Molecular cytogenetic analysis reveals the existence of two independent neo-XY sex chromosome systems in Anatolian Pamphagidae grasshoppers

Structure and Evolution of Ribosomal Genes of Insect Chromosomes

Currently, clusters of 45S and 5S ribosomal DNA (rDNA) have been studied in about 1000 and 100 species of the class Insecta, respectively. Although the number of insect species with known 45S rDNA clusters (also referred to as nucleolus-organizing regions, or NORs) constitutes less than 0.1 percent of the described members of this enormous group, certain conclusions can already be drawn. Since haploid karyotypes with single 45S and 5S rDNA clusters predominate in both basal and derived insect groups, this character state is apparently ancestral for the class Insecta in general. Nevertheless, the number, chromosomal location, and other characteristics of both 45S and 5S rDNA sites substantially vary across different species, and sometimes even within the same species. There are several main factors and molecular mechanisms that either maintain these parameters or alter them on the short-term and/or long-term scale. Chromosome structure (i.e., monocentric vs. holokinetic chromosomes), excessive numbers of rRNA gene copies per cluster, interactions with transposable elements, pseudogenization, and meiotic recombination are perhaps the most important among them.

New insights into the chromosomes of stoneflies: I. Karyotype, C-banding and localization of ribosomal and telomeric DNA markers in Skwalacompacta (McLachlan, 1872) (Polyneoptera, Plecoptera, Perlodidae) from Siberia

This study provides data on chromosome number (2n♂♀=26), sex determination mechanism (XY♂/XX♀), C-banding pattern, distribution of clusters of telomeric TTAGG repeats and 18S ribosomal DNA in the karyotype of the stonefly Skwalacompacta (McLachlan, 1872). For the first time in the history of stoneflies cytogenetics, we provide photos of the chromosomes of the Plecoptera insects. The karyotype of males and females of S.compacta consists of 12 pairs of autosomes. Three pairs of large autosomes and four pairs of medium-sized autosomes are subacrocentric. The remaining pairs of autosomes are small, with unclear morphology. Pericentromeric C-bands were revealed in all autosomes. The sex chromosomes are also subacrocentric. The short arms of X and Y chromosomes are entirely heterochromatic and are rich in ribosomal DNA sequences. In the X chromosome this arm is larger than in the Y chromosome. It is likely that this arm associated with the nucleolar organizer (NOR). Telomeric DNA (TTAGG)n repeats were detected in the terminal regions of all chromosomes.

On the Origin of Neo-Sex Chromosomes in the Neotropical Dragonflies Rhionaeschna bonariensis and R. planaltica (Aeshnidae, Odonata)

Odonata have holokinetic chromosomes. About 95% of species have an XX/X0 sex chromosome system, with heterogametic males. There are species with neo-XX/neo-XY sex chromosomes resulting from an X chromosome/autosome fusion. The genus Rhionaeschna includes 42 species found in the Americas. We analyzed the distribution of the nucleolar organizer region (NOR) using FISH with rDNA probes in Rhionaeschna bonariensis (n = 12 + neo-XY), R. planaltica (n = 7 + neo-XY), and Aeshna cyanea (n = 13 + X0). In R. bonariensis and A. cyanea, the NOR is located on a large pair of autosomes, which have a secondary constriction in the latter species. In R. planaltica, the NOR is located on the ancestral part of the neo-X chromosome. Meiotic analysis and FISH results in R. planaltica led to the conclusion that the neo-XY system arose by insertion of the ancestral X chromosome into an autosome. Genomic in situ hybridization, performed for the first time in Odonata, highlighted the entire neo-Y chromosome in meiosis of R. bonariensis, suggesting that it consists mainly of repetitive DNA. This feature and the terminal chiasma localization suggest an ancient origin of the neo-XY system. Our study provides new information on the origin and evolution of neo-sex chromosomes in Odonata, including new types of chromosomal rearrangements, NOR transposition, and heterochromatin accumulation.

