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Supernumerary chromosomes (B chromosomes) have been an intriguing subject of study. Our understanding of the molecular differentiation of B chromosomes from an interpopulation perspective remains limited, with most analyses involving chromosome banding and mapping of a few sequences. To gain insights into the molecular composition, origin, and evolution of B chromosomes, we conducted cytogenetic and next-generation sequencing analysis of the repeatome in the grasshopper Abracris flavolineata across various populations. Our results unveiled the presence of B chromosomes in two newly investigated populations and described new satellite DNA sequences. While we observed some degree of genetic connection among A. flavolineata populations, our comparative analysis of genomes with and without B chromosomes provided evidence of two new B chromosome variants. These variants exhibited distinct compositions of various repeat classes, including transposable elements and satellite DNAs. Based on shared repeats, their chromosomal location, and the C-positive heterochromatin content on the B chromosome, these variants likely share a common origin but have undergone distinct molecular differentiation processes, resulting in varying degrees of heterochromatinization. Our data serve as a detailed example of the dynamic and differentiated nature of B chromosome molecular content at the interpopulation level, even when they share a common origin.
Assuntos
Cromossomos de Insetos , Gafanhotos , Animais , Gafanhotos/genética , Cromossomos de Insetos/genética , Heterocromatina/genética , Evolução Molecular , DNA Satélite/genética , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Elementos de DNA TransponíveisRESUMO
Ancistrus presents a wide karyotypic diversity, resulting from numeric and structural chromosomal rearrangements. It has been proposed that some genome-specific regions containing repetitive units could organize prone-to-break DNA sites in Loricariidae, triggering chromosomal rearrangements such as Robertsonian fusions (Rb fusions), centric fissions, translocations, and inversions. The tandemly repeats of the small nuclear RNAs (snRNAs) gene families are considered good cytogenetic markers for understanding chromosomal remodeling events among closely related species, but these snRNAs have been scarcely analyzed in Ancistrus. This study presented the nucleotide sequencing and comparative in situ location of U snRNA sequences from Ancistrus aguaboensis, Ancistrus cf. multispinis, and Ancistrus sp. (2n = 50, 52, and 50, respectively), aiming to provide information about snRNA clusters in the genome and chromosome evolution in Ancistrus. U snRNA nucleotide sequences of Ancistrus presented identity to orthologous copies and folded their secondary structures correctly. In situ localization and karyotyping of the three Ancistrus species revealed clustered copies of U2 and U5 snRNA gene families to a single chromosome site, one chromosome pair bearing U1 snRNA sequence, and one main locus of U4 snRNA sequence, besides scattered signals along the chromosomes. Previous studies related the participation of the rRNA gene families in centric fusion events, contributing to chromosome rearrangements and karyotype plasticity present in Loricariidae. In this study, homeologies in U snRNA loci chromosomal locations were detected, indicating the occurrence of conserved sites of these gene families in these three Ancistrus species with 2n = 50 or 52 chromosomes.
Assuntos
Peixes-Gato , Animais , Peixes-Gato/genética , Peixe-Zebra/genética , Cariótipo , Cariotipagem , RNA Nuclear Pequeno/genética , Análise de Sequência , NucleotídeosRESUMO
Brazil is the largest producer of soybeans in the world. The vast extent of soybean plantations across the Brazilian territory exposes this crop to attack by several insects, including the velvetbean caterpillar, Anticarsia gemmatalis. One of the alternatives used to control this insect are the toxins produced by Bacillus thuringiensis (Bt). However, in some cases, resistance to these toxins has been reported in the laboratory. Despite the ecological and economic impact of the velvetbean caterpillar, there are few studies on the genetic structure of this species, especially with regard to microsatellites. In this paper, we carried out a comparative transcriptional analysis of microsatellites in resistant (RES) and susceptible (SUS) strains of A. gemmatalis challenged and not challenged with Bt toxins. According to the number of sequences analyzed in each group, a 7.9% simple sequence repeat (SSR) rate was identified for the SUS library, and 7.4% for SUSBt. For the RES group, this value was 8.5% and for the RESBt 7.7%. Most of the fragments found showed a shorter repeat pattern, located in mono- and trinucleotide motifs. Among the 128 types of SSR motifs, it was possible to notice a large amount of adenine and thymine in relation to guanine and cytosine, which was also seen in chromosomes after staining with base-specific fluorochromes DAPI/CMA3, highlighting DAPI-positive regions. Although the participation of microsatellites in the resistance mechanism of A. gemmatalis to Bt is not clear, the results obtained in this work contribute to a better understanding of the repetitive DNA found in transcribed regions of a non-model organism.
