Physical mapping of the Nile tilapia (Oreochromis niloticus) genome by fluorescent in situ hybridization of repetitive DNAs to metaphase chromosomes - a review

The Nile tilapia (Oreochromis niloticus) has received increasing scientific interest over the past few decades for two reasons: first, tilapia is an enormously important species in aquaculture worldwide, especially in regions where there is a chronic shortage of animal protein; and second, this teleost fish belongs to the fascinating group of cichlid fishes that have undergone a rapid and extensive radiation of much interest to evolutionary biologists. Currently, studies based on physical and genetic mapping of the Nile tilapia genome offer the best opportunities for applying genomics to such diverse questions and issues as phylogeography, isolation of quantitative trait loci involved in behaviour, morphology, and disease, and overall improvement of aquacultural stocks. In this review, we have integrated molecular cytogenetic data for the Nile tilapia describing the chromosomal location of the repetitive DNA sequences, satellite DNAs, telomeres, 45S and 5S rDNAs, and the short and long interspersed nucleotide elements [short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINEs)], and provide the beginnings of a physical genome map for this important teleost fish. (C) 2004 Elsevier B.V. All rights reserved.

Genomic organization of repetitive DNAs in the cichlid fish Astronotus ocellatus

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Chromosomal Variability among Allopatric Populations of Erythrinidae Fish Hoplias malabaricus: Mapping of Three Classes of Repetitive DNAs

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Chromosomal mapping of repetitive DNAs in the beetle Dichotomius geminatus provides the first evidence for an association of 5S rRNA and histone H3 genes in insects, and repetitive DNA similarity between the B chromosome and A complement

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Chromosomal Mapping of Repetitive DNAs in the Grasshopper Abracris flavolineata Reveal Possible Ancestry of the B Chromosome and H3 Histone Spreading

Supernumerary chromosomes (B chromosomes) occur in approximately 15% of eukaryote species. Although these chromosomes have been extensively studied, knowledge concerning their specific molecular composition is lacking in most cases. The accumulation of repetitive DNAs is one remarkable characteristic of B chromosomes, and the occurrence of distinct types of multigene families, satellite DNAs and some transposable elements have been reported. Here, we describe the organization of repetitive DNAs in the A complement and B chromosome system in the grasshopper species Abracris flavolineata using classical cytogenetic techniques and FISH analysis using probes for five multigene families, telomeric repeats and repetitive C0t-1 DNA fractions. The 18S rRNA and H3 histone multigene families are highly variable and well distributed in A. flavolineata chromosomes, which contrasts with the conservation of U snRNA genes and less variable distribution of 5S rDNA sequences. The H3 histone gene was an extensively distributed with clusters occurring in all chromosomes. Repetitive DNAs were concentrated in C-positive regions, including the pericentromeric region and small chromosomal arms, with some occurrence in C-negative regions, but abundance was low in the B chromosome. Finally, the first demonstration of the U2 snRNA gene in B chromosomes in A. flavolineata may shed light on its possible origin. These results provide new information regarding chromosomal variability for repetitive DNAs in grasshoppers and the specific molecular composition of B chromosomes. © 2013 Bueno et al.

A tandemly repetitive centromeric DNA sequence of the fish Hoplias malabaricus (Characiformes : Erythrinidae) is derived from 5S rDNA

A substantial fraction of the eukaryotic genome consists of repetitive DNA sequences that include satellites, minisatellites, microsatellites, and transposable elements. Although extensively studied for the past three decades, the molecular forces that generate, propagate and maintain repetitive DNAs in the genomes are still discussed. To further understand the dynamics and the mechanisms of evolution of repetitive DNAs in vertebrate genome, we searched for repetitive sequences in the genome of the fish species Hoplias malabaricus. A satellite sequence, named 5SHindIII-DNA, which has a conspicuous similarity with 5S rRNA genes and spacers was identified. FISH experiments showed that the 5S rRNA bona fide gene repeats were clustered in the interstitial position of two chromosome pairs of H. malabaricus, while the satellite 5SHindIII-DNA sequences were clustered in the centromeric position in nine chromosome pairs of the species. The presence of the 5SHindIII-DNA sequences in the centromeres of several chromosomes indicates that this satellite family probably escaped from the selective pressure that maintains the structure and organization of the 5S rDNA repeats and become disperse into the genome. Although it is not feasible to explain how this sequence has been maintained in the centromeric regions, it is possible to hypothesize that it may be involved in some structural or functional role of the centromere organization.

