelho, 2010; Collares‐Pereira, Matos, Morgado‐Santos, & Coelho, 2013; Morgado‐Santos et al., 2017; Pereira, Ráb, & Collares‐Pereira, 2013)], Misgurnus anguillicaudatus (e.g., Kuroda et al., 2018; Kuroda, Fujimoto, Murakami, Yamaha, & Arai, 2019; Kwan, Ko, Jeon, Kim, & Won, 2019; Yamada et al., 2015) and Cobitius spp. (Choleva et al., 2012; Cunha, Doadrio, Abrantes, & Coelho, 2011; Janko et al., 2012, 2018; Ko, Yoon, Kim, & Park, 2015; Majtánová et al., 2016) for further information.…”

“…This is because (a) they are gynogens, meaning they will have genetically identical offspring barring new mutation, unlike hybridogens [e.g., Poeciliopsis (Schultz, 1969), Hexagrammos (Suzuki, Arai, & Munehara, 2017), and Hypseleotris spp. (Schmidt et al, 2011)], (b) they are mainly diploid, facilitating genomic studies hoping to disentangle the effects of ploidy and hybridization‐induced asexuallity, unlike Carassius gynogenic triploid clones (Gui & Zhou, 2010) and many triploid gynogenetic Cobitis lineages (Majtánová et al., 2016), (c) they are externally fertilized, unlike the livebearing Poecillidae clones ( Poeciliopsis and Poecilia ), facilitating controlled laboratory breeding, and (d) their gynogenetic mode of inheritance appears to be more stable than some other clonal fish species [e.g., Chrosomus (Dawley et al., 1987), Squalius alburnoides (Pereira et al., 2013), Misgurnusis (Kuroda et al., 2019)]. Furthermore, there is a great deal of information about Fundulus spp.…”

Chromosomes of Asian Cyprinid Fishes: Genomic Differences in Conserved Karyotypes of ‘Poropuntiinae’ (Teleostei, Cyprinidae)

“…Molecular cytogenetics have emerged as an essential tool for describing evolutionary patterns, particularly in clades where species maintain a shared diploid number. The abundance and the chromosomal location of the repetitive DNA fraction change significantly between genomes of closely related species, and these variations are generally species-specific [ 17 ]. In this context, comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH) mapping of repetitive DNAs were extensively used in teleost chromosomal research [ 18 , 19 , 20 , 21 , 22 , 23 ].…”