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State-of-the-Art in Insect Cytogenetics
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State-of-the-Art in Insect Cytogenetics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Cytogenomics".

Deadline for manuscript submissions: closed (10 November 2023) | Viewed by 11110

Special Issue Editors

Prof. Dr. Pedro Lorite Martínez

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Guest Editor
Department of Experimental Biology, Genetic Area, University of Jaén, 23071 Jaén, Spain
Interests: insects; chromosome; heterochromatin; repetitive DNA; molecular cytogenetics; cytogenomics
Prof. Dr. Teresa Palomeque

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Guest Editor
Department of Experimental Biology, University of Jaén, 23071 Jaén, Spain
Interests: insects; chromosome; heterochromatin; repetitive DNA; molecular cytogenetics; cytogenomics
Dr. Eugenia E. Montiel

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Guest Editor
Department of Experimental Biology, University of Jaén, 23071 Jaén, Spain
Interests: insects; chromosome; heterochromatin; repetitive DNA; molecular cytogenetics; cytogenomics
Dr. Pablo Mora

E-Mail Website
Guest Editor
Laboratory of Chromosomics, University of South Bohemia, České Budějovice, Czech Republic
Interests: insects; chromosome; heterochromatin; repetitive DNA; molecular cytogenetics; cytogenomics

Special Issue Information

Dear Colleagues,

Insects represent the most wonderful and variable and numerous group of organisms that populate the Earth. Insect habitat spans the entire planet, with more than five million potentially recognized species, and most of them are cytogenetically unknown. Insects play an important role for humans as transmitters of certain diseases, as both crop pests and allies to combat pests of crops of economic interest, among other human–insect interactions. In recent years, several groups of insects have been considered as sensors of climate change, since climate change can affect their life cycles and population sizes.

Chromosomal banding and the application of molecular cytogenetics techniques (e.g., fluorescence in situ hybridization (FISH) with specific probes, genomic in situ hybridization (GISH) or chromosome painting) to insect chromosomes have made it possible to identify specific regions on the chromosomes and analyze chromosome rearrangements and chromosome evolution. These studies have demonstrated the diversity in the function and structure of insect chromosomes, on many occasions linked to the varied and complex life cycles of insects.

Knowledge of the typical evolutionarily important characteristics of karyotypes, such as sex chromosomes, heterochromatin, supernumerary elements, number and location of rDNA genes, among others, has undergone rapid development. The joint application of the indicated techniques with next-generation sequencing (NGS) data already applied in insects is providing numerous important data on the composition and structure of insect chromosomes. The application of other new techniques can significantly increase knowledge of insect chromosomes. Among these techniques, we highlight molecular combing, designed to identify amplifications, microdeletions, and rearrangements in a DNA sequence and to study the process of DNA replication. Equally interesting are chromosome orientation FISH (CO-FISH), which makes it possible to selectively mark one of the two homologous strands of a chromosome; and Comet-FISH, a fluorescence-microscopy-based technique used to measure DNA damage and repair at the level of individual cells. Finally, the combined application of FISH with the CRISPR/Cas9 system can provide important data on the cytogenetics of insects.

For this Special Issue, original research articles and reviews addressing important questions related to these fields using standard or new molecular cytogenetic techniques are welcome.

Prof. Dr. Pedro Lorite
Prof. Dr. Teresa Palomeque
Dr. Eugenia E. Montiel
Dr. Pablo Mora
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • chromosome organization
  • chromosome evolution
  • chromosome composition
  • heterochromatin
  • fluorescence in situ hybridization
  • molecular cytogenetics
  • cytogenomics

Published Papers (6 papers)