New insights into the six decades of Mesa’s hypothesis of chromosomal evolution in Ommexechinae grasshoppers (Orthoptera: Acridoidea)

In Acridoidea grasshoppers, chromosomal rearrangements are frequently found as deviations from the standard acrocentric karyotype (2n = 23♂/24♀, FN = 23♂/24♀) in either phylogenetically unrelated species or shared by closely related ones, i.e. genus. In the South American subfamily Ommexechinae, most of the species show a unique karyotype (2n = 23♂/24♀, FN = 25♂/26♀) owing to the occurrence of a large autosomal pair (L1) with submetacentric morphology. In the early 1960s, Alejo Mesa proposed the hypothesis of an ancestral pericentric inversion to explain this karyotype variation. Furthermore, in Ommexechinae, extra chromosomal rearrangements (e.g. centric fusions) are recorded between the ancestral X chromosome and autosomes that originated the so-called neo-sex chromosomes. However, the evolutionary significance of the pericentric inversions and centric fusions in Ommexechinae remains poorly explored. Aiming for a better understanding of chromosomal evolution in Ommexechinae, we performed a detailed cytogenetic analysis in five species. Our findings support the hypothesis about the occurrence of an early pericentric inversion in the ancestor of Ommexechinae. Moreover, our results show a complex karyotype diversification pattern due to several chromosome rearrangements, variations in heterochromatin and repetitive DNA dynamics. Finally, the chromosomal mapping of U2 snDNA in L1 provided new insights about the morphological evolution of this autosomal pair and revealed unnoticed chromosome reorganizations.

High karyotypic variation in Orthemis Hagen, 1861 species, with insights about the neo-XY in Orthemisambinigra Calvert, 1909 (Libellulidae, Odonata)

The American dragonfly genus Orthemis Hagen, 1861 is mainly found in the Neotropical region. Seven of 28 taxonomically described species have been reported from Argentina. Chromosome studies performed on this genus showed a wide variation in chromosome number and a high frequency of the neoXY chromosomal sex-determination system, although the sexual pair was not observed in all cases. This work analyzes the spermatogenesis of Orthemisdiscolor (Burmeister, 1839), O.nodiplaga Karsch, 1891 and O.ambinigra Calvert, 1909 in individuals from the provinces of Misiones and Buenos Aires, Argentina. Orthemisdiscolor has 2n=23, n=11+X and one larger bivalent. Orthemisnodiplaga exhibits the largest chromosome number of the order, 2n=41, n=20+X and small chromosomes. Orthemisambinigra shows a reduced complement, 2n=12, n=5+neo-XY, large-sized chromosomes, and a homomorphic sex bivalent. Fusions and fragmentations are the main evolutionary mechanisms in Odonata, as well as in other organisms with holokinetic chromosomes. Orthemisnodiplaga would have originated by nine autosomal fragmentations from the ancestral karyotype of the genus (2n=22A+X in males). We argue that the diploid number 23 in Orthemis has a secondary origin from the ancestral karyotype of family Libellulidae (2n=25). The complement of O.ambinigra would have arisen from five autosomal fusions and the insertion of the X chromosome into a fused autosome. C-banding and DAPI/CMA₃ staining allowed the identification of the sexual bivalent, which revealed the presence of constitutive heterochromatin. We propose that the chromosome with intermediate C-staining intensity and three medial heterochromatic regions corresponds to the neo-Y and that the neo-system of this species has an ancient evolutionary origin. Moreover, we discuss on the mechanisms involved in the karyotypic evolution of this genus, the characteristics of the neo sex-determining systems and the patterns of heterochromatin distribution, quantity and base pair richness.

Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis, a zoophytophagous predatory bug that is both a biological control agent and a pest

Nesidiocoris tenuis (Reuter) is an efficient predatory biological control agent used throughout the Mediterranean Basin in tomato crops but regarded as a pest in northern European countries. From the family Miridae, it is an economically important insect yet very little is known in terms of genetic information and no genomic or transcriptomic studies have been published. Here, we use a linked-read sequencing strategy on a single female N. tenuis. From this, we assembled the 355 Mbp genome and delivered an ab initio, homology-based and evidence-based annotation. Along the way, the bacterial "contamination" was removed from the assembly. In addition, bacterial lateral gene transfer (LGT) candidates were detected in the N. tenuis genome. The complete gene set is composed of 24 688 genes; the associated proteins were compared to other hemipterans (Cimex lectularis, Halyomorpha halys and Acyrthosiphon pisum). We visualized the genome using various cytogenetic techniques, such as karyotyping, CGH and GISH, indicating a karyotype of 2n = 32. Additional analyses include the localization of 18S rDNA and unique satellite probes as well as pooled sequencing to assess nucleotide diversity and neutrality of the commercial population. This is one of the first mirid genomes to be released and the first of a mirid biological control agent.

Karyotypes diversity in some Iranian Pamphagidae grasshoppers (Orthoptera, Acridoidea, Pamphagidae): new insights on the evolution of the neo-XY sex chromosomes

For the first time, cytogenetic features of grasshoppers from Iran have been studied. In this paper we conducted a comparative cytogenetic analysis of six species from the family Pamphagidae. The species studied belong to subfamilies Thrinchinae Stål, 1876 (Eremopeza bicoloripes (Moritz, 1928), E. saussurei (Uvarov, 1918)) and Pamphaginae (Saxetania paramonovi (Dirsh, 1927), Tropidauchen escalerai Bolívar, 1912, Tropidauchen sp., and Paranothrotes citimus Mistshenko, 1951). We report information about the chromosome number and morphology, C-banding patterns, and localization of ribosomal DNA clusters and telomeric (TTAGG)n repeats. Among these species, only S. paramonovi had an ancestral Pamphagidae karyotype (2n=18+X0♂; FN=19♂). The karyotypes of the remaining species differed from the ancestral karyotypes. The karyotypes of E. bicoloripes and E. saussurei, despite having the same chromosome number (2n=18+X0♂) had certain biarmed chromosomes (FN=20♂ and FN=34♂ respectively). The karyotypes of T. escalerai and Tropidauchen sp. consisted of eight pairs of acrocentric autosomes, one submetacentric neo-X chromosome and one acrocentric neo-Y chromosome in males (2n=16+neo-X neo-Y♂). The karyotype of P. citimus consisted of seven pairs of acrocentric autosomes, submetacentric the neo-X1 and neo-Y and acrocentric the neo-X2 chromosomes (2n=14+neo-X1 neo-X2 neo-Y♂). Comparative analysis of the localization and size of C-positive regions, the position of ribosomal clusters and the telomeric DNA motif in the chromosomes of the species studied, revealed early unknown features of their karyotype evolution. The data obtained has allowed us to hypothesize that the origin and early phase of evolution of the neo-Xneo-Y♂ sex chromosome in the subfamily Pamphaginae, are linked to the Iranian highlands.

Snake W Sex Chromosome: The Shadow of Ancestral Amniote Super-Sex Chromosome

: Heteromorphic sex chromosomes, particularly the ZZ/ZW sex chromosome system of birds and some reptiles, undergo evolutionary dynamics distinct from those of autosomes. The W sex chromosome is a unique karyological member of this heteromorphic pair, which has been extensively studied in snakes to explore the origin, evolution, and genetic diversity of amniote sex chromosomes. The snake W sex chromosome offers a fascinating model system to elucidate ancestral trajectories that have resulted in genetic divergence of amniote sex chromosomes. Although the principal mechanism driving evolution of the amniote sex chromosome remains obscure, an emerging hypothesis, supported by studies of W sex chromosomes of squamate reptiles and snakes, suggests that sex chromosomes share varied genomic blocks across several amniote lineages. This implies the possible split of an ancestral super-sex chromosome via chromosomal rearrangements. We review the major findings pertaining to sex chromosomal profiles in amniotes and discuss the evolution of an ancestral super-sex chromosome by collating recent evidence sourced mainly from the snake W sex chromosome analysis. We highlight the role of repeat-mediated sex chromosome conformation and present a genomic landscape of snake Z and W chromosomes, which reveals the relative abundance of major repeats, and identifies the expansion of certain transposable elements. The latest revolution in chromosomics, i.e., complete telomere-to-telomere assembly, offers mechanistic insights into the evolutionary origin of sex chromosomes.