Assuntos
Bacillus thuringiensis , Mariposas , Animais , Toxinas de Bacillus thuringiensis , Bacillus thuringiensis/química , Bacillus thuringiensis/genética , Glycine max/genética , Brasil , LarvaRESUMO
Miniature fishes have always been a challenge for cytogenetic studies due to the difficulty in obtaining chromosomal preparations, making them virtually unexplored. An example of this scenario relies on members of the family Lebiasinidae which include miniature to medium-sized, poorly known species, until very recently. The present study is part of undergoing major cytogenetic advances seeking to elucidate the evolutionary history of lebiasinids. Aiming to examine the karyotype diversification more deeply in Pyrrhulina, here we combined classical and molecular cytogenetic analyses, including Giemsa staining, C-banding, repetitive DNA mapping, comparative genomic hybridization (CGH), and whole chromosome painting (WCP) to perform the first analyses in five Pyrrhulina species (Pyrrhulina aff. marilynae, Pyrrhulina sp., P. obermulleri, P. marilynae and Pyrrhulina cf. laeta). The diploid number (2n) ranged from 40 to 42 chromosomes among all analyzed species, but P. marilynae is strikingly differentiated by having 2n = 32 chromosomes and a karyotype composed of large meta/submetacentric chromosomes, whose plesiomorphic status is discussed. The distribution of microsatellites does not markedly differ among species, but the number and position of the rDNA sites underwent significant changes among them. Interspecific comparative genome hybridization (CGH) found a moderate divergence in the repetitive DNA content among the species' genomes. Noteworthy, the WCP reinforced our previous hypothesis on the origin of the X1X2Y multiple sex chromosome system in P. semifasciata. In summary, our data suggest that the karyotype differentiation in Pyrrhulina has been driven by major structural rearrangements, accompanied by high dynamics of repetitive DNAs.
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Multigene families are essential components of eukaryotic genomes and play key roles either structurally and functionally. Their modes of evolution remain elusive even in the era of genomics, because multiple multigene family sequences coexist in genomes, particularly in large repetitive genomes. Here, we investigate how the multigene families 18S rDNA, U2 snDNA, and H3 histone evolved in 10 species of Schistocerca grasshoppers with very large and repeat-enriched genomes. Using sequenced genomes and fluorescence in situ hybridization mapping, we find substantial differences between species, including the number of chromosomal clusters, changes in sequence abundance and nucleotide composition, pseudogenization, and association with transposable elements (TEs). The intragenomic analysis of Schistocerca gregaria using long-read sequencing and genome assembly unveils conservation for H3 histone and recurrent pseudogenization for 18S rDNA and U2 snDNA, likely promoted by association with TEs and sequence truncation. Remarkably, TEs were frequently associated with truncated copies, were also among the most abundant in the genome, and revealed signatures of recent activity. Our findings suggest a combined effect of concerted and birth-and-death models driving the evolution of multigene families in Schistocerca over the last 8 million years, and the occurrence of intra- and interchromosomal rearrangements shaping their chromosomal distribution. Despite the conserved karyotype in Schistocerca, our analysis highlights the extensive reorganization of repetitive DNAs in Schistocerca, contributing to the advance of comparative genomics for this important grasshopper genus.