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Research

13 pages, 657 KiB  
Article
Expanding the Chromosomal Evolution Understanding of Lygaeioid True Bugs (Lygaeoidea, Pentatomomorpha, Heteroptera) by Classical and Molecular Cytogenetic Analysis
by Natalia V. Golub, Anna Maryańska-Nadachowska, Boris A. Anokhin and Valentina G. Kuznetsova
Genes 2023, 14(3), 725; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14030725 - 15 Mar 2023
Cited by 3 | Viewed by 1353
Abstract
The Lygaeoidea comprise about 4660 species in 790 genera and 16 families. Using standard chromosome staining and FISH with 18S rDNA and telomeric (TTAGG)n probes, we studied male karyotypes and meiosis in 10 species of Lygaeoidea belonging to eight genera of the [...] Read more.
The Lygaeoidea comprise about 4660 species in 790 genera and 16 families. Using standard chromosome staining and FISH with 18S rDNA and telomeric (TTAGG)n probes, we studied male karyotypes and meiosis in 10 species of Lygaeoidea belonging to eight genera of the families Blissidae, Cymidae, Heterogastridae, Lygaeidae, and Rhyparochromidae. Chromosome numbers were shown to range from 12 to 28, with 2n = 14 being predominant. All species have an XY system and all but one have a pair of m-chromosomes. The exception is Spilostethus saxatilis (Lygaeidae: Lygaeinae); in another species of Lygaeinae, Thunbergia floridulus, m-chromosomes were present, which represents the first finding for this subfamily. All species have an inverted sequence of sex chromosome divisions (“post-reduction”). The 18S rDNA loci were observed on one or both sex chromosomes in Kleidocerys resedae and Th. floridulus, respectively (Lygaeidae), while on an autosomal bivalent in all other species. The rDNA loci tended to be close to the end of the chromosome. Using (TTAGG)n—FISH, we were able to show for the first time that the Lygaeoidea lack the canonical “insect” telomere motif (TTAGG)n. We speculate that this ancestral motif is absent from the entire infraorder Pentatomomorpha being replaced by some other telomere repeat motif sequences. Full article
(This article belongs to the Special Issue State-of-the-Art in Insect Cytogenetics)
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12 pages, 2717 KiB  
Article
The Satellite DNAs Populating the Genome of Trigona hyalinata and the Sharing of a Highly Abundant satDNA in Trigona Genus
by Jaqueline A. Pereira, Diogo C. Cabral-de-Mello and Denilce M. Lopes
Genes 2023, 14(2), 418; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14020418 - 6 Feb 2023
Cited by 3 | Viewed by 1471
Abstract
Among Meliponini species, c-heterochromatin can occupy large portions of chromosomes. This characteristic could be useful for understanding evolutionary patterns of satellite DNAs (satDNAs), although few sequences have been characterized in these bees. In Trigona, phylogenetically represented by clades A and B, [...] Read more.
Among Meliponini species, c-heterochromatin can occupy large portions of chromosomes. This characteristic could be useful for understanding evolutionary patterns of satellite DNAs (satDNAs), although few sequences have been characterized in these bees. In Trigona, phylogenetically represented by clades A and B, the c-heterochromatin is mostly located in one chromosome arm. Here we used different techniques, including restriction endonucleases and genome sequencing followed by chromosomal analysis, to identify satDNAs that may be contributing to the evolution of c-heterochromatin in Trigona. Our results revealed a highly abundant ThyaSat01-301 satDNA, corresponding to about 13.77% of the Trigona hyalinata genome. Another seven satDNAs were identified, one corresponding to 2.24%, and the other six corresponding to 0.545% of the genome. The satDNA ThyaSat01-301 was shown to be one of the main constituents of the c-heterochromatin of this species, as well as of other species belonging to clade B of Trigona. However, this satDNA was not observed on the chromosomes of species from clade A, demonstrating that the c-heterochromatin is evolving divergently between species of clade A and B, as a consequence of the evolution of repetitive DNA sequences. Finally, our data suggest the molecular diversification of the karyotypes, despite a conservated macrochromosomal structure on the genus. Full article
(This article belongs to the Special Issue State-of-the-Art in Insect Cytogenetics)
