TY - JOUR
T1 - A long-term conserved satellite DNA that remains unexpanded in several genomes of Characiformes fish is actively transcribed
AU - Dos Santos, Rodrigo Zeni
AU - Calegari, Rodrigo Milan
AU - Silva, Duílio Mazzoni Zerbinato de Andrade
AU - Ruiz-Ruano, Francisco J.
AU - Melo, Silvana
AU - Oliveira, Claudio
AU - Foresti, Fausto
AU - Uliano-Silva, Marcela
AU - Porto-Foresti, Fábio
AU - Utsunomia, Ricardo
PY - 2021/2/3
Y1 - 2021/2/3
N2 - Eukaryotic genomes contain large amounts of repetitive DNA sequences, such as tandemly repeated satellite DNAs (satDNAs). These sequences are highly dynamic and tend to be genus- or species-specific due to their particular evolutionary pathways, although there are few unusual cases of conserved satDNAs over long periods of time. Here, we used multiple approaches to reveal that an satDNA named CharSat01-52 originated in the last common ancestor of Characoidei fish, a superfamily within the Characiformes order, ∼140-78 Ma, whereas its nucleotide composition has remained considerably conserved in several taxa. We show that 14 distantly related species within Characoidei share the presence of this satDNA, which is highly amplified and clustered in subtelomeric regions in a single species (Characidium gomesi), while remained organized as small clusters in all the other species. Defying predictions of the molecular drive of satellite evolution, CharSat01-52 shows similar values of intra- and interspecific divergence. Although we did not provide evidence for a specific functional role of CharSat01-52, its transcriptional activity was demonstrated in different species. In addition, we identified short tandem arrays of CharSat01-52 embedded within single-molecule real-time long reads of Astyanax paranae (536 bp-3.1 kb) and A. mexicanus (501 bp-3.9 kb). Such arrays consisted of head-to-tail repeats and could be found interspersed with other sequences, inverted sequences, or neighbored by other satellites. Our results provide a detailed characterization of an old and conserved satDNA, challenging general predictions of satDNA evolution.
AB - Eukaryotic genomes contain large amounts of repetitive DNA sequences, such as tandemly repeated satellite DNAs (satDNAs). These sequences are highly dynamic and tend to be genus- or species-specific due to their particular evolutionary pathways, although there are few unusual cases of conserved satDNAs over long periods of time. Here, we used multiple approaches to reveal that an satDNA named CharSat01-52 originated in the last common ancestor of Characoidei fish, a superfamily within the Characiformes order, ∼140-78 Ma, whereas its nucleotide composition has remained considerably conserved in several taxa. We show that 14 distantly related species within Characoidei share the presence of this satDNA, which is highly amplified and clustered in subtelomeric regions in a single species (Characidium gomesi), while remained organized as small clusters in all the other species. Defying predictions of the molecular drive of satellite evolution, CharSat01-52 shows similar values of intra- and interspecific divergence. Although we did not provide evidence for a specific functional role of CharSat01-52, its transcriptional activity was demonstrated in different species. In addition, we identified short tandem arrays of CharSat01-52 embedded within single-molecule real-time long reads of Astyanax paranae (536 bp-3.1 kb) and A. mexicanus (501 bp-3.9 kb). Such arrays consisted of head-to-tail repeats and could be found interspersed with other sequences, inverted sequences, or neighbored by other satellites. Our results provide a detailed characterization of an old and conserved satDNA, challenging general predictions of satDNA evolution.
KW - neotropical fish
KW - repetitive DNA
KW - satDNA
KW - tandem repeats
UR - http://www.scopus.com/inward/record.url?scp=85102153723&partnerID=8YFLogxK
U2 - 10.1093/gbe/evab002
DO - 10.1093/gbe/evab002
M3 - Article
C2 - 33502491
AN - SCOPUS:85102153723
SN - 1759-6653
VL - 13
JO - Genome Biology and Evolution
JF - Genome Biology and Evolution
IS - 2
M1 - evab002
ER -