Chromosome and Genome Diversity in the Genus Trifolium (Fabaceae)

Trifolium L. is an economically important genus that is characterized by variable karyotypes relating to its ploidy level and basic chromosome numbers. The advent of genomic resources combined with molecular cytogenetics provides an opportunity to develop our understanding of plant genomes in general. Here, we summarize the current state of knowledge on Trifolium genomes and chromosomes and review methodologies using molecular markers that have contributed to Trifolium research. We discuss possible future applications of cytogenetic methods in research on the Trifolium genome and chromosomes.

Cytogenetically Elusive Sex Chromosomes in Scincoidean Lizards

The lizards of the species-rich clade Scincoidea including cordylids, gerrhosaurids, skinks, and xantusiids, show an almost cosmopolitan geographical distribution and a remarkable ecological and morphological divergence. However, previous studies revealed limited variability in cytogenetic traits. The sex determination mode was revealed only in a handful of gerrhosaurid, skink, and xantusiid species, which demonstrated either ZZ/ZW or XX/XY sex chromosomes. In this study, we explored the karyotypes of six species of skinks, two species of cordylids, and one gerrhosaurid. We applied conventional and molecular cytogenetic methods, including C-banding, fluorescence in situ hybridization with probes specific for telomeric motifs and rDNA loci, and comparative genomic hybridization. The diploid chromosome numbers are rather conserved among these species, but the chromosome morphology, the presence of interstitial telomeric sequences, and the topology of rDNA loci vary significantly. Notably, XX/XY sex chromosomes were identified only in Tiliqua scincoides, where, in contrast to the X chromosome, the Y chromosome lacks accumulations of rDNA loci. We confirm that within the lizards of the scincoidean clade, sex chromosomes remained in a generally poor stage of differentiation.

Cytogenetic Evidence for Sex Chromosomes and Karyotype Evolution in Anguimorphan Lizards

Anguimorphan lizards are a morphologically variable group of squamate reptiles with a wide geographical distribution. In spite of their importance, they have been cytogenetically understudied. Here, we present the results of the cytogenetic examination of 23 species from five anguimorphan families (Anguidae, Helodermatidae, Shinisauridae, Varanidae and Xenosauridae). We applied both conventional (Giemsa staining and C-banding) and molecular cytogenetic methods (fluorescence in situ hybridization with probes for the telomeric motifs and rDNA loci, comparative genome hybridization), intending to describe the karyotypes of previously unstudied species, to uncover the sex determination mode, and to reveal the distribution of variability in cytogenetic characteristics among anguimorphan lizards. We documented that karyotypes are generally quite variable across anguimorphan lineages, with anguids being the most varying. However, the derived chromosome number of 2n = 40 exhibits a notable long-term evolutionary stasis in monitors. Differentiated ZZ/ZW sex chromosomes were documented in monitors and helodermatids, as well as in the anguids Abronia lythrochila, and preliminary also in Celestus warreni and Gerrhonotus liocephalus. Several other anguimorphan species have likely poorly differentiated sex chromosomes, which cannot be detected by the applied cytogenetic methods, although the presence of environmental sex determination cannot be excluded. In addition, we uncovered a rare case of spontaneous triploidy in a fully grown Varanus primordius.

Analysis of the structure of developmental delay and intellectual disability among patients of the Research Centre for Medical Genetics

