Research Article |
Corresponding author: Natalia D. M. Carvalho ( nathydayane@gmail.com ) Academic editor: Larissa Kupriyanova
© 2016 Natalia D. M. Carvalho, Edson Carmo, Rogerio O. Neves, Carlos Henrique Schneider, Maria Claudia Gross.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Carvalho NDM, Carmo EJ, Neves RO, Schneider CH, Gross MC (2016) Differential repetitive DNA composition in the centromeric region of chromosomes of Amazonian lizard species in the family Teiidae. Comparative Cytogenetics 10(2): 203-217. https://doi.org/10.3897/CompCytogen.v10i2.7081
|
Differences in heterochromatin distribution patterns and its composition were observed in Amazonian teiid species. Studies have shown repetitive DNA harbors heterochromatic blocks which are located in centromeric and telomeric regions in Ameiva ameiva (Linnaeus, 1758), Kentropyx calcarata (Spix, 1825), Kentropyx pelviceps (Cope, 1868), and Tupinambis teguixin (Linnaeus, 1758). In Cnemidophorus sp.1, repetitive DNA has multiple signals along all chromosomes. The aim of this study was to characterize moderately and highly repetitive DNA sequences by Cot1-DNA from Ameiva ameiva and Cnemidophorus sp.1 genomes through cloning and DNA sequencing, as well as mapping them chromosomally to better understand its organization and genome dynamics. The results of sequencing of DNA libraries obtained by Cot1-DNA showed that different microsatellites, transposons, retrotransposons, and some gene families also comprise the fraction of repetitive DNA in the teiid species. FISH using Cot1-DNA probes isolated from both Ameiva ameiva and Cnemidophorus sp.1 showed these sequences mainly located in heterochromatic centromeric, and telomeric regions in Ameiva ameiva, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin chromosomes, indicating they play structural and functional roles in the genome of these species. In Cnemidophorus sp.1, Cot1-DNA probe isolated from Ameiva ameiva had multiple interstitial signals on chromosomes, whereas mapping of Cot1-DNA isolated from the Ameiva ameiva and Cnemidophorus sp.1 highlighted centromeric regions of some chromosomes. Thus, the data obtained showed that many repetitive DNA classes are part of the genome of Ameiva ameiva, Cnemidophorus sp.1, Kentroyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin, and these sequences are shared among the analyzed teiid species, but they were not always allocated at the same chromosome position.
centromere, Cot1-DNA, FISH, heterochromatin, telomere
Teiidae are a Neotropical lizard family characterized by karyotype diversity with a diploid number ranging from 34 to 52 chromosomes, as well as differences in heterochromatin composition and distribution patterns (
These heterochromatin blocks usually contain repetitive DNA, such as ribosomal DNA 5S, telomeric sequences, tropomyosin 1 genes, and the retrotransposons Rex 1 and SINE (
Repetitive DNA may be isolated by various strategies, among them Cot1-DNA is used to isolate total fraction of moderately and highly repetitive DNA sequences in the genome (
The aim of this study was to characterize sequences of moderately and highly repetitive DNA sequences in Ameiva ameiva and Cnemidophorus sp.1 genomes. These teiid species have a large amount of heterochromatin that is organized differentially. Libraries enriched with repetitive DNA were cloned, sequenced, used as probes, and chromosomally mapped in Ameiva ameiva, Cnemidophorus sp.1, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin. Furthermore, they assisted in the understanding of genomic sequence organization and dynamics in karyotypes of these Amazonian teiid species.
Samples of Ameiva ameiva, Cnemidophorus sp.1, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin were collected in Amazonas State, Brazil, in different locations (Table
Species of the Teinae and Tupinambinae subfamilies: collection sites, number and the analyzed animals and voucher specimens (lots) are listed. AM: Amazonas.