Assuntos
Evolução Molecular , Rearranjo Gênico , Gafanhotos , Animais , Genoma de Inseto , Gafanhotos/genética , Hibridização in Situ Fluorescente , Cariótipo , Família MultigênicaRESUMO
Tandem repeats are important parts of eukaryotic genomes being crucial e.g., for centromere and telomere function and chromatin modulation. In Lepidoptera, knowledge of tandem repeats is very limited despite the growing number of sequenced genomes. Here we introduce seven new satellite DNAs (satDNAs), which more than doubles the number of currently known lepidopteran satDNAs. The satDNAs were identified in genomes of three species of Crambidae moths, namely Ostrinia nubilalis, Cydalima perspectalis, and Diatraea postlineella, using graph-based computational pipeline RepeatExplorer. These repeats varied in their abundance and showed high variability within and between species, although some degree of conservation was noted. The satDNAs showed a scattered distribution, often on both autosomes and sex chromosomes, with the exception of both satellites in D. postlineella, in which the satDNAs were located at a single autosomal locus. Three satDNAs were abundant on the W chromosomes of O. nubilalis and C. perspectalis, thus contributing to their differentiation from the Z chromosomes. To provide background for the in situ localization of the satDNAs, we performed a detailed cytogenetic analysis of the karyotypes of all three species. This comparative analysis revealed differences in chromosome number, number and location of rDNA clusters, and molecular differentiation of sex chromosomes.
RESUMO
Satellite DNAs (satDNA) are fast-evolving repetitive sequences organized in large tandem arrays, with characteristic enrichment in heterochromatin. Knowledge about evolutionary dynamics of this genome fraction is mostly restricted to its characterization in species with monocentric chromosomes, i.e., localized centromeres. In holocentric species, with non-localized centromeres, satDNAs have been largely ignored. Here we advance the understanding of satDNA evolution among holocentric species by characterization of the most abundant satDNAs in the hemipteran Holhymenia histrio, integrating genomic and chromosomal analyses. High plasticity at chromosomal and molecular levels was noticed for 34 satDNAs populating H. histrio genome. One satDNA family in particular (HhiSat01-184) was highly amplified on multiple chromosomes and also highly polymorphic. Our data support the emergence of a new satDNA family from this abundant satDNA, confined to a single chromosome. Moreover, we present new information about composition of a peculiar chromosome in Coreidae, the m-chromosome, and of the X chromosome. Overall, the molecular and chromosomal patterns for satDNAs in the holocentric species H. histrio seem to be similar to those observed in monocentric species.
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Cromossomos de Insetos , DNA Satélite , Evolução Molecular , Genoma de Inseto , Genômica , Insetos/genética , Animais , Biologia Computacional/métodos , Genômica/métodos , Heterocromatina/genética , Sequenciamento de Nucleotídeos em Larga Escala , Hibridização in Situ FluorescenteRESUMO
Pimelodidae has a high number of species, but cytogenetic studies are generally restricted to classical chromosomal characterization and in situ localization of ribosomal DNA (rDNA) genes. This study was developed to compare Pimelodus microstoma and Pimelodus pohli focusing on chromosomal diversification provided by the transposition of DNA sequences containing multigene families. Both species share 56 chromosomes, with centromeric and terminal heterochromatic blocks. The silver nucleolus organizer regions (Ag-NORs)/45S rDNA was located in the chromosome pair 24 for both species. The 5S rDNA sites were evidenced in the pair 8 of P. microstoma, and in the pairs 1, 17, and 18 in P. pohli. The U1 small nuclear RNA (snRNA) was located at terminal site in the first subtelocentric pair in both species. The U2 snRNA site was syntenic to 5S rDNA in non-homeologue chromosomes between analyzed species. The histones H3 and H4 were clustered in chromosome pairs 19 and 23 in P. microstoma, and 21 and 22 in P. pohli. Our study proposes that the movement of DNA sequences carrying multigene families has been driven on the chromosomal diversification of Pimelodidae. These multigene location in the genomes can explain most of the visualized chromosomal rearrangements in Pimelodidae and it is useful to understand the chromosomal changes and their distinctive karyotype formulae.
