The role of rDNA genes in X chromosome association in the aphid Acyrthosiphon pisum

Comparative mapping of a new repetitive DNA sequence and chromosome region-specific probes unveiling rearrangements in an Amazonian frog complex

The frog species Physalaemus ephippifer exists in the Amazonian region and harbors heteromorphic Z and W chromosomes. A genetic lineage closely related to this species was recognized based on its mitochondrial DNA and RADseq-style markers, but its taxonomic status is still unclear and has been referred to as Lineage 1 of "P. cuvieri". The heteromorphic sex chromosomes found in P. ephippifer are not present in this lineage and which of its chromosome pairs is homologous to the sex chromosomes of P. ephippifer remain to be elucidated as well as the role of such a karyotypic divergence in the evolution of these frogs. Here, we described a new family of repetitive DNA and used its chromosomal sites along with the markers detected by a probe constructed from the microdissected segment of the Z chromosome of P. ephippifer to infer chromosomal homology. We also analyzed an unnamed species that is considered to be the sister group of the clade composed of Lineage 1 of "P. cuvieri" and P. ephippifer. Our results suggest that complex rearrangements involving the chromosomes that were inferred to be homeologous to the sex chromosomes of P. ephippifer have occurred during the divergence of this group of frogs.

Evolutionary pattern of karyotypes and meiosis in pholcid spiders (Araneae: Pholcidae): implications for reconstructing chromosome evolution of araneomorph spiders

BACKGROUND

Despite progress in genomic analysis of spiders, their chromosome evolution is not satisfactorily understood. Most information on spider chromosomes concerns the most diversified clade, entelegyne araneomorphs. Other clades are far less studied. Our study focused on haplogyne araneomorphs, which are remarkable for their unusual sex chromosome systems and for the co-evolution of sex chromosomes and nucleolus organizer regions (NORs); some haplogynes exhibit holokinetic chromosomes. To trace the karyotype evolution of haplogynes on the family level, we analysed the number and morphology of chromosomes, sex chromosomes, NORs, and meiosis in pholcids, which are among the most diverse haplogyne families. The evolution of spider NORs is largely unknown.

RESULTS

Our study is based on an extensive set of species representing all major pholcid clades. Pholcids exhibit a low 2n and predominance of biarmed chromosomes, which are typical haplogyne features. Sex chromosomes and NOR patterns of pholcids are diversified. We revealed six sex chromosome systems in pholcids (X0, XY, X1X20, X1X2X30, X1X2Y, and X1X2X3X4Y). The number of NOR loci ranges from one to nine. In some clades, NORs are also found on sex chromosomes.

CONCLUSIONS

The evolution of cytogenetic characters was largely derived from character mapping on a recently published molecular phylogeny of the family. Based on an extensive set of species and mapping of their characters, numerous conclusions regarding the karyotype evolution of pholcids and spiders can be drawn. Our results suggest frequent autosome-autosome and autosome-sex chromosome rearrangements during pholcid evolution. Such events have previously been attributed to the reproductive isolation of species. The peculiar X1X2Y system is probably ancestral for haplogynes. Chromosomes of the X1X2Y system differ considerably in their pattern of evolution. In some pholcid clades, the X1X2Y system has transformed into the X1X20 or XY systems, and subsequently into the X0 system. The X1X2X30 system of Smeringopus pallidus probably arose from the X1X20 system by an X chromosome fission. The X1X2X3X4Y system of Kambiwa probably evolved from the X1X2Y system by integration of a chromosome pair. Nucleolus organizer regions have frequently expanded on sex chromosomes, most probably by ectopic recombination. Our data suggest the involvement of sex chromosome-linked NORs in achiasmatic pairing.

Comparative Gene Mapping as a Tool to Understand the Evolution of Pest Crop Insect Chromosomes

The extent of the conservation of synteny and gene order in aphids has been previously investigated only by comparing a small subset of linkage groups between the pea aphid Acyrthosiphon pisum and a few other aphid species. Here we compared the localization of eight A. pisum scaffolds (covering more than 5 Mb and 83 genes) in respect to the Drosophila melanogaster Muller elements identifying orthologous loci spanning all the four A. pisum chromosomes. Comparison of the genetic maps revealed a conserved synteny across different loci suggesting that the study of the fruit fly Muller elements could favour the identification of chromosomal markers useful for the study of chromosomal rearrangements in aphids. A. pisum is the first aphid species to have its genome sequenced and the finding that there are several chromosomal regions in synteny between Diptera and Hemiptera indicates that the genomic tools developed in A. pisum will be broadly useful not only for the study of other aphids but also for other insect species.

