Introduction: Eukaryotic genomes are composed of simple, repetitive sequences, including satellite DNAs (satDNA), which are noncoding sequences arranged in tandem arrays. These sequences play a crucial role in genomic functions and innovations, influencing processes such as the maintenance of nuclear material, the formation of heterochromatin and the differentiation of sex chromosomes. In this genomic era, advances in next-generation sequencing and bioinformatics tools have facilitated the exhaustive cataloging of repetitive elements in genomes, particularly in non-model species. This study focuses on the satDNA content of Ancistrus sp., a diverse species of fish from the Loricariidae family. The genus Ancistrus shows significant karyotypic evolution, with extensive variability from the ancestral diploid number. Methods: By means of bioinformatic approaches, 40 satDNA families in Ancistrus sp., constituting 5.19% of the genome were identified. Analysis of the abundance and divergence landscape revealed diverse profiles, indicating recent amplification and homogenization of these satDNA sequences. Results: The most abundant satellite, AnSat1-142, constitutes 2.1% of the genome, while the least abundant, AnSat40-52, represents 0.0034%. The length of the monomer repeat varies from 16 to 142 base pairs, with an average length of 61 bp. These results contribute to understanding the genomic dynamics and evolution of satDNAs in Ancistrus sp. Conclusion: The study underscores the variability of satDNAs between fish species and provides valuable information on chromosome organization and the evolution of repetitive elements in non-model organisms.

1.
Thakur
J
,
Packiaraj
J
,
Henikoff
S
.
Sequence, chromatin and evolution of satellite DNA
.
Int J Mol Sci
.
2021
;
22
(
9
):
4309
.
2.
López-Flores
I
,
Garrido-Ramos
M
.
The repetitive DNA content of eukaryotic genomes
.
Genome Dyn
.
2012
;
7
:
1
28
.
3.
Plohl
M
,
Mestrovic
N
,
Mravinac
B
.
Satellite DNA evolution
.
Genome Dyn
.
2012
;
7
:
126
52
.
4.
dos Santos
RZ
,
Calegari
RM
,
Silva
DMZA
,
Ruiz-Ruano
FJ
,
Melo
S
,
Oliveira
C
, et al
.
A long-term conserved satellite DNA that remains unexpanded in several genomes of Characiformes fish is actively transcribed
.
Genome Biol Evol
.
2021
;
13
(
2
):
evab002
.
5.
Garrido-Ramos
MA
.
Satellite DNA in plants: more than just rubbish
.
Cytogenet Genome Res
.
2015
;
146
(
2
):
153
70
.
6.
Kuhn
GCS
.
Satellite DNA transcripts have diverse biological roles in Drosophila
.
Heredity
.
2015
;
115
(
1
):
1
2
.
7.
Ruiz-Ruano
FJ
,
López-León
MD
,
Cabrero
J
,
Camacho
JPM
.
High-throughput analysis of the satellitome illuminates satellite DNA evolution
.
Sci Rep
.
2016
;
6
(
1
):
28333
.
8.
Silva
DMZA
,
Utsunomia
R
,
Ruíz-Ruano
FJ
,
Daniel
SN
,
Porto-Foresti
F
,
Hashimoto
DT
, et al
.
High-throughput analysis unveils a highly shared satellite DNA library among three species of fish genus Astyanax
.
Sci Rep
.
2017
;
7
(
1
):
12726
.
9.
Miga
KH
,
Koren
S
,
Rhie
A
,
Vollger
MR
,
Gershman
A
,
Bzikadze
A
, et al
.
Telomere-to-telomere assembly of a complete human X chromosome
.
Nature
.
2020
;
585
(
7823
):
79
84
.
10.
Díaz-Castillo
C
.
Junk DNA contribution to evolutionary capacitance can drive species dynamics
.
Evol Biol
.
2016
;
44
(
2
):
190
205
.
11.
Lower
SE
,
Dion-Côté
AM
,
Clark
AG
,
Barbash
DA
.
Special issue: repetitive DNA sequences
.
Genes
.
2019
;
10
(
11
):
896
.
12.
Martins
C
.