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18 pages, 4409 KiB  
Article
Tandem Repeat DNA Provides Many Cytological Markers for Hybrid Zone Analysis in Two Subspecies of the Grasshopper Chorthippus parallelus
by Beatriz Navarro-Domínguez, Josefa Cabrero, María Dolores López-León, Francisco J. Ruiz-Ruano, Miguel Pita, José L. Bella and Juan Pedro M. Camacho
Genes 2023, 14(2), 397; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14020397 - 3 Feb 2023
Cited by 3 | Viewed by 1902
Abstract
Recent advances in next generation sequencing (NGS) have greatly increased our understanding of non-coding tandem repeat (TR) DNA. Here we show how TR DNA can be useful for the study of hybrid zones (HZ), as it serves as a marker to identify introgression [...] Read more.
Recent advances in next generation sequencing (NGS) have greatly increased our understanding of non-coding tandem repeat (TR) DNA. Here we show how TR DNA can be useful for the study of hybrid zones (HZ), as it serves as a marker to identify introgression in areas where two biological entities come in contact. We used Illumina libraries to analyse two subspecies of the grasshopper Chorthippus parallelus, which currently form a HZ in the Pyrenees. We retrieved a total of 152 TR sequences, and used fluorescent in situ hybridization (FISH) to map 77 families in purebred individuals from both subspecies. Our analysis revealed 50 TR families that could serve as markers for analysis of this HZ, using FISH. Differential TR bands were unevenly distributed between chromosomes and subspecies. Some of these TR families yielded FISH bands in only one of the subspecies, suggesting the amplification of these TR families after the geographic separation of the subspecies in the Pleistocene. Our cytological analysis of two TR markers along a transect of the Pyrenean hybrid zone showed asymmetrical introgression of one subspecies into the other, consistent with previous findings using other markers. These results demonstrate the reliability of TR-band markers for hybrid zone studies. Full article
(This article belongs to the Special Issue State-of-the-Art in Insect Cytogenetics)
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20 pages, 13468 KiB  
Article
Making the Genome Huge: The Case of Triatoma delpontei, a Triatominae Species with More than 50% of Its Genome Full of Satellite DNA
by Pablo Mora, Sebastián Pita, Eugenia E. Montiel, José M. Rico-Porras, Teresa Palomeque, Francisco Panzera and Pedro Lorite
Genes 2023, 14(2), 371; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14020371 - 31 Jan 2023
Cited by 8 | Viewed by 1734
Abstract
The genome of Triatoma delpontei Romaña & Abalos 1947 is the largest within Heteroptera, approximately two to three times greater than other evaluated Heteroptera genomes. Here, the repetitive fraction of the genome was determined and compared with its sister species Triatoma infestans Klug [...] Read more.
The genome of Triatoma delpontei Romaña & Abalos 1947 is the largest within Heteroptera, approximately two to three times greater than other evaluated Heteroptera genomes. Here, the repetitive fraction of the genome was determined and compared with its sister species Triatoma infestans Klug 1834, in order to shed light on the karyotypic and genomic evolution of these species. The T. delpontei repeatome analysis showed that the most abundant component in its genome is satellite DNA, which makes up more than half of the genome. The T. delpontei satellitome includes 160 satellite DNA families, most of them also present in T. infestans. In both species, only a few satellite DNA families are overrepresented on the genome. These families are the building blocks of the C-heterochromatic regions. Two of these satellite DNA families that form the heterochromatin are the same in both species. However, there are satellite DNA families highly amplified in the heterochromatin of one species that in the other species are in low abundance and located in the euchromatin. Therefore, the present results depicted the great impact of the satellite DNA sequences in the evolution of Triatominae genomes. Within this scenario, satellitome determination and analysis led to a hypothesis that explains how satDNA sequences have grown on T. delpontei to reach its huge genome size within true bugs. Full article
(This article belongs to the Special Issue State-of-the-Art in Insect Cytogenetics)