Subfamily | Species | Collection sites | Number and sex the analyzed animals | Voucher specimens (lots) |
---|---|---|---|---|
Teiinae | Ameiva ameiva | São Sebastião do Uatumã, AM Santa Isabel do Rio Negro, AM Tapauá, AM São Sebastião de Cuieiras, AM Reserva Adolpho Ducke, AM |
30 (thirteen males; thirteen females; four without sex identification) |
INPA H33213 |
Cnemidophorus sp.1 | Manaus, AM | 13 (five males; eight females) | INPA H35018 | |
Kentropyx calcarata | São Sebastião do Uatumã, AM São Sebastião de Cuieiras, AM |
7 (three males; four females) |
INPA H31712 | |
Kentropyx pelviceps | Tapauá, AM | 3 (three females) | INPA H34841 | |
Tupinambinae | Tupinambis teguixin | São Sebastião do Uatumã, AM Tapauá, AM Reserva Adolpho Ducke, AM |
5 (four females; one without sex identification) |
INPA H34791 |
The animals were euthanized after capture in the field with a lethal dose of the anesthetic sodium thiopental to avoid being deprived of food or water. This research was approved by the Ethics Committee for Animal Experimentation of the Fundação Universidade do Amazonas/Universidade Federal do Amazonas (UFAM) (number 041/2013). No endangered or protected species were used in this research. The animals underwent cytogenetic procedures, were fixed with 10% formaldehyde (injected in the coelom and digestive tract), and preserved in 70% alcohol. Voucher specimens were deposited in the Herpetological Collection of the Instituto Nacional de Pesquisas da Amazônia (INPA H31712, 33213, 34791, 34841, 35018). All samples were identified by the researcher Dr. Federico Arias.
Mitotic chromosomes were obtained from bone marrow cell suspensions in vitro using colchicine (
Cot1-DNA libraries were tagged using digoxigenin-11-dUTP for nick translation reaction, according to manufacturer’s instructions (Dig-Nick Translation mix Roche). Anti-digoxigenin rhodamine (Roche) was used for signal detection. Cot1-DNA libraries from Ameiva ameiva tagged using digoxigenin-11-dUTP were hybridized with chromosomes of the species. Further, homologous hybridizations were performed with Cot1-DNA libraries in Cnemidophorus sp.1. Probes obtained from Cot1-DNA of Ameiva ameiva and Cot1-DNA of Cnemidophorus sp.1 were also hybridized with chromosomes of other analyzed teiid species. FISH was performed under 77% stringency (2.5 ng/probe, 50% formamide, 10% dextran sulfate, and 2× SSC at 37°C for 18 h) (
Chromosomes were analyzed using an epifluorescence microscope (Leica DFC 3000G). Metaphase stages were photographed; the karyotypes were loaded in Adobe Photoshop CS4 software and measured using Image J software. Afterward, the karyotypes were organized following the karyotype formula in karyotypes from Ameiva ameiva, Kentropyx calcarata and Kentropyx pelviceps were classified as gradual series of acrocentric chromosomes; those of Cnemidophorus sp.1 as biarmed, uniarmed, and microchromosomes; and those of Tupinambis teguixin as macro and microchromosomes.
A total of 40 Ameiva ameiva Cot1-DNA clones were sequenced wherein 12 sequences corresponded 8 to microsatellites, 1 to transposons, 1 to retrotransposons, and 1 genes, all having high similarity with repetitive DNA deposited in public DNA banks (Table
Repetitive sequences obtained fraction Cot1-DNA Ameiva ameiva with deposited sequences in the NCBI databases and GIRI.
Clone | Homology | Similarity | Identity |
---|---|---|---|
AA 1 | DNA Transposons | Tc1-like de Labeo rohita (GenBank AY083617.1) | 100% |
AA 2 | Microsatellite | Betula platyphylla var. japonica (GenBank AB084484.1) | 100% |
AA 3 | Gene | TAP2 mRNA de Oryzias latipes (GenBank AB033382.1) | 100% |
AA 4 | Microsatellite | Coffea canephora (GenBank EU526584.1) | 100% |
AA 5 | Microsatellite | Salmo salar (GenBank Y11457.1) | 96% |
AA 6 | Microsatellite | Serranus cabrilla (GenBank AM049431.1) | 95% |
AA 7 | Microsatellite | Hypericum perforatum (GenBank FR732510.1) | 93% |
AA 8 | Microsatellite | Apteronemobius asahinai (GenBank AB621739.1) | 100% |
AA 9 | Non-LTR Retrotransposons | CR 1 (RepBase/GIRI*) | 88% |
AA 10 | Microsatellite | Bos taurus (GenBank AF271953.1) | 81% |
AA 11 | Microsatellite | Colias behrii (GenBank FN552755.1) | 100% |
AA 12 | DNA Transposons | Tc1/mariner (RepBase/GIRI*) | 80% |
Repetitive sequences obtained fraction Cot1-DNA Cnemidophorus sp.1 with deposited sequences in the NCBI databases and GIRI.