Physical chromosome mapping of repetitive DNA sequences in Nile tilapia Oreochromis niloticus: Evidences for a differential distribution of repetitive elements in the sex chromosomes

Repetitive DNAs have been extensively applied as physical chromosome markers on comparative studies, identification of chromosome rearrangements and sex chromosomes, chromosome evolution analysis, and applied genetics. Here we report the characterization of repetitive DNA sequences from the Nile tilapia (Oreochromis niloticus) genome by construction and screening of plasmid library enriched with repetitive DNAs, analysis of a BAC-based physical map, and hybridization to chromosomes. The physical mapping of BACs enriched with repetitive sequences and C(o)t-1 DNA (DNA enriched for highly and moderately repetitive DNA sequences) to chromosomes using FISH showed a predominant distribution of repetitive elements in the centromeric and telomeric regions and along the entire length of the largest chromosome pair (X and Y sex chromosomes) of the species. The distribution of repetitive DNAs differed significantly between the p arm of X and Y chromosomes. These findings suggest that repetitive DNAs have had an important role in the differentiation of sex chromosomes. (c) 2007 Elsevier Ltd. All rights reserved.

Tracking the evolution of sex chromosome systems in Melanoplinae grasshoppers through chromosomal mapping of repetitive DNA sequences

Background: The accumulation of repetitive DNA during sex chromosome differentiation is a common feature of many eukaryotes and becomes more evident after recombination has been restricted or abolished. The accumulated repetitive sequences include multigene families, microsatellites, satellite DNAs and mobile elements, all of which are important for the structural remodeling of heterochromatin. In grasshoppers, derived sex chromosome systems, such as neo-XY♂/XX♀ and neo-X1X2Y♂/X 1X1X2X2♀, are frequently observed in the Melanoplinae subfamily. However, no studies concerning the evolution of sex chromosomes in Melanoplinae have addressed the role of the repetitive DNA sequences. To further investigate the evolution of sex chromosomes in grasshoppers, we used classical cytogenetic and FISH analyses to examine the repetitive DNA sequences in six phylogenetically related Melanoplinae species with X0♂/XX♀, neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X 2X2♀ sex chromosome systems. Results: Our data indicate a non-spreading of heterochromatic blocks and pool of repetitive DNAs (C 0 t-1 DNA) in the sex chromosomes; however, the spreading of multigene families among the neo-sex chromosomes of Eurotettix and Dichromatos was remarkable, particularly for 5S rDNA. In autosomes, FISH mapping of multigene families revealed distinct patterns of chromosomal organization at the intra- and intergenomic levels. Conclusions: These results suggest a common origin and subsequent differential accumulation of repetitive DNAs in the sex chromosomes of Dichromatos and an independent origin of the sex chromosomes of the neo-XY and neo-X1X2Y systems. Our data indicate a possible role for repetitive DNAs in the diversification of sex chromosome systems in grasshoppers. © 2013Palacios-Gimenez et al.; licensee BioMed Central Ltd.

Chromosomal organization of repetitive DNA sequences in Astyanax bockmanni (Teleostei, Characiformes): dispersive location, association and co-localization in the genome

Repetitive DNA sequences constitute a great portion of the genome of eukaryotes and are considered key components to comprehend evolutionary mechanisms and karyotypic differentiation. Aiming to contribute to the knowledge of chromosome structure and organization of some repetitive DNA classes in the fish genome, chromosomes of two allopatric populations of Astyanax bockmanni were analyzed using classic cytogenetics techniques and fluorescent in situ hybridization, with probes for ribosomal DNA sequences, histone DNA and transposable elements. These Astyanax populations showed the same diploid number (2n = 50), however with differences in chromosome morphology, distribution of constitutive heterochromatin, and location of 18S rDNA and retroelement Rex3 sites. In contrast, sites for 5S rDNA and H1, H3 and H4 histones showed to be co-located and highly conserved. Our results indicate that dispersion and variability of 18S rDNA and heterochromatin sites are not associated with macro rearrangements in the chromosome structure of these populations. Similarly, distinct evolutionary mechanisms would act upon histone genes and 5S rDNA, contributing to chromosomal association and co-location of these sequences. Data obtained indicate that distinct mechanisms drive the spreading of repetitive DNAs in the genome of A. bockmanni. Also, mobile elements may account for the polymorphism of the major rDNA sites and heterochromatin in this genus. © 2013 Springer Science+Business Media Dordrecht.

Dinâmica evolutiva de DNAs repetitivos com ênfase em espécies da tribo Phanaeini

Pós-graduação em Ciências Biológicas (Genética) - IBB

Repetitive DNA chromosomal organization in the cricket Cycloptiloides americanus: a case of the unusual X(1)X(2)0 sex chromosome system in Orthoptera

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A step to the gigantic genome of the desert locust: chromosome sizes and repeated DNAs