Chromosomes and repetitive DNAs: a contribution to the knowledge of the fish genome
. In:
Pisano
E
,
Ozouf-Costaz
C
,
Foresti
F
,
Kapoor
B
, editors.
Fish cytogenetics
;
2007
.
13.
Traynor
S
,
Møllegaard
NE
,
Jørgensen
MG
,
Brückmann
NH
,
Pedersen
CB
,
Terp
MG
, et al
.
Remodeling and destabilization of chromosome 1 pericentromeric heterochromatin by SSX proteins
.
Nucleic Acids Res
.
2019
;
47
(
13
):
6668
84
.
14.
Otake
K
,
Ohzeki
J
,
Shono
N
,
Kugou
K
,
Okazaki
K
,
Nagase
T
, et al
.
CENP-B creates alternative epigenetic chromatin states permissive for CENP-A or heterochromatin assembly
.
J Cell Sci
.
2020
;
133
(
15
):
jcs243303
.
15.
Utsunomia
R
,
Ruiz-Ruano
FJ
,
Silva
DMZA
,
Serrano
ÉA
,
Rosa
IF
,
Scudeler
PES
, et al
.
A glimpse into the satellite DNA library in characidae fish (Teleostei, Characiformes)
.
Front Genet
.
2017
;
8
:
103
.
16.
Vozdova
M
,
Kubickova
S
,
Cernohorska
H
,
Fröhlich
J
,
Martínková
N
,
Rubes
J
.
Sequence analysis and FISH mapping of four satellite DNA families among cervidae
.
Genes
.
2020
;
11
(
5
):
584
.
17.
Parise-Maltempi
PP
,
Da Silva
E
,
Rens
W
,
Dearden
FL
,
O’Brien
PCM
,
Trifonov
VA
, et al
.
Comparative analysis of sex chromosomes in Leporinus species (Teleostei, Characiformes) using chromosome painting
.
BMC Genet
.
2013
;
14
(
1
):
60
.
18.
Plohl
M
,
Meštrović
N
,
Mravinac
B
.
Centromere identity from the DNA point of view
.
Chromosoma
.
2014
;
123
(
4
):
313
25
.
19.
Pucci
MB
,
Barbosa
P
,
Nogaroto
V
,
Almeida
MC
,
Artoni
RF
,
Pansonato-Alves
JC
, et al
.
Population differentiation and speciation in the genus Characidium (Characiformes: Crenuchidae): effects of reproductive and chromosomal barriers
.
Biol J Linn Soc
.
2014
;
111
(
3
):
541
53
.
20.
Jagannathan
M
,
Yamashita
YM
.
Function of junk: pericentromeric satellite DNA in chromosome maintenance
.
Cold Spring Harb Symp Quant Biol
.
2017
;
82
:
319
27
.
21.
Utsunomia
R
,
Silva
DMZA
,
Ruiz-Ruano
FJ
,
Goes
CAG
,
Melo
S
,
Ramos
LP
, et al
.
Satellitome landscape analysis of Megaleporinus macrocephalus (Teleostei, Anostomidae) reveals intense accumulation of satellite sequences on the heteromorphic sex chromosome
.
Sci Rep
.
2019
;
9
(
1
):
5856
.
22.
Crepaldi
C
,
Parise-Maltempi
PP
.
Heteromorphic sex chromosomes and their DNA content in fish: an insight through satellite DNA accumulation in Megaleporinus elongatus
.
Cytogenet Genome Res
.
2020
;
160
(
1
):
38
46
.
23.
da Silva
MJ
,
Fogarin Destro
R
,
Gazoni
T
,
Narimatsu
H
,
Pereira Dos Santos
PS
,
Haddad
C
, et al
.
Great abundance of satellite DNA in Proceratophrys (Anura, Odontophrynidae) revealed by genome sequencing
.
Cytogenet Genome Res
.
2020
;
160
(
3
):
141
7
.
24.
Ferretti
ABSM
,
Milani
D
,
Palacios-Gimenez
OM
,
Ruiz-Ruano
FJ
,
Cabral-de-Mello
DC
.
High dynamism for neo-sex chromosomes: satellite DNAs reveal complex evolution in a grasshopper
.
Heredity
.
2020
;
125
(
3
):
124
37
.