Occurrence of Rabl-like telomere clustering in the holocentric chromosomes of the peach potato aphid Myzus persicae (Hemiptera; Aphididae)

Several studies demonstrated that chromosome anchoring to nuclear structures is involved in the organization of the interphase nucleus. The Rabl configuration, a well-studied chromosome organization in the interphase nucleus, has been deeply studied in organisms with monocentric chromosomes but just slightly touched in species with holocentric chromosomes. In the present paper, by means of the isolation and chromosomal mapping of the C0t DNA fraction and chromatin immunoprecipitation with anti-LEM-2 antibodies, we evidenced the presence of few foci where telomeres and subtelomeric regions cluster in the aphid interphase nuclei, suggesting the occurrence of a Rabl-like chromosome configuration. The same experimental approaches also evidenced that most of the repetitive DNA of the 2 X chromosomes is located at the periphery of the nucleus, whereas the ribosomal genes, located at 1 telomere of each X chromosome, are present towards the inner portion of the nucleus, favoring their transcriptional activity.

The cytogenetic architecture of the aphid genome

In recent years aphids, with their well-defined polyphenism, have become favoured as model organisms for the study of epigenetic processes. The availability of the pea aphid (Acyrthosiphon pisum) genome sequence has engendered much research aimed at elucidating the mechanisms by which the phenotypic plasticity of aphids is inherited and controlled. Yet so far this research effort has paid little attention to the cytogenetic processes that play a vital part in the organisation, expression and inheritance of the aphid genome. Aphids have holocentric chromosomes, which have very different properties from the chromosomes with localised centromeres that are found in most other organisms. Here we review the diverse forms of aphid chromosome behaviour that occur during sex determination and male and female meiosis, often in response to environmental changes and mediated by endocrine factors. Remarkable differences occur, even between related species, that could have significant effects on the inheritance of all or parts of the genome. In relation to this, we review the particular features of the distribution of heterochromatin, rDNA genes and other repetitive DNA in aphid chromosomes, and discuss the part that these may play in the epigenetic modification of chromatin structure and function.

Widespread selection across coding and noncoding DNA in the pea aphid genome

Genome-wide patterns of diversity and selection are critical measures for understanding how evolution has shaped the genome. Yet, these population genomic estimates are available for only a limited number of model organisms. Here we focus on the population genomics of the pea aphid (Acyrthosiphon pisum). The pea aphid is an emerging model system that exhibits a range of intriguing biological traits not present in classic model systems. We performed low-coverage genome resequencing of 21 clonal pea aphid lines collected from alfalfa host plants in North America to characterize genome-wide patterns of diversity and selection. We observed an excess of low-frequency polymorphisms throughout coding and noncoding DNA, which we suggest is the result of a founding event and subsequent population expansion in North America. Most gene regions showed lower levels of Tajima's D than synonymous sites, suggesting that the majority of the genome is not evolving neutrally but rather exhibits significant constraint. Furthermore, we used the pea aphid's unique manner of X-chromosome inheritance to assign genomic scaffolds to either autosomes or the X chromosome. Comparing autosomal vs. X-linked sequence variation, we discovered that autosomal genes show an excess of low frequency variants indicating that purifying selection acts more efficiently on the X chromosome. Overall, our results provide a critical first step in characterizing the genetic diversity and evolutionary pressures on an aphid genome.

Continuous occurrence of intra-individual chromosome rearrangements in the peach potato aphid, Myzus persicae (Sulzer) (Hemiptera: Aphididae)

Analysis of the holocentric mitotic chromosomes of the peach-potato aphid, Myzus persicae (Sulzer), from clones labelled 50, 51 and 70 revealed different chromosome numbers, ranging from 12 to 14, even within each embryo, in contrast to the standard karyotype of this species (2n = 12). Chromosome length measurements, combined with fluorescent in situ hybridization experiments, showed that the observed chromosomal mosaicisms are due to recurrent fragmentations of chromosomes X, 1 and 3. Contrary to what has generally been reported in the literature, X chromosomes were frequently involved in recurrent fragmentations, in particular at their telomeric ends opposite to the nucleolar organizer region. Supernumerary B chromosomes have been also observed in clones 50 and 51. The three aphid clones showed recurrent fissions of the same chromosomes in the same regions, thereby suggesting that the M. persicae genome has fragile sites that are at the basis of the observed changes in chromosome number. Experiments to induce males also revealed that M. persicae clones 50, 51 and 70 are obligately parthenogenetic, arguing that the reproduction by apomictic parthenogenesis favoured the stabilization and inheritance of the observed chromosomal fragments.