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Peixes-Gato/genética , Mapeamento Cromossômico , Análise Citogenética , Família Multigênica , Animais , DNA Ribossômico/genética , Feminino , Masculino , Região Organizadora do Nucléolo/genética , RNA Nuclear Pequeno/genéticaRESUMO
Neotropical cichlid fishes are one of the most diversified and evolutionarily successful species assemblages. Extremely similar forms and intraspecific polychromatism present challenges for the taxonomy of some of these groups. Several species complexes have a largely unknown origin and unresolved evolutionary processes. Dwarf cichlids of the genus Apistogramma, comprising more than a hundred species, exhibit intricate taxonomic and biogeographic patterns, with both allopatric and sympatric distributions. However, karyotype evolution and the role of chromosomal changes in Apistogramma are still unknown. In the present study, nine South American Apistogramma species were analyzed using conventional cytogenetic methods and the mapping of repetitive DNA sequences [18S rDNA, 5S rDNA, and (TTAGGG)n] by fluorescence in situ hybridization (FISH). Our results showed that Apistogramma has unique cytogenetic characteristics in relation to closely related groups, such as a reduced 2n and a large number of bi-armed chromosomes. Interspecific patterns revealed a scenario of remarkable karyotypic changes, including a reduction of 2n, the occurrence of B-chromosomes and evolutionary dynamic of rDNA tandem repeats. In addition to the well-known pre-zygotic reproductive isolation, the karyotype reorganization in the genus suggests that chromosomal changes could act as postzygotic barriers in areas where Apistogramma congeners overlap.
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Sequências Repetitivas de Ácido Nucleico/genética , Animais , Ciclídeos , DNA Ribossômico/genética , Evolução Molecular , CariótipoRESUMO
BACKGROUND: Species with 'young' or nascent sex chromosomes provide unique opportunities to understand early evolutionary mechanisms (e.g. accumulation of repetitive sequences, cessation of recombination and gene loss) that drive the evolution of sex chromosomes. Among vertebrates, fishes exhibit highly diverse and a wide spectrum of sex-determining mechanisms and sex chromosomes, ranging from cryptic to highly differentiated ones, as well as, from simple to multiple sex chromosome systems. Such variability in sex chromosome morphology and composition not only exists within closely related taxa, but often within races/populations of the same species. Inside this context, the wolf fish Hoplias malabaricus offers opportunity to investigate the evolution of morphologically variable sex chromosomes within a species complex, as homomorphic to highly differentiated sex chromosome systems occur among its different karyomorphs. MATERIALS & METHODS: To discover various evolutionary stages of sex chromosomes and to compare their sequence composition among the wolf fish´s karyomorphs, we applied multipronged molecular cytogenetic approaches, including C-banding, repetitive DNAs mapping, Comparative Genomic Hybridization (CGH) and Whole Chromosomal Painting (WCP). Our study was able to characterize a cryptically differentiated XX/XY sex chromosome system in the karyomorph F of this species. CONCLUSION: The Y chromosome was clearly identified by an interstitial heterochromatic block on the short arms, primarily composed of microsatellite motifs and retrotransposons. Additionally, CGH also identified a male specific chromosome region in the same chromosomal location, implying that the accumulation of these repeats may have initiated the Y chromosome differentiation, as well as played a critical role towards the evolution and differentiation of sex chromosomes in various karyomorphs of this species.
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Although fishes exhibit the greatest biodiversity among the vertebrates, a large percentage of this fauna is still underexplored on evolutionary cytogenetic questions, particularly the miniature species. The Lebiasinidae family is a particular example for such case. This study is the first one presenting differential cytogenetic methods, such as C-banding, repetitive DNAs mapping, comparative genomic hybridization (CGH), and whole chromosome painting in lebiasinid species. Pyrrhulina australis and Pyrrhulina aff. australis were deeply investigated concerning their chromosomal patterns and evolutionary relationships. These species have a very similar morphology, but they can be distinguished by a longitudinal midlateral faintly dark stripe exclusive for Pyrrhulina aff. australis. Both species presented 2n = 40 chromosomes (4st +36a), without heteromorphic sex chromosomes. However, despite their morphological and karyotype resemblance, it was evidenced that both species have already gone through a significant genomic divergence, thus corresponding to distinct evolutionary units. Furthermore, to give additional support to some proposals on evolutionary relationship among Lebiasinidae with other fish families, a chromosomal comparative approach with Erythrinus erythrinus, a representative species of the Erythrinidae family, was also performed. In addition to have similar karyotype structure, mainly composed by acrocentric chromosomes, both species share uncommon genomic similarities, such as (i) syntenic location of 5S and 18S rDNA sequences; (ii) huge dispersion of multiple 5S rDNA sites in the karyotypes; and (iii) complex association between 5S rDNA and Rex3 elements. CGH experiments, despite reinforcing some shared genomic homologies, also highlighted that both Pyrrhulina and Erythrinus have a range of nonoverlapping species-specific signals. The overall chromosomal data proved to be effective markers for the cytotaxonomy and evolutionary process among Lebiasinidae fishes.