25.
Crepaldi
C
,
Martí
E
,
Gonçalves
ÉM
,
Martí
DA
,
Parise-Maltempi
PP
.
Genomic differences between the sexes in a fish species seen through satellite DNAs
.
Front Genet
.
2021
;
12
:
728670
.
26.
Hughes
SE
,
Hawley
RS
.
Heterochromatin: a rapidly evolving species barrier
.
PLoS Biol
.
2009
;
7
(
10
):
e1000233
.
27.
Camacho
J
,
Cabrero
J
,
López-León
MD
,
Martín-Peciña
M
,
Perfectti
F
,
Garrido-Ramos
MA
, et al
.
Satellitome comparison of two Oedipodine grasshoppers highlights the contingent nature of satellite DNA evolution
.
BMC Biol
.
2022
;
20
(
1
):
36
.
28.
João da Silva
M
,
Gazoni
T
,
Haddad
CFB
,
Parise-Maltempi
PP
.
Analysis in Proceratophrys boiei genome illuminates the satellite DNA content in a frog from the Brazilian Atlantic forest
.
Front Genet
.
2023
;
14
:
1101397
.
29.
Serrano-Freitas
ÉA
,
Silva
DMZA
,
Ruiz-Ruano
FJ
,
Utsunomia
R
,
Araya-Jaime
C
,
Oliveira
C
, et al
.
Satellite DNA content of B chromosomes in the characid fish Characidium gomesi supports their origin from sex chromosomes
.
Mol Genet Genomic
.
2020
;
295
(
1
):
195
207
.
30.
Suntronpong
A
,
Singchat
W
,
Kruasuwan
W
,
Prakhongcheep
O
,
Sillapaprayoon
S
,
Muangmai
N
, et al
.
Characterization of centromeric satellite DNAs (MALREP) in the Asian swamp eel (Monopterus albus) suggests the possible origin of repeats from transposable elements
.
Genomics
.
2020
;
112
(
5
):
3097
107
.
31.
Goes
CAG
,
Dos Santos
RZ
,
Aguiar
WRC
,
Alves
DCV
,
Silva
DMZA
,
Foresti
F
, et al
.
Revealing the satellite DNA history in Psalidodon and Astyanax characid fish by comparative satellitomics
.
Front Genet
.
2022
;
13
:
884072
.
32.
Kretschmer
R
,
Goes
CAG
,
Bertollo
LAC
,
Ezaz
T
,
Porto-Foresti
F
,
Toma
GA
, et al
.
Satellitome analysis illuminates the evolution of ZW sex chromosomes of Triportheidae fishes (Teleostei: characiformes)
.
Chromosoma
.
2022
;
131
(
1–2
):
29
45
.
33.
Santos da Silva
K
,
Glugoski
L
,
Vicari
MR
,
de Souza
ACP
,
Noronha
RCR
,
Pieczarka
JC
, et al
.
Chromosomal diversification in Ancistrus species (Siluriformes: Loricariidae) inferred from repetitive sequence analysis
.
Front Genet
.
2022
;
13
:
838462
.
34.
Goes
CAG
,
dos Santos
N
,
Rodrigues
PHM
,
Stornioli
JHF
,
Silva
AB
,
dos Santos
RZ
, et al
.
The satellite DNA catalogues of two serrasalmidae (Teleostei, Characiformes): conservation of general satDNA features over 30 million years
.
Genes
.
2022
;
14
(
1
):
91
.
35.
Fricke
R
,
Eschmeyer
W
,
Van Der Laan
R
.
Eschmeyer’s catalog of fishes: genera, species, references
.
2022
[cited 2022 Apr]; Available from: http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp.
36.
Fisch-Muller
S
.
Subfamily ancistrinae (armored catfishes)
. In:
Reis
R
,
Kullander
S
,
Ferraris
C
, editors.
Check list of the freshwater fishes of South and Central America
.
Edipucrs
;
2003
. p.
373
400
.
37.
Oliveira
RR
,
Feldberg
E
,
Anjos
MB
,
Zuanon
J
.
Karyotype characterization and ZZ/ZW sex chromosome heteromorphism in two species of the catfish genus Ancistrus Kner, 1854 (Siluriformes: Loricariidae) from the Amazon basin
.