Clone | Homology | Similarity | Identity |
---|---|---|---|
Cn 1 | Gene | TAP2 mRNA de Oryzias latipes (GenBank AB033382.1) | 100% |
Cn 2 | Microsatellite | Betula platyphylla var. japonica (GenBank AB084484.1) | 100% |
Cn 3 | DNA Transposons | Tc1-like de Labeo rohita (GenBank AY083617.1) | 100% |
Cn 4 | Microsatellite | Colias behrii (GenBank FN552755.1) | 93% |
Cn 5 | Microsatellite | Glaucosoma hebraicum (GeneNank FJ409080.1) | 97% |
Cn 6 | Microsatellite | Colias behrii (GenBank FN552755.1) | 99% |
Cn 7 | Microsatellite | Apteronemobius asahinai (GenBank AB621739.1) | 90% |
Cn 8 | Microsatellite | Salmo salar (GenBank Y11457.1) | 96% |
By using the homologous probe of Cot1-DNA, Ameiva ameiva hybridization signals were located in the centromeric region/short arm of pairs 1 to 18, except pairs 9, 16, and 17, which showed interstitial signals (Figures
Karyotypes with Ameiva ameiva Cot1-DNA probe hybridized (signal red). a A. ameiva b Cnemidophorus sp.1 c Kentropyx calcarata d Kentropyx pelviceps and e Tupinambis teguixin. The chromosomes were counterstained with DAPI. a = gradual series of acrocentric chromosomes. m = Macrochromosome, mi = microchromosome. Scale bar: 10 μm.
Hybrization using the heterologous probe of Cot1-DNA obtained from Ameiva ameiva in Cnemidophorus sp.1 presented multiple signals along all chromosomes, with compartmentalized blocks mainly in interstitial regions (Figure
Several classes of repetitive DNA are included in the genome of Amazonian teiid species, such as ribosomal DNA 5S, telomeric sequences, tropomyosin 1 genes, and retrotransposons Rex 1 and SINE. Most of these repetitive DNA sequences are allocated to heterochromatin regions, in addition to acting structurally in the centromeric and telomeric organization for Ameiva ameiva, Cnemidophorus sp.1, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin (
However, heterochromatin of teiids is not limited to ribosomal DNA 5S, telomeric sequences, tropomyosin 1 gene, retrotransposons Rex 1 and SINE, and presents a complex composition with various repetitive DNA. In libraries obtained by Cot1-DNA sequencing, it was evidenced that different microsatellites, transposons, retrotransposons, some gene families and other type of sequences (e.g. satellite DNAs) are also present in this fraction of moderately and highly repetitive DNA. They were allocated preferentially to the centromeric and telomeric regions of Ameiva ameiva, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin. These sequences are also present in Cnemidophorus sp.1; however, they were present in euchromatic regions, similar to the pattern observed for telomeric sequences, tropomyosin 1 genes, and retrotransposons Rex 1 and SINE.