Задержка психического развития (ЗПР) и умственная отсталость (УО) являются частыми симптомами у пациентов, консультируемых врачом-генетиком. Цель исследования: оценка структуры и разнообразия нозологических форм ЗПР и УО и их динамики среди пациентов, проконсультированных в ФГБНУ МГНЦ. Работа выполнена на материале, извлеченном из медико-генетических карт пациентов, проконсультированных врачами-генетиками консультативного и научно-консультативного отделов в 2006 и 2007 годах и через 10 лет -в 2016 и 2017 годах. Общее число обработанных медико-генетических карт за 4 анализируемых года составило 14301 по всем нозологиям, общее число карт пациентов с ЗПР или УО за 4 года составило 2321 карту. Общее количество пациентов с ЗПР или УО за 4 года составило 2350, при этом доли пациентов с ЗПР или УО, проконсультированных в 2016-2017 годах, достоверно увеличились по сравнению с долями таких пациентов, проконсультированных в 2006-2007 годах. В исследуемые периоды структура ЗПР и УО осталась практически неизменной по таким критериям, как пол и возраст. Доли пациентов с ЗПР и УО, обусловленными факторами окружающей среды и генетическими причинами, также не претерпели изменений. Наблюдается значительное увеличение числа пациентов с ЗПР или УО в 2016 и 2017 гг. с диагнозом, подтвержденным биохимическими, молекулярно-генетическими или цитогенетическими методами. Количество нозологических форм ЗПР и УО, подтвержденных молекулярно-генетическими или цитогенетическими методами, возросло почти в 5 раз за исследуемый десятилетний период. Существенное увеличение числа пациентов с лабораторно верифицированными генетическими формами ЗПР или УО в 2016 и 2017 годах обусловлено значительным прогрессом в области ДНК-диагностики синдромов, включающих ЗПР и УО, а также появлением новых методов исследований: хромосомного микроматричного анализа и секвенирования нового поколения. Background: Developmental delay (DD) and intellectual disability (ID) are frequent symptoms in patients consulted by a geneticist. Purpose of the research: evaluation of the structure and variety of nosological forms of DD and ID and their dynamics among patients consulted by geneticists of the counseling unit and research and counseling department of the Research Centre for Medical Genetics in 2006, 2007, 2016 and 2017. Materials and methods: The present work was performed on the material taken from the medical genetic cards of patients of the Research Centre for Medical Genetics consulted by geneticists of the counseling unit and research and counseling department in 2006 and 2007 and 10 years later in 2016 and 2017. The total number of medical genetic cards processed during the 4 analyzed years was 14301 for all nosologies; the total number of cards of patients with DD or ID during the 4 years was 2321 cards. The total number of patients with DD or ID over the 4 analyzed years was 2350. Meanwhile the proportions of patients with DD or ID consulted in 2016-2017 increased significantly compared to the proportions of such patients consulted in 2006-2007. Results: During the research period (2006, 2007, 2016, and 2017) the structure of DD and ID remained almost unchanged for criteria such as gender and age. The proportions of patients with DD or ID caused by environmental factors and genetic causes also did not change. There was a significant increase in the number of patients with DD or ID in 2016 and 2017 with a diagnosis confirmed by biochemical, molecular genetic or cytogenetic methods. The number of nosological forms of PD and OA confirmed by molecular genetic or cytogenetic methods increased almost 5-fold over the ten-year period research. Conclusions: The significant increase in the number of patients with laboratory verified genetic forms of DD or ID in 2016 and 2017 is explained by significant advances in DNA diagnostics of syndromes manifesting in DD or ID, as well as the appearance of new research methods - chromosome microarray analysis and next-generation sequencing.

First Report of Sex Chromosomes in Plated Lizards (Squamata: Gerrhosauridae)

Squamate reptiles show high diversity in sex determination ranging from environmental sex determination to genotypic sex determination with varying degrees of differentiation of sex chromosomes. Unfortunately, we lack even basic information on sex determination mode in several lineages of squamates, which prevents full understanding of their diversity and evolution of sex determination. One of the reptilian lineages with missing information on sex determination is the family Gerrhosauridae, commonly known as the plated lizards. Several species of gerrhosaurids have been studied in the past by conventional cytogenetic methods, but sex-specific differences were not identified. In this study, we applied both conventional and molecular cytogenetic methods to metaphases from both sexes of the Peters’ keeled plated lizard (Tracheloptychus petersi). We identified accumulations of rDNA loci in a pair of microchromosomes in metaphases from males, but only in a single microchromosome in females. The restriction of the observed heterozygosity to females suggests a putative ZZ/ZW system of sex chromosomes, which represents the first report of sex chromosomes in a gerrhosaurid lizard. The lack of sex-specific signals in all other cytogenetic methods implies that the sex chromosomes of T. petersi are poorly differentiated in sequence content.