Assuntos
Evolução Biológica , Caraciformes/classificação , Caraciformes/genética , Análise Citogenética/métodos , Animais , Mapeamento Cromossômico/métodos , Coloração Cromossômica , Hibridização Genômica Comparativa/métodos , Cariotipagem , RNA Ribossômico 18S , RNA Ribossômico 5S , Especificidade da EspécieRESUMO
Multigene families correspond to a group of genes tandemly repeated, showing enormous diversity in both number of units and genomic organization. In fishes, unlike rDNAs that have been well explored in cytogenetic studies, U2 small nuclear RNA (snRNA) genes are poorly investigated concerning their chromosomal localization. All Triportheus species (Characiformes, Triportheidae) studied so far carry a ZZ/ZW sex chromosomes system, where the W chromosome contains a huge 18S rDNA cistron. In some species the syntenic organization of rDNAs on autosomes was also verified. To explore this particular organization, we performed three-color-fluorescence in situ hybridization using 5S, 18S rDNA, and U2 snRNA genes as probes in eight Triportheus species. This work represents the first one analyzing the chromosomal distribution of U2 snRNA genes in genomes of Triportheidae. The variability in number of rDNA clusters, and the divergent syntenies for these three multigene families, put in evidence their evolutionary dynamism, revealing a much more complex organization of these genes than previously supposed for closely related species. Our study also provides additional data on the accumulation of repetitive sequences in the sex-specific chromosome. Besides, the chromosomal organization of U2 snDNAs among fish species is also reviewed.
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Caraciformes/genética , DNA Ribossômico/genética , Evolução Molecular , Variação Genética , RNA Nuclear Pequeno/genética , Sintenia/genética , Animais , Mapeamento Cromossômico , Feminino , Genoma , Cariótipo , Cariotipagem , Masculino , Família Multigênica , Especificidade da EspécieRESUMO
Cytogenetic studies in fish of the Rineloricaria genus have already shown a high variation in diploid number (2n). Along with fusion/fission events for 2n alteration, inversions contribute to the diversification of chromosome formulae within this group. The present study assessed different populations/species of the Rineloricaria aiming to describe the karyotype organization of its members and understand the mechanisms that lead to the variation of chromosome numbers. Cytogenetic data showed distinct karyotype organization among Rineloricaria populations/species studied, ranging in diploid number from 46 to 64 chromosomes, syntopic species and two karyomorphs in Rineloricaria pentamaculata. Using ribosomal DNAs (rDNAs) and TTAGGGn probes by fluorescence in situ hybridization in species with low diploid numbers, we detected sites of 18S rDNA, 5S rDNA, and TTAGGGn in centromeric regions of metacentric chromosomes, which participated in chromosome rearrangements like centric fusions. In species with high 2n, centric fissions probably occurred in karyotypic diversification. In this study, we assessed the telomeric instability, chromosomal breaks, and rearrangements due to interstitial telomeric site vestiges detection, in addition to the probable role of rDNAs in chromosome fusions in karyotypic diversification of this group.