Cytogenetic and molecular analysis of the holocentric chromosomes of the potato aphid Macrosiphum euphorbiae (Thomas, 1878)

Cytogenetic and molecular investigations on the holocentric chromosomes of the aphid Macrosiphum euphorbiae (Thomas, 1878)have been carried out using silver staining and C-banding (followed by chromomycin A3 and DAPI staining) in order to improve our knowledge about the structure of aphid chromosomes. The C-banding pattern is peculiar since only the two X chromosomes and a single pair of autosomes presented heterochromatic bands. Silver staining and FISH with the 28S rDNA probe localized the rDNA genes on one telomere of each X chromosome that were also brightly fluorescent after chromomycin A3 staining of C-banded chromosomes, whereas all other heterochromatic bands were DAPI positive. Interestingly, a remarkable nucleolar organizing region (NOR) heteromorphism was present making the two X chromosomes easily distinguishable. Southern blotting and FISH assessed the presence of the (TTAGG)n repeat at the ends of all the Macrosiphum euphorbiae chromosomes. Karyotype analysis showed that all males possessed the X chromosome with the larger amount of rDNA suggesting a non-Mendelian inheritance of the two X chromosomes.

Genome sequence of the pea aphid Acyrthosiphon pisum

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

Heterochromatin characterization in five species of Heteroptera

The amount, composition and location of heterochromatin in Athaumastus haematicus (Stål, 1859), Leptoglossus impictus (Stål, 1859), Phthia picta (Drury, 1770) (Coreidae), Largus rufipennis Laporte, 1832 (Largidae) and Jadera sanguinolenta (Fabricius, 1775) (Rhopalidae) are analyzed by C-banding and DAPI/ CMA fluorescent banding. As the rule for Heteroptera the possession of holokinetic chromosomes and a pre-reductional type of meiosis cytogenetically characterize these five species. Besides, all of them (except L. rufipennis) present a pair of m chromosomes. C-banding technique reveals the absence of constitutive heterochromatin in A. haematicus, scarce C-positive blocks in L. impictus and J. sanguinolenta, and C-positive heterochromatin terminally located in P. picta and L. rufipennis. All C-bands are DAPI bright, except for a DAPI dull/CMA bright band at one telomeric end of the X chromosome in L. rufipennis, which probably corresponds to a nucleolar organizing region. The results of the banding techniques are analyzed in relation to the chiasma frequency and distribution in the five species, and it is concluded that there should exist some constraints to the acquisition and/ or accumulation of heterochromatin in their karyotypes.

Genetic mapping of aphicarus -- a sex-linked locus controlling a wing polymorphism in the pea aphid (Acyrthosiphon pisum)

We have initiated research to determine the genetic basis of a male wing polymorphism in the pea aphid Acyrthosiphon pisum (Hemiptera: Aphididae). Previous studies showed that this polymorphism is controlled by a single biallelic locus, which we name aphicarus (api), on the X chromosome. Our objectives were to confirm that api segregates as a polymorphism of a single gene on the X chromosome, and to obtain molecular markers flanking api that can be used as a starting point for high-resolution genetic and physical mapping of the target region, which will ultimately allow the cloning of api. We have established an F2 population segregating for api and have generated X-linked AFLP markers. The segregation pattern of api in the F2 population shows that the male wing polymorphism segregates as a polymorphism of a single gene, or set of closely linked genes on the X chromosome. Using a subset of 78 F2 males, we have constructed a linkage map of the chromosomal region encompassing api using seven AFLP markers. The map spans 74.1 cM and we have mapped api to an interval of 10 cM. In addition, we confirmed X linkage of our AFLP markers and api by using one X-linked marker developed in an earlier study. Our study presents the first mapping of a gene with known function in aphids, and the results indicate that target gene mapping in aphids is feasible.

Cytogenetic and molecular characterization of the MBSAT1 satellite DNA in holokinetic chromosomes of the cabbage moth, Mamestra brassicae (Lepidoptera)

Digestion of Mamestra brassicae DNA with DraI produced a prominent fragment of approximately 200 bp and a ladder of electrophoretic bands with molecular weights which are a multiple of 200 bp. Southern blotting revealed that this ladder is composed of DNA fragments that are multimers of the 200-bp DraI band suggesting that DraI isolated a satellite that has been called Mamestra brassicae satellite DNA1 (MBSAT1). MBSAT1 is the first satellite DNA isolated in Lepidoptera. In-situ DraI digestion of chromosome spreads, together with fluorescent in-situ hybridization, showed that MBSAT1 sequences are clustered in heterochromatin of the sex chromosomes, Z and W. MBSAT1 was 234 bp long with an AT content of 60.7%. The curvature-propensity plot suggested a curvature in the MBSAT1 structure.