The Role of Cytogenetic Methods in the Diagnosis of Haematological Diseases

Introduction: Conventional cytogenetics by the use of standard karyotyping allows the study of numerical and structural chromosomal aberrations. Haematological malignancies include a number of cancer types that originate in the blood cells of the bone marrow or of the lymphatic system. Cytogenetic methods are traditionally used for the sake of diagnosis and prognosis of these diseases. However, with the ever more frequent use of molecular methods in the diagnostic laboratories, the importance of the conventional cytogenetic analysis in the diagnosis of haematological diseases needs to be reassessed. Aim: To evaluate the role of cytogenetic methods in the diagnosis of haematological malignancies. Materials and Methods: A retrospective analysis of cytogenetic findings of 146 patients with various haematological malignancies was performed. All of the findings were made over a period of three years at the Centre for Genetics at the Medical Faculty of the University of Sarajevo in Bosnia and Herzegovina. Microsoft Excel 2019 was used for the analysis and presentation of data in the form of tables and graphs. Results: The results of the present study showed that the use of conventional cytogenetic analysis is a good diagnostic method for 50.68% (74) of patients in whom chromosomal aberrations were detected. Conclusion: Cytogenetics remains the most comprehensive method for assessing chromosomal abnormalities due to its ability to detect clinically relevant aneuploidies and additional cytogenetic abnormalities that cannot be detected by locus-specific assays.

GC and Repeats Profiling along Chromosomes—The Future of Fish Compositional Cytogenomics

The study of fish cytogenetics has been impeded by the inability to produce G-bands that could assign chromosomes to their homologous pairs. Thus, the majority of karyotypes published have been estimated based on morphological similarities of chromosomes. The reason why chromosome G-banding does not work in fish remains elusive. However, the recent increase in the number of fish genomes assembled to the chromosome level provides a way to analyse this issue. We have developed a Python tool to visualize and quantify GC percentage (GC%) of both repeats and unique DNA along chromosomes using a non-overlapping sliding window approach. Our tool profiles GC% and simultaneously plots the proportion of repeats (rep%) in a color scale (or vice versa). Hence, it is possible to assess the contribution of repeats to the total GC%. The main differences are the GC% of repeats homogenizing the overall GC% along fish chromosomes and a greater range of GC% scattered along fish chromosomes. This may explain the inability to produce G-banding in fish. We also show an occasional banding pattern along the chromosomes in some fish that probably cannot be detected with traditional qualitative cytogenetic methods.

Lessons of studies of karyotypic and genomic evolution in animals, application of developed technique in the studies of karyotype and genome organization in plants

The present report is devoted to analysis of results obtained with modern molecular and molecular-cytogenetic methods in studies of karyotype and genome organization in various animal species. Perspectives of their application for the study of karyotype and genome organization in plants are considered and discussed.

The use of molecular cytogenetic methods in the investigation of distant potato hybrids

This paper reviews the results of studies of interspecies hybridization, polyploidization, as well as phylogenetic relationships of Solanum species and members of closely related taxa by such molecular cytogenetic techniques as genomic (GISH) and fluorescent (FISH) DNA-DNA in situ hybridization. The latter was used to determine the genomic composition and origin of wild species of the Petota section, while the FISH technique was used for detecting intergenomic collinearity. The combination of these two types of research made possible a comparative analysis of karyotypes and genomes, thus allowing a better understanding of the meiotic interchromosomal interactions in hybrids. This review primarily focuses on the studies of wild allopolyploid potato species and artificially created intergeneric and interspecific hybrids of the genus Solanum and their offspring.