Neotrop Ichthyol
.
2007
;
5
(
3
):
301
6
.
38.
de Oliveira
RR
,
Feldberg
E
,
dos Anjos
MB
,
Zuanon
J
.
Occurrence of multiple sexual chromosomes (XX/XY1Y2 and Z1Z1Z2Z2/Z1Z2W1W2) in catfishes of the genus Ancistrus (Siluriformes: Loricariidae) from the Amazon basin
.
Genetica
.
2008
;
134
(
2
):
243
9
.
39.
de Oliveira
RR
,
Feldberg
E
,
Dos Anjos
M
,
Zuanon
J
.
Mechanisms of chromosomal evolution and its possible relation to natural history characteristics in Ancistrus catfishes (Siluriformes: Loricariidae)
.
J Fish Biol
.
2009
;
75
(
9
):
2209
25
.
40.
Mariotto
S
,
Centofante
L
,
Miyazawa
CS
,
Bertollo
LAC
,
Moreira Filho
O
.
Chromosome polymorphism in Ancistrus cuiabae Knaack, 1999 (Siluriformes: Loricariidae: Ancistrini)
.
Neotrop Ichthyol
.
2009
;
7
(
4
):
595
600
.
41.
Mariotto
S
,
Centofante
L
,
Vicari
M
,
Artoni
R
,
Moreira-Filho
O
.
Chromosomal diversification in ribosomal DNA sites in Ancistrus Kner, 1854 (Loricariidae, Ancistrini) from three hydrographic basins of Mato Grosso, Brazil
.
Comp Cytogenet
.
2011
;
5
(
4
):
289
300
.
42.
Thums Konerat
J
,
Bueno
V
,
Margarido
VP
,
Portela-Castro
ALB
,
Martins-Santos
IC
.
Diversity of sex chromosome systems in Ancistrini (Loricariidae, Hypostominae): ZZ/ZW in Ancistrus taunayi Miranda Ribeiro, 1918
.
Cytogenet Genome Res
.
2015
;
146
(
4
):
306
10
.
43.
Ribeiro
MO
,
Noleto
RB
,
Lorscheider
CA
,
Porto
FE
,
Prizon
AC
,
Zawadzki
CH
, et al
.
Cytogenetic description of Ancistrus abilhoai (Siluriformes: Loricariidae) from Iguaçu River Basin, southern Brazil
.
Genet Mol Res
.
2015
;
14
(
2
):
4051
7
.
44.
Barros
AV
,
Wolski
MAV
,
Nogaroto
V
,
Almeida
MC
,
Moreira-Filho
O
,
Vicari
MR
.
Fragile sites, dysfunctional telomere and chromosome fusions: what is 5S rDNA role
.
Gene
.
2017
;
608
:
20
7
.
45.
Favarato
RM
,
Ribeiro
LB
,
Feldberg
E
,
Matoso
DA
.
Chromosomal mapping of transposable elements of the rex family in the bristlenose catfish, Ancistrus (Siluriformes, Loricariidae), from the amazonian region
.
J Hered
.
2017
;
108
(
3
):
254
61
.
46.
Glugoski
L
,
Deon
G
,
Schott
S
,
Vicari
MR
,
Nogaroto
V
,
Moreira-Filho
O
.
Comparative cytogenetic analyses in Ancistrus species (Siluriformes: Loricariidae)
.
Neotrop Ichthyol
.
2020
;
18
(
2
).
47.
Alves
AL
,
Oliveira
C
,
Foresti
F
.
Karyotype variability in eight species of the subfamilies Loricariinae and Ancistrinae (Teleostei, Siluriformes, Loricariidae)
.
Caryologia
.
2003
;
56
(
1
):
57
63
.
48.
Alves
AL
,
Oliveira
C
,
Nirchio
M
,
Granado
A
,
Foresti
F
.
Karyotypic relationships among the tribes of Hypostominae (Siluriformes: Loricariidae) with description of XO sex chromosome system in a Neotropical fish species
.
Genetica
.
2006
;
128
(
1–3
):
1
9
.
49.