Cytogenetic characterization of telomeres in the holocentric chromosomes of the lepidopteran Mamestra brassicae

Telomeres of the Mamestra brassica holocentric chromosomes were studied by Southern blotting, in-situ hybridization and Bal31 assay evidencing the presence of the telomeric (TTAGG)n repeat. Successively, molecular analysis of telomeres showed that TRAS1 transposable elements were present at the subtelomeric regions of autosomes but not in the NOR-bearing telomeres of the Z and W sex chromosomes. TRAS1 appeared to be transcriptionally active and non-methylated, as evaluated by RT-PCR and digestion with MspI and HpaII. Finally, dot-blotting experiments showed that the 2.8 +/- 0.5% of the M. brassicae genome consists of TRAS1.

Cytogenetic and molecular analysis of the pufferfish Tetraodon fluviatilis (Osteichthyes)

In view of their compact genome, pufferfish (Tetraodontiformes) have been proposed as model animal for the study of the vertebrate genome. Despite such interest, cytogenetic information about puffers is still scanty. To fill this gap, a cytogenetic analysis of T. fluviatilis has been performed using both classical and molecular techniques. C-banding, followed by DAPI staining, evidenced that in T. fluviatilis, like all other puffer species so far examined, heterochromatin is essentially AT-rich and it is located at centromeres, whereas staining with CMA3, silver staining and FISH with a 28S ribosomal RNA gene DNA probe showed 2-4 nucleolar organizing regions (NORs) located in heterochromatic regions in the considered puffer species. FISH with the 5S probe put in evidence both in T. fluviatilis and in T. nigroviridis only a 5S cluster per haploid genome that is physically unlinked with the major ribosomal RNA genes including the 28S rRNA genes. Hybridization with the (TTAGGG)n probe showed in all the puffers brightly fluorescent signals uniform both in size and intensity at the end of all the chromosomes. Finally, mariner-like elements (MLEs) have been identified in T. fluviatilis and they have located into the NOR-associated heterochromatin.

Cytogenetic analysis of the pufferfish Tetraodon fluviatilis (Osteichthyes)

Because of their compact genome, pufferfish (Tetraodontiformes) have been proposed as a model for the study of the vertebrate genome. The genome of pufferfish is peculiar as it has the structural complexity of the genomes of higher vertebrates, but has small introns and lacks large clusters of highly repetitive sequences. Despite such interest, information about the genetics of pufferfish is still scanty. To fill this gap, we have performed a cytogenetic analysis of the pufferfish, Tetraodon fluviatilis, which can be maintained in an aquarium for a long time and, unlike the pufferfish, Fugu rubripes, it is not difficult to obtain. Karyotype analysis shows that T. fluviatilis has 2n = 42 with two metacentric chromosomes, four submetacentrics, two subtelocentrics and 34 acrocentrics. C-banding, followed by DAPI staining, showed that heterochromatin is essentially AT-rich and is located at centromeres. Staining of the same metaphase plates with CMA3 showed the presence of four heterochromatic regions located on two pairs of submetacentric chromosomes. Silver staining and FISH with a 28S rDNA probe showed that these GC-rich regions are nucleolar organizing regions (NORs). Finally, regardless of the technique used, no difference in the chromosome complement was found between males and females.

NOR heteromorphism within a parthenogenetic lineage of the aphid Megoura viciae

In parthenogenetic females of a clone of the aphid Megoura viciae (Homoptera, Aphididae), more than 50% of the cells show heteromorphism between homologous NORs which are located on one telomeric region of the two X chromosomes. Using different techniques, such as staining with the CG-specific fluorochrome chromomycin A3, silver staining and in-situ hybridization with an rDNA probe, we have shown that the observed heteromorphism is due to an unequal distribution of ribosomal genes between homologous NOR regions. The total number of rDNA genes per individual aphid remained constant. Moreover, the analysis of cells from single embroys has shown that the observed heteromorphism is not only intraclonal but also intraindividual. These data, together with the finding of X chromosomes connected by chromatin bridges between their NORs, allow us to suggest that mitotic unequal crossing over could be the main cause of NOR heteomorphism in this taxon.