Genome Size of 17 Species From Caelifera (Orthoptera) and Determination of Internal Standards With Very Large Genome Size in Insecta

Comparative studies of insect genome size show that Orthoptera is a unique group of Insecta with a significantly enlarged genome. To determine a suitable internal standard for a large genome and to compare the effects of different internal standards on estimates of genome size, we used four internal standards to estimate nuclear DNA content in nine insect species with large genomes. The results showed that the combination of two internal standards, Locusta migratoria (♂1C = 6.20 pg, ♀1C = 6.60 pg) and Periplaneta americana♂ (1C = 3.41 pg), was suitable for estimating large genome of Caelifera by flow cytometry. Using these two internal standards, we estimated the genome sizes of 17 species of Caelifera (12 genera in Acrididae, 2 genera in Pamphagidae, 1 genus in Pyrgomorphidae) using flow cytometry. Genomes ranged from 6.57 pg (Shirakiacris shirakii) to 18.64 pg (Bryodemella holdereri), the largest described in insects to date. These species showed significant genomic dimorphism based on sex: females had a 0.56 pg larger genome than males on average, which might be due to the sex chromosome determinism mechanism of X0(♂)/XX(♀). To test the results obtained by flow cytometry, we used k-mers of Illumina sequencing data to gauge the C-value of Calliptamus abbreviatus and Haplotropis brunneriana. The results of the two methods are slightly different. Genomes were estimated to be about 0.28 and 0.26 pg smaller, respectively, than the flow cytometry values. Furthermore, we also reconstructed the evolutionary relationships of these taxa and discuss the genome size evolution in a phylogenetic framework.

Patterns of Sex Chromosome Differentiation in Spiders: Insights from Comparative Genomic Hybridisation

Spiders are an intriguing model to analyse sex chromosome evolution because of their peculiar multiple X chromosome systems. Y chromosomes were considered rare in this group, arising after neo-sex chromosome formation by X chromosome-autosome rearrangements. However, recent findings suggest that Y chromosomes are more common in spiders than previously thought. Besides neo-sex chromosomes, they are also involved in the ancient X1X2Y system of haplogyne spiders, whose origin is unknown. Furthermore, spiders seem to exhibit obligatorily one or two pairs of cryptic homomorphic XY chromosomes (further cryptic sex chromosome pairs, CSCPs), which could represent the ancestral spider sex chromosomes. Here, we analyse the molecular differentiation of particular types of spider Y chromosomes in a representative set of ten species by comparative genomic hybridisation (CGH). We found a high Y chromosome differentiation in haplogyne species with X1X2Y system except for Loxosceles spp. CSCP chromosomes exhibited generally low differentiation. Possible mechanisms and factors behind the observed patterns are discussed. The presence of autosomal regions marked predominantly or exclusively with the male or female probe was also recorded. We attribute this pattern to intraspecific variability in the copy number and distribution of certain repetitive DNAs in spider genomes, pointing thus to the limits of CGH in this arachnid group. In addition, we confirmed nonrandom association of chromosomes belonging to particular CSCPs at spermatogonial mitosis and spermatocyte meiosis and their association with multiple Xs throughout meiosis. Taken together, our data suggest diverse evolutionary pathways of molecular differentiation in different types of spider Y chromosomes.

Comparative analysis of C-heterochromatin, ribosomal and telomeric DNA markers in chromosomes of Pamphagidae grasshoppers from Morocco

The karyotypes and the localization of C-bands, clusters of ribosomal DNA and telomeric repeats of 10 species of the family Pamphagidae from Morocco are described for the first time. The species studied belong to the subfamilies Pamphaginae and Thrinchinae. All species have karyotypes consisting of 19 and 20 acrocentric chromosomes and X0/XX sex chromosome system in males and females, respectively (2n♂=19, NF=19; 2n♀=20, NF=20). Despite the karyotype conservatism, we revealed differences in the location and size of C-heterochromatin blocks and ribosomal DNA clusters. A comparative analysis of these differences shows that karyotype divergences in this group is connected not to structural chromosome rearrangements, but to the evolution of repetitive DNA.

