Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet<b> </b>(<b><i>Acipenser ruthenus</i></b>)

Abstract

Acipenseriformes represent a phylogenetically basal clade of ray-finned fish characterized by unusual genomic traits, including paleopolyploid states of extant genomes with high chromosome numbers and slow rates of molecular evolution. Despite a high interest in this fish group, only a limited number of studies have been accomplished on the isolation and characterization of repetitive DNA, karyotype standardization is not yet complete, and sex chromosomes are still to be identified. Here, we applied next-generation sequencing and cluster analysis to characterize major fractions of sterlet (Acipenser ruthenus) repetitive DNA. Using FISH, we mapped 16 tandemly arranged sequences on sterlet chromosomes and found them to be unevenly distributed in the genome with a tendency to cluster in particular regions. Some of the satellite DNAs might be used as specific markers to identify individual chromosomes and their paralogs, resulting in the unequivocal identification of at least 18 chromosome pairs. Our results provide an insight into the characteristic genomic distribution of the most common sterlet repetitive sequences. Biased accumulation of repetitive DNAs in particular chromosomes makes them especially interesting for further search for cryptic sex chromosomes. Future studies of these sequences in other acipenserid species will provide new perspectives regarding the evolution of repetitive DNA within the genomes of this fish order.

Next Generation Sequencing of Chromosome-Specific Libraries Sheds Light on Genome Evolution in Paleotetraploid Sterlet (Acipenser ruthenus)

“…Following the previously-proposed nomenclature [ 14 ], the 10 largest chromosomes in the sterlet karyotype were referred to as macrochromosomes; the chromosomes ARUT11–30 were referred to as mid-sized chromosomes, and ARUT31–60 (highly enriched with repetitive DNA) were referred to as microchromosomes ( Figure 1 ).…”

“…While one of the parent genomes remains conserved, the chromosome of the second subgenome evolved much faster and underwent multiple rearrangements and pseudogenization [ 8 ]. Although we still do not know whether auto- or allo- polyploidization took place in the sturgeon ancestor, an uneven accumulation of tandemly-arranged repetitive elements took place on paralogous chromosomes [ 14 ]. It is noteworthy that chromosomes of different sizes underwent specific evolutionary pathways: the largest karyotype elements seem to be much more conserved in sterlet evolution than the smaller elements, and a similar process has been described in birds [ 38 ] and reptiles [ 39 , 40 ].…”

“…It is noteworthy that chromosomes of different sizes underwent specific evolutionary pathways: the largest karyotype elements seem to be much more conserved in sterlet evolution than the smaller elements, and a similar process has been described in birds [ 38 ] and reptiles [ 39 , 40 ]. Accumulation of repetitive elements was also different in various sterlet chromosome groups with large chromosomes accumulating interstitial repetitive blocks and small chromosomes enriched in dispersed repeats and accumulating pericentromeric tandem repetitive sequences [ 14 ].…”

“…The genes involved in embryo development regulation (such as Hox genes) are especially interesting for this purpose, because they are often retained after duplications and receive new functions. Besides, it was previously shown that fluorescence in situ hybridization (FISH) with chromosome-specific probes [ 12 , 13 ] and repetitive elements [ 8 , 14 ] also might be very useful for detecting extended paralogous regions in polyploids. Moreover, the chromosome-specific libraries used for probe generation can be sequenced and aligned to the reference genome [ 15 ], providing information on gene content and revealing syntenic blocks.…”

Chromosomes of Asian cyprinid fishes: cytogenetic analysis of two representatives of small paleotetraploid tribe Probarbini

“…However, studies performing cytogenetic mapping of e.g. several markers such as Hox genes or satellite DNAs, in conjunction with recent advances in genome sequencing and bioinformatics, are also starting to be implemented typically in non-teleost acipenserids [60, 61]. Regarding rDNA profiles, they proved useful especially in deciphering the origin of rather recent homoploid or polyploid hybrids, because the intermediate pattern might help to identify the parental species [62–66].…”