Mariotto
S
,
Artoni
RF
,
Miyazawa
CS
.
Occurrence of sexual chromosome, of the type ZZ/ZW, in Ancistrus cf. dubius (Loricariidae, Ancistrinae) of the Paraguay River Basin, Mato Grosso, Brazil
.
Caryologia
.
2004
;
57
(
4
):
327
31
.
50.
Mariotto
S
,
Miyazawa
CS
.
Ancistrus cf. dubius (Siluriformes, Ancistrinae), a complex of species. 1. Chromosomic characterization of four populations and occurrence of sexual chromosomes of type XX/XY, in the Pantanal basin of Mato Grosso, Brazil
.
Caryologia
.
2006
;
59
(
4
):
299
304
.
51.
Mariotto
S
,
Centofante
L
,
Moreira-Filho
O
.
Diversity and chromosomal evolution in the genus Ancistrus Kner, 1854 (Loricariidae: Ancistrini) from three hydrographic basins of Mato Grosso state, Brazil
.
Neotrop Ichthyol
.
2013
;
11
(
1
):
125
31
.
52.
Prizon
AC
,
Bruschi
DP
,
Borin-Carvalho
LA
,
Cius
A
,
Barbosa
LM
,
Ruiz
HB
, et al
.
Hidden diversity in the populations of the armored catfish Ancistrus Kner, 1854 (Loricariidae, Hypostominae) from the Paraná River Basin revealed by molecular and cytogenetic data
.
Front Genet
.
2017
;
8
:
185
.
53.
Belyayev
A
,
Jandová
M
,
Josefiová
J
,
Kalendar
R
,
Mahelka
V
,
Mandák
B
, et al
.
The major satellite DNA families of the diploid Chenopodium album aggregate species: arguments for and against the “library hypothesis”
.
PLoS One
.
2020
;
15
(
10
):
e0241206
6
.
54.
Novák
P
,
Neumann
P
,
Macas
J
.
Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2
.
Nat Protoc
.
2020
;
15
(
11
):
3745
76
.
55.
Novák
P
,
Ávila Robledillo
L
,
Koblížková
A
,
Vrbová
I
,
Neumann
P
,
Macas
J
.
TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads
.
Nucleic Acids Res
.
2017
;
45
(
12
):
e111
1
.
56.
Novák
P
,
Neumann
P
,
Pech
J
,
Steinhaisl
J
,
Macas
J
.
RepeatExplorer: a galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads
.
Bioinformatics
.
2013
;
29
(
6
):
792
3
.
57.
Novák
P
,
Neumann
P
,
Macas
J
.
Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
.
BMC Bioinform
.
2010
;
11
(
1
):
378
.
58.
Drummond
A
,
Aston
B
,
Cheung
M
,
Heled
J
,
Kearse
M
,
Moir
R
, et al
. Geneious v4. 8. [Internet].
2009
. [cited 2022 Mar]. Available from: http://www.geneious.com.
59.
Junier
T
,
Pagni
M
.
Dotlet: diagonal plots in a Web browser
.
Bioinformatics
.
2000
;
16
(
2
):
178
9
.
60.
Benson
G
.
Tandem repeats finder: a program to analyze DNA sequences
.
Nucleic Acids Res
.
1999
;
27
(
2
):
573
80
.
61.
Smit
AFA
,
Hubley
R
,
Green
P
. RepeatMasker.
2013
. Available from: http://www.repeatmasker.org.
62.
Lorite
P
,
Carrillo
JA
,
Tinaut
A
,
Palomeque
T
.
Evolutionary dynamics of satellite DNA in species of the genus Formica (Hymenoptera, Formicidae)
.
Gene
.
2004
;
332
:
159
68
.
63.
Ruíz-Ruano
FJ
,
Castillo-Martínez
J
,
Cabrero
J
,
Gómez
R
,
Camacho
JPM
,
López-León
MD
.
High-throughput analysis of satellite DNA in the grasshopper Pyrgomorpha conica reveals abundance of homologous and heterologous higher-order repeats
.
Chromosoma
.
2018
;
127
(
3
):
323
40
.
64.