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11 pages, 1523 KiB  
Article
Tempo and Mode of Genome Structure Evolution in Insects
by James M. Alfieri, Michelle M. Jonika, Jennifer N. Dulin and Heath Blackmon
Genes 2023, 14(2), 336; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14020336 - 28 Jan 2023
Cited by 3 | Viewed by 1758
Abstract
The division of the genome into discrete chromosomes is a fundamental characteristic of eukaryotic life. Insect taxonomists’ early adoption of cytogenetics has led to an incredible amount of data describing genome structure across insects. In this article, we synthesize data from thousands of [...] Read more.
The division of the genome into discrete chromosomes is a fundamental characteristic of eukaryotic life. Insect taxonomists’ early adoption of cytogenetics has led to an incredible amount of data describing genome structure across insects. In this article, we synthesize data from thousands of species and use biologically realistic models to infer the tempo and mode of chromosome evolution among insect orders. Our results show that orders vary dramatically in the overall rate of chromosome number evolution (a proxy of genome structural stability) and the pattern of evolution (e.g., the balance between fusions and fissions). These findings have important implications for our understanding of likely modes of speciation and offer insight into the most informative clades for future genome sequencing. Full article
(This article belongs to the Special Issue State-of-the-Art in Insect Cytogenetics)
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16 pages, 2938 KiB  
Article
Why Are X Autosome Rearrangements so Frequent in Beetles? A Study of 50 Cases
by Bernard Dutrillaux and Anne-Marie Dutrillaux
Genes 2023, 14(1), 150; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14010150 - 5 Jan 2023
Cited by 2 | Viewed by 1643
Abstract
Amongst the 460 karyotypes of Polyphagan Coleoptera that we studied, 50 (10.8%) were carriers of an X autosome rearrangement. In addition to mitotic metaphase analysis, the correct diagnosis was performed on meiotic cells, principally at the pachytene stage. The percentages of these inter-chromosomal [...] Read more.
Amongst the 460 karyotypes of Polyphagan Coleoptera that we studied, 50 (10.8%) were carriers of an X autosome rearrangement. In addition to mitotic metaphase analysis, the correct diagnosis was performed on meiotic cells, principally at the pachytene stage. The percentages of these inter-chromosomal rearrangements, principally fusions, varied in relation to the total diploid number of chromosomes: high (51%) below 19, null at 19, low (2.7%) at 20 (the ancestral and modal number), and slightly increasing from 7.1% to 16.7% from 22 to above 30. The involvement of the X in chromosome fusions appears to be more than seven-fold higher than expected for the average of the autosomes. Examples of karyotypes with X autosome rearrangements are shown, including insertion of the whole X in the autosome (ins(A;X)), which has never been reported before in animals. End-to-end fusions (Robertsonian translocations, terminal rearrangements, and pseudo-dicentrics) are the most frequent types of X autosome rearrangements. As in the 34 species with a 19,X formula, there was no trace of the Y chromosome in the 50 karyotypes with an X autosome rearrangement, which demonstrates the dispensability of this chromosome. In most instances, C-banded heterochromatin was present at the X autosome junction, which suggests that it insulates the gonosome from the autosome portions, whose genes are subjected to different levels of expression. Finally, it is proposed that the very preferential involvement of the X in inter-chromosome rearrangements is explained by: (1) the frequent acrocentric morphology of the X, thus the terminal position of constitutive heterochromatin, which can insulate the attached gonosomal and autosomal components; (2) the dispensability of the Y chromosome, which considerably minimizes the deleterious consequences of the heterozygous status in male meiosis, (3) following the rapid loss of the useless Y chromosome, the correct segregation of the X autosome–autosome trivalent, which ipso facto is ensured by a chiasma in its autosomal portion. Full article
(This article belongs to the Special Issue State-of-the-Art in Insect Cytogenetics)
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