The desert locust (Schistocerca gregaria) has been used as material for numerous cytogenetic studies. Its genome size is estimated to be 8.55 Gb of DNA comprised in 11 autosomes and the X chromosome. Its X0/XX sex chromosome determinism therefore results in females having 24 chromosomes whereas males have 23. Surprisingly, little is known about the DNA content of this locust's huge chromosomes. Here, we use the Feulgen Image Analysis Densitometry and C-banding techniques to respectively estimate the DNA quantity and heterochromatin content of each chromosome. We also identify three satellite DNAs using both restriction endonucleases and next-generation sequencing. We then use fluorescent in situ hybridization to determine the chromosomal location of these satellite DNAs as well as that of six tandem repeat DNA gene families. The combination of the results obtained in this work allows distinguishing between the different chromosomes not only by size, but also by the kind of repetitive DNAs that they contain. The recent publication of the draft genome of the migratory locust (Locusta migratoria), the largest animal genome hitherto sequenced, invites for sequencing even larger genomes. S. gregaria is a pest that causes high economic losses. It is thus among the primary candidates for genome sequencing. But this species genome is about 50 % larger than that of L. migratoria, and although next-generation sequencing currently allows sequencing large genomes, sequencing it would mean a greater challenge. The chromosome sizes and markers provided here should not only help planning the sequencing project and guide the assembly but would also facilitate assigning assembled linkage groups to actual chromosomes.

麂属动物以及六带犰狳DNA重复序列家族的克隆、序列分析和染色体定位

1．黑麂和费氏麂卫星DNA的克隆、序列分析和染色体定位 麂属动物在很短的时间内经历了快速的物种辐射，并且种间染色体数目存在巨大差异，是研究动物核型进化和物种起源的理想模型。近二十年来的分子细胞遗传学研究已基本上证实染色体串联融合(端粒－着丝粒融合)是麂属动物核型演化的主要染色体重排方式。尽管染色体串联融合的分子机制仍不清楚，但研究提示着丝粒区域的卫星DNA可能介导染色体的非同源重组。因此，着丝粒卫星DNA的克隆、分析序列以及染色体定位研究不仅有助于阐明麂属染色体核型演化规律，还可能揭示染色体串联融合的分子机制。迄今为止，上述研究工作已经在赤麂、小麂和小麂台湾亚种开展过。但是，尚无有关黑麂、费氏麂和贡山麂卫星 DNA 克隆、序列分析以及染色体定位研究的报道。 在本研究中，我成功地克隆了黑麂的卫星DNA I、II和IV，分别命名为BMC5、BM700和BM1.1k，并且从费氏麂中克隆了卫星DNA II，命名为FM700。对这些卫星DNA克隆进行序列分析，并将这些克隆探针分别与黑麂、费氏麂、贡山麂和小麂的染色体杂交。研究结果表明： 1)黑麂的卫星DNA I(BMC5)与小麂卫星DNA I(C5)序列高度相似，并且在小麂、黑麂、费氏麂和贡山麂染色体上的大部分串联融合位点处均有分布，因此卫星DNA I可能代表着染色体发生串联融合后保存下来，来源于麂属动物祖先染色体着丝粒的一种卫星DNA。卫星DNA I在这四种麂属动物染色体上的分布也表明黑麂、费氏麂和贡山麂与赤麂的核型演化过程相似，很可能从一个2n ＝ 70的共同祖先通过一系列的串联易位进化而来。 2) 将卫星DNA II（BM700和FM700）克隆探针分别杂交到黑麂和费氏麂的染色体上，只检测到几对间隔分布的信号。这提示在核型进化过程中不同卫星DNA间可能发生了广泛的重组，从而导致卫星DNA II大量丢失。大部分重组断裂位点可能位于卫星DNA I 与卫星DNA II之间，或者在卫星DNA II 区域内。 2．六带犰狳重复序列家族的克隆、序列分析和染色体定位 六带犰狳属于犰狳科、贫齿目，是六带犰狳属中唯一的一个代表物种。系统发育研究认为贫齿目与非洲兽总目是有胎盘哺乳动物中最原始的两个类群。C显带结果揭示六带犰狳30%的基因组是由组成性异染色质构成的，并且C带分布的位置也较复杂，提示在六带犰狳基因组中存在多种重复序列元件。 为了研究六带犰狳异染色质的组成，我从六带犰狳的基因组中克隆了七种位点特异性的重复序列。根据测序结果以及它们在染色体上的分布，将这些重复序列分为五个重复序列家族。其中AMD-EcoRI 837与AMD-BglII 811的序列相似，都是由大小约116 bp的单位组成，分布在大多数染色体的着丝粒区域，同时在一些染色体臂也有分布。AMD-EcoRI 832，AMD-EcoRI 836和AMD-EcoRI 934是特定染色体的重复序列，并且都分布于着丝粒区域。另外，AMD-BglII 634，AMD-EcoRI 731两个克隆都属于长散在分布重复序列(L1)，倾向于分布在G带阳性、富含AT碱基的区域，并且这两种重复序列在染色体上的定位与C带阳性的非着丝粒的异染色质区域很相似。本研究提供了六带犰狳异染色质区域的部分基因组信息，并且这些重复序列家族也可以用于研究六带犰狳及其近缘物种的系统发育关系。