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Peixes-Gato/genética , Mapeamento Cromossômico/métodos , Cromossomos/genética , Regulação da Expressão Gênica , Variação Genética , Animais , DNA Ribossômico/genética , Hibridização in Situ Fluorescente , Especificidade da EspécieRESUMO
The 5S ribosomal DNA (rDNA) sequences are subject of dynamic evolution at chromosomal and molecular levels, evolving through concerted and/or birth-and-death fashion. Among grasshoppers, the chromosomal location for this sequence was established for some species, but little molecular information was obtained to infer evolutionary patterns. Here, we integrated data from chromosomal and nucleotide sequence analysis for 5S rDNA in two Abracris species aiming to identify evolutionary dynamics. For both species, two arrays were identified, a larger sequence (named type-I) that consisted of the entire 5S rDNA gene plus NTS (non-transcribed spacer) and a smaller (named type-II) with truncated 5S rDNA gene plus short NTS that was considered a pseudogene. For type-I sequences, the gene corresponding region contained the internal control region and poly-T motif and the NTS presented partial transposable elements. Between the species, nucleotide differences for type-I were noticed, while type-II was identical, suggesting pseudogenization in a common ancestor. At chromosomal point to view, the type-II was placed in one bivalent, while type-I occurred in multiple copies in distinct chromosomes. In Abracris, the evolution of 5S rDNA was apparently influenced by the chromosomal distribution of clusters (single or multiple location), resulting in a mixed mechanism integrating concerted and birth-and-death evolution depending on the unit.
Assuntos
Mapeamento Cromossômico/métodos , DNA Ribossômico/genética , Gafanhotos/genética , RNA Ribossômico 5S/genética , Animais , Cromossomos/genética , Evolução Molecular , Feminino , Masculino , Pseudogenes , Análise de Sequência de DNA , Análise de Sequência de ProteínaRESUMO
The genus Astyanax is widely distributed from the southern United States to northern Patagonia, Argentina. While cytogenetic studies have been performed for this genus, little is known about the histone gene families. The aim of this study was to examine the chromosomal relationships among the different species of Astyanax. The chromosomal locations of the 5S rRNA and H3 histone genes were determined in A. abramis, A. asuncionensis, A. altiparanae, A. bockmanni, A. eigenmanniorum, A. mexicanus (all 2n = 50), A. fasciatus (2n = 46), and A. schubarti (2n = 36). All eight species exhibited H3 histone clusters on two chromosome pairs. In six species (A. abramis, A. asuncionensis, A. altiparanae, A. bockmanni, A. eigenmanniorum, and A. fasciatus), syntenic clusters of H3 histone and 5S rDNA were observed on metacentric (m) or submetacentric (sm) chromosomes. In seven species, clusters of 5S rDNA sequences were located on one or two chromosome pairs. In A. mexicanus, 5S rDNA clusters were located on four chromosome pairs. This study demonstrates that H3 histone clusters are conserved on two chromosome pairs in the genus Astyanax, and specific chromosomal features may contribute to the genomic organization of the H3 histone and 5S rRNA genes.
Assuntos
Caraciformes/genética , Mapeamento Cromossômico , Genes de RNAr , Histonas/genética , Sintenia , Animais , Caraciformes/classificação , Diploide , Hibridização in Situ Fluorescente , Cariótipo , RNA Ribossômico 5S/genéticaRESUMO
B chromosomes are frequently enriched for a wide variety of repetitive DNAs. Among grasshoppers in the species Abracris flavolineata (Ommatolampidinae) the B chromosomes are submetacentric, C-negative and harbor repetitive DNAs such as, U2 snDNA, C 0 t-1 DNA, two Mariner-like elements and some microsatellites. Here, we provide evidence showing the intragenome similarity between the B chromosome and the A complement in A. flavolineata, combining analysis of microdissection and chromosome painting and B chromosome-specific amplification through polymerase chain reaction (PCR) of U2 snDNA. Chromosome painting revealed signals spread through the C-negative regions, including the A and B chromosomes. Moreover, significant clustered signals forming bands were observed in some A chromosomes, and for the B chromosome, significant signals were located on both arms, which could be caused by accumulation of repetitive DNA sequences. The C-positive regions did not reveal any signals. Sequence comparison of U2 snDNA between that obtained from a genome without the B chromosome and that from µB-DNA revealed high similarity with the occurrence of four shared haplotypes, one of them (i.e., Hap1) being highly prevalent and putatively ancestral. The highest divergence from Hap1 was observed for Hap3, which was caused by only six mutational steps. These data support an intraspecific origin of the B chromosome in A. flavolineata that is highly similar with the A complement, and the low U2 snDNA sequence diversity observed in the B chromosome could be related to its recent origin, besides intrachromosomal concerted evolution for U2 snDNA repeats in the B chromosome.