Repetitive DNA in the Catfish Genome: rDNA, Microsatellites, and Tc1-Mariner Transposon Sequences in Imparfinis Species (Siluriformes, Heptapteridae)

Abstract

Physical mapping of repetitive DNA families in the karyotypes of fish is important to understand the organization and evolution of different orders, families, genera, or species. Fish in the genus Imparfinis show diverse karyotypes with various diploid numbers and ribosomal DNA (rDNA) locations. Here we isolated and characterized Tc1-mariner nucleotide sequences from Imparfinis schubarti, and mapped their locations together with 18S rDNA, 5S rDNA, and microsatellite probes in Imparfinis borodini and I. schubarti chromosomes. The physical mapping of Tc1/Mariner on chromosomes revealed dispersed signals in heterochromatin blocks with small accumulations in the terminal and interstitial regions of I. borodini and I. schubarti. Tc1/Mariner was coincident with rDNA chromosomes sites in both species, suggesting that this transposable element may have participated in the dispersion and evolution of these sequences in the fish genome. Our analysis suggests that different transposons and microsatellites have accumulated in the I. borodini and I. schubarti genomes and that the distribution patterns of these elements may be related to karyotype evolution within Imparfinis.

Evolutionary insights in Amazonian turtles (Testudines, Podocnemididae): co-location of 5S rDNA and U2 snRNA and wide distribution of Tc1/Mariner

“…Heterochromatic accumulations of Tc1/Mariner were also previously reported in some fish (Ayres-Alves et al, 2017;Gouveia et al, 2017). This may indicate that there is a selection pressure against inserting TEs into euchromatin; this could reflect ectopic exchanges (Oliveira et al, 2013) and the low recombination rates of these regions, which reduces insertion damage (Delaurière et al, 2009).…”

“…The largest group of Class II eukaryotic transposons is composed of members related to the Mariner and Tc1 families (Benjamin et al, 2007). In terms of an organizational pattern, Tc1/Mariner is described as being predominantly dispersed along the karyotypes of several species (Schemberger et al, 2016); however, accumulations have been reported in heterochromatic regions (Ayres-Alves et al, 2017), terminal regions (Schemberger et al, 2016;Gouveia et al, 2017), and sex chromosomes (possibly caused by lack of recombination) (Schemberger et al, 2016). In addition, co-location of rDNA sites with Tc1/Mariner clusters has been observed and it has been proposed that the transposon can participate in rDNA dispersion through recombination events and/or transposition-derived mobilization (Ayres-Alves et al, 2017;Gouveia et al, 2017).…”

Establishment and Characterization of Canine Mammary Gland Carcinoma Cell Lines With Vasculogenic Mimicry Ability in vitro and in vivo

“…Subsequent washes and centrifugations were performed at 4 • C, and the cells were fixed to slides and stained using the Wright-Giemsa staining method for karyotype assembly. Seventy different images were captured from each cell culture (n = 10) and at least 20 metaphases of each culture were analyzed, according to Gouveia et al (34).…”

The Diversity of Sequence and Chromosomal Distribution of New Transposable Element-Related Segments in the Rye Genome Revealed by FISH and Lineage Annotation

“…In addition, due to the complex organization of TEs and the assembly problem caused by them, the whole genome-wide analysis may not accurately reflect the TE distribution and abundance for any region of the genome ( Bergman et al, 2006 ), especially for genomes haven’t been successfully assembled. The fluorescence in situ hybridization (FISH) technique, which was developed by Langer-Safer et al (1982) , was popular for physical mapping of high copy number sequences clustered in plant genomes ( Iwata-Otsubo et al, 2016 ; Gouveia et al, 2017 ). Thus the FISH technique provided an efficient tool to locate the hardly assembled TE sequences on chromosomes of rye ( Li et al, 2016 ).…”