The sequences of repetitive DNA that were more abundant in moderately and highly repetitive fractions of the genome obtained using Cot1-DNA in Ameiva ameiva and Cnemidophorus sp.1 were microsatellites, which were homologous with sequences of other organisms deposited in public databases, including plants, fish, mammals, bird and insect (Tables
Microsatellite or simple sequence repeats (SSRs) are short sequences organized in long segments made up of tandem repeat units and are found in coding or non-coding regions in diverse species genomes (
SSRs have functional roles in the genome, such as gene regulation, replication in transcription, protein function, and genome organization (
In addition to microsatellites, about 50% of sequences obtained by Cot1-DNA from two species, exhibited similarities to transposable elements (transposons and retrotransposons). One important characteristic of these transposable elements is the transposition mechanism; retrotransposons transpose via an intermediate from RNA and transposons move up the genome through DNA copies that may be contributing to diversity and plasticity of the genome during evolution (
An retrotransposon, non-LTR retrotransposon CR1 (Chicken Repeat 1) was identified only in the Ameiva ameiva genome; however, this does not indicate that it was not present in the genome of Cnemidophorus sp.1, because it simply may not have been identified in this study. Retroelement CR1 is a LINE family that is widely distributed in various organisms, including vertebrates (birds, reptiles, and fish) and invertebrates (
Repetitive DNA rDNA 5s, tropomyosin 1 genes, and retroelements Rex 1 and SINE (
Some clones presented similarity with part of the gene TAP-2 (transporter associated with antigen processing). TAP is encoded by class I major histocompatibility complex (MHC) genes and are responsible for the transport of antigen peptides from the cytoplasm to endoplasmic reticulum (
The physical chromosomal map of homologous probes and/or heterologous of Cot1-DNA showing signals associated with heterochromatic regions in centromeric and telomeric regions in chromosomes of Ameiva ameiva, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin; and corroborated partially the standard heterochromatic (
In Cnemidophorus sp.1, hybridization of moderately and highly repetitive sequences obtained from Cot1-DNA from Ameiva ameiva presented multiple signals along chromosomes with compartmentalized blocks in interstitial regions, which probably are located in euchromatic regions since they are not located in centromeric and telomeric heterochromatic regions of chromosomes (
On the other hand, FISH using Cot1-DNA homologous probe revealed signals mainly in centromeric regions of chromosomes of Cnemidophorus sp.1. Thus, heterochromatic centromeric fraction of Cnemidophorus sp.1 seems to be composed of microsatellites and transposable elements obtained by Cot1-DNA of the specie itself and elucidated by its sequencing, being different of the sequences obtained by Cot1-DNA of Ameiva ameiva, despite belonging to same categories. Yet Cot1-DNA contains a variety of different sequences, including the satellite DNA which are among the major component of centromeric heterochromatin, conversely to TE or microsatellite which are interspersed along chromosomes. Other repetitive elements may be present in the heterochromatic fraction of this species, which have not been detected by Cot1-DNA (
Although its function and multiprotein components are conserved among organisms, these repetitive DNA are extremely divergent regarding its structure, organization, dynamics, and propagation mechanisms, influencing the diversification and evolution of centromeres (
This study contributes to understanding the heterochromatic fraction composition and structure and organization of repetitive DNA of teiid genomes and indicates that the different classes of moderately and highly repetitive DNA are part of Ameiva ameiva, Cnemidophorus sp.1, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin genome. This means that these sequences are shared among the analyzed teiid species, although not always allocated on the same chromosome region. Nevertheless, the physical mapping of repetitive DNA revealed similarity among the species Ameiva ameiva, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin and showed that the centromeric fraction of Cnemidophorus sp.1 is different from that of the other analyzed species.
This work was supported by the Universidade Federal do Amazonas (UFAM), the graduate program of INPA Genética, Conservação e Biologia Evolutiva, Rede BioPHAM (CNPq/FAPEAM grant number: 563348/2010-0); Conselho Nacional de Pesquisa e Desenvolvimento Tecnológico (grant number: 474617/2013-0); FAPEAM (020/2013); CAPES (Pró-Amazônia – grant number 23038.009447/2013-45, 3295/2013). Species were collected with a permit issued by the Chico Mendes Institute for Biodiversity Conservation (ICMBio/SISBIO license number 41825-1). NDMC received funding from the Fundação de Amparo a Pesquisas do Estado do Amazonas. The authors are grateful to Dra. Eliana Feldberg for the epifluorescence microscope. Cactus Communications reviewed this paper.