B Chromosomes in Grasshoppers: Different Origins and Pathways to the Modern Bs

B chromosomes (B_s) were described in most taxa of eukaryotes and in around 11.9% of studied Orthopteran species. In some grasshopper species, their evolution has led to many B chromosome morphotypes. We studied the B_s in nine species (Nocaracris tardus, Nocaracris cyanipes, Aeropus sibiricus, Chorthippus jacobsoni, Chorthippus apricarius, Bryodema gebleri, Asiotmethis heptapotamicus songoricus, Podisma sapporensis, and Eyprepocnemis plorans), analyzing their possible origin and further development. The studied B_s consisted of C-positive or C-positive and C-negative regions. Analyzing new data and considering current hypotheses, we suggest that B_s in grasshoppers could arise through different mechanisms and from different chromosomes of the main set. We gave our special attention to the B_s with C-negative regions and suggest a new hypothesis of B chromosome formation from large or medium autosomes. This hypothesis includes dissemination of repetitive sequences and development of intercalary heterochromatic blocks in euchromatic chromosome arm followed by deletion of euchromatic regions located between them. The hypothesis is based on the findings of the Eyprepocnemis plorans specimens with autosome containing numerous intercalary repeat clusters, analysis of C-positive B_s in Eyprepocnemis plorans and Podisma sapporensis containing intercalary and terminal C-negative regions, and development of heterochromatic neo-Y chromosome in some Pamphagidae grasshoppers.

Origin and Evolution of the Neo-Sex Chromosomes in Pamphagidae Grasshoppers through Chromosome Fusion and Following Heteromorphization

In most phylogenetic lineages, the evolution of sex chromosomes is accompanied by their heteromorphization and degradation of one of them. The neo-sex chromosomes are useful model for studying early stages of these processes. Recently two lineages of the neo-sex chromosomes on different stages of heteromorphization was discovered in Pamphagidae family. The neo-sex chromosome heteromorphization was analyzed by generation of DNA probes derived from the neo-Xs and neo-Ys followed with chromosome painting in nineteen species of Pamphagidae family. The homologous regions of the neo-sex chromosomes were determined in closely related species with the painting procedure and image analysis with application of the Visualization of the Specific Signal in Silico software package. Results of these analyses and distribution of C-positive regions in the neo-sex chromosomes revealed details of the heteromorphization of the neo-sex chromosomes in species from both phylogenetic lineages of Pamphagidae grasshoppers. The hypothetical mechanism of the neo-Y degradation was suggested. It includes expansion of different repeats from the proximal neo-Y chromosome region by inversions, spreading them towards distal region. Amplification of these repeats leads to formation of C-positive regions and elimination of the C-negative regions located between them.

Comparative analysis of chromosomal localization of ribosomal and telomeric DNA markers in three species of Pyrgomorphidae grasshoppers

The karyotypes of three species of Pyrgomorphidae grasshoppers were studied: Zonocerus elegans (Thunberg, 1815), Pyrgomorpha guentheri (Burr, 1899) and Atractomorpha lata (Mochulsky, 1866). Data on karyotypes of P. guentheri and Z. elegans are reported here for the first time. All species have karyotypes consisting of 19 acrocentric chromosomes in males and 20 acrocentric chromosomes in females (2n♂=19, NF=19; 2n♀=20, NF=20) and X0/XX sex determination system. A comparative analysis of the localization of C-heterochromatin, clusters of ribosomal DNA, and telomere repeats revealed inter-species diversity in these cytogenetic markers. These differences indicate that the karyotype divergence in the species studied is not associated with structural chromosome rearrangements, but with the evolution of repeated DNA sequences.