Mora
P
,
Vela
J
,
Ruiz-Ruano
FJ
,
Ruiz-Mena
A
,
Montiel
EE
,
Palomeque
T
, et al
.
Satellitome analysis in the ladybird beetle Hippodamia variegata (Coleoptera, Coccinellidae)
.
Genes
.
2020
;
11
(
7
):
783
.
65.
Ruiz-Ruano
FJ
,
Navarro-Domínguez
B
,
Camacho
JPM
,
Garrido-Ramos
MA
.
Characterization of the Satellitome in lower vascular plants: the case of the endangered fern Vandenboschia speciosa
.
Ann Bot
.
2019
;
123
(
4
):
587
99
.
66.
Gutiérrez
J
,
Aleix-Mata
G
,
Montiel
EE
,
Cabral-de-Mello
DC
,
Marchal
JA
,
Sánchez
A
.
Satellitome analysis on Talpa aquitania genome and inferences about the satDNAs evolution on some Talpidae
.
Genes
.
2022
;
14
(
1
):
117
.
67.
Bardella
VB
,
Milani
D
,
Cabral-de-Mello
DC
.
Analysis of Holhymenia histrio genome provides insight into the satDNA evolution in an insect with holocentric chromosomes
.
Chromosome Res
.
2020
;
28
(
3–4
):
369
80
.
68.
Montiel
EE
,
Mora
P
,
Rico-Porras
JM
,
Palomeque
T
,
Lorite
P
.
Satellitome of the red palm weevil, Rhynchophorus ferrugineus (Coleoptera: Curculionidae), the most diverse among insects
.
Front Ecol Evol
.
2022
;
10
:
826808
.
69.
Ugarković
Ð
,
Plohl
M
.
Variation in satellite DNA profiles - causes and effects
.
EMBO J
.
2002
;
21
(
22
):
5955
9
.
70.
Garrido-Ramos
M
.
Satellite DNA: an evolving topic
.
Genes
.
2017
;
8
(
9
):
230
.
71.
Chalopin
D
,
Volff
JN
,
Galiana
D
,
Anderson
JL
,
Schartl
M
.
Transposable elements and early evolution of sex chromosomes in fish
.
Chromosome Res
.
2015
;
23
(
3
):
545
60
.
72.
Palacios-Gimenez
OM
,
Marti
DA
,
Cabral-de-Mello
DC
.
Neo-sex chromosomes of Ronderosia bergi: insight into the evolution of sex chromosomes in grasshoppers
.
Chromosoma
.
2015
;
124
(
3
):
353
65
.
73.
Wright
AE
,
Dean
R
,
Zimmer
F
,
Mank
JE
.
How to make a sex chromosome
.
Nat Commun
.
2016
;
7
(
1
):
12087
.
74.
Yano
CF
,
Bertollo
LAC
,
Ezaz
T
,
Trifonov
V
,
Sember
A
,
Liehr
T
, et al
.
Highly conserved Z and molecularly diverged W chromosomes in the fish genus Triportheus (Characiformes, Triportheidae)
.
Heredity
.
2017
;
118
(
3
):
276
83
.
75.
Sember
A
,
Bertollo
C
,
Ráb
P
,
Yano
CF
,
Hatanaka
T
,
de Oliveira
EA
, et al
.
Sex chromosome evolution and genomic divergence in the fish Hoplias malabaricus (Characiformes, Erythrinidae)
.
Front Genet
.
2018
;
9
(
71
):
71
.
76.
Charlesworth
D
.
When and how do sex‐linked regions become sex chromosomes
.
Evolution
.
2021
;
75
(
3
):
569
81
.
77.
Kratochvíl
L
,
Stöck
M
,
Rovatsos
M
,
Bullejos
M
,
Herpin
A
,
Jeffries
DL
, et al
.
Expanding the classical paradigm: what we have learnt from vertebrates about sex chromosome evolution
.
Philos Trans R Soc Lond B Biol Sci
.
2021
;
376
(
1833
):
20200097
.
78.
Henikoff
S
,
Ahmad
K
,
Malik
HS
.
The centromere paradox: stable inheritance with rapidly evolving DNA
.
Science
.
2001
;
293
(
5532
):
1098
102
.
You do not currently have access to this content.