Evolution of Tandemly Arranged Repetitive DNAs in Three Species of Cyprinoidei with Different Ploidy Levels

Abstract

Polyploid species represent a challenge for both cytogenetic and genomic studies due to their high chromosome numbers and the morphological similarity between their paralogous chromosomes. This paper describes the use of low-coverage high-throughput sequencing to identify the 14 most abundant tandemly arranged repetitive elements in the paleotetraploid genome of the crucian carp (Carassius carassius, 2n = 100). These repetitive elements were then used for molecular cytogenetic studies of a closely related functionally triploid form of the Prussian carp (Carassius gibelio, 3n = 150 + Bs) and a relatively distant diploid species, the tench (Tinca tinca, 2n = 48). According to their distribution on the chromosomes of the 3 aforementioned species, the repetitive elements here identified can be divided into 5 groups: (1) those specific to a single genomic locus in both Carassius species, despite the recent carp-specific genome duplication; (2) those located in a single genomic locus of T. tinca, but amplified in one or both Carassius species; (3) those massively amplified in the B chromosomes of C. gibelio; (4) those located in a single locus in C. gibelio, but amplified in many blocks in C. carassius; and (5) those located in multiple pericentromeric loci in both Carassius species. Our data indicate that some of the repetitive elements are highly conserved in cyprinoid species and may serve as good cytogenetic and genomic markers for discriminating paralogous chromosomes, while others are evolutionarily recent, and their amplification may be related to the last whole-genome duplication event.

Cytogenetic Analysis of the Fish Genus Carassius Indicates Divergence, Fission, and Segmental Duplication as Drivers of Tandem Repeat and Microchromosome Evolution

“…The presence of clearly highlighted chromosomes indicates that the probe and competitor DNA collaborated properly and that nonspecific hybridization of the probe to repetitive regions was inhibited. The Carassius microchromosomes did not show a high degree of heterochromatization, as is typical for B chromosomes, which are sometimes considered to be microchromosomes ( Bishani et al 2021 ; Gvoždík et al 2023 ). Our finding is consistent with a high gene content and a low proportion of a repetitive fraction within the microchromosomes.…”

Identification of Iguania Ancestral Syntenic Blocks and Putative Sex Chromosomes in the Veiled Chameleon (Chamaeleo calyptratus, Chamaeleonidae, Iguania)

“…Identification of repetitive DNA clusters was carried out using RepeatExplorer2 [ 59 ] and TAREAN 2.3.8 tools [ 60 ] as described previously [ 61 ]. Only tandem repeats predicted by TAREAN were localized in metaphase chromosomes of C. calyptratus .…”

“…Primers were designed to cover the largest part of the repetitive unit with fragments ranging in size from 38 (CCA_s4) to 469 bp (CCA_s1). PCR amplification was performed as described previously [ 61 ]. The annealing temperature was 60 °C for all primer pairs.…”

Chromosomes of Asian cyprinid fishes: Novel insight into the chromosomal evolution of Labeoninae (Teleostei, Cyprinidae)

“…This suggests that pericentric inversions played a significant role in their karyotype evolution. In this context, molecular cytogenetics emerges as a crucial tool to identify the karyotype dynamics in fishes, as has already been demonstrated for several Cyprinidae species [11][12][13][14][15][16][17][18]. Indeed, the mapping of repetitive sequences, which make up the majority of the eukaryotic genome, is widely utilized in fish cytogenetics and has a significant potential to further understand the origin process of sex and B chromosomes, as well as karyotype differentiation [19].…”