Chromosome Pairing Research Articles

Chromosomes of Asian Cyprinid Fishes: Genomic Differences in Conserved Karyotypes of 'Poropuntiinae' (Teleostei, Cyprinidae).

The representatives of cyprinid lineage 'Poropuntiinae' with 16 recognized genera and around 100 species form a significant part of Southeast Asian ichthyofauna. Cytogenetics are valuable when studying fish evolution, especially the dynamics of repetitive DNAs, such as ribosomal DNAs (5S and 18S) and microsatellites, that can vary between species. Here, karyotypes of seven 'poropuntiin' species, namely Cosmochilus harmandi, Cyclocheilichthys apogon, Hypsibarbus malcomi, H. wetmorei, Mystacoleucus chilopterus, M. ectypus, and Puntioplties proctozysron occurring in Thailand were examined using conventional and molecular cytogenetic protocols. Variable numbers of uni- and bi-armed chromosomes indicated widespread chromosome rearrangements with a stable diploid chromosome number (2n) of 50. Examination with fluorescence in situ hybridization using major and minor ribosomal probes showed that Cosmochilus harmandi, Cyclocheilichthys apogon, and Puntioplites proctozystron all had one chromosomal pair with 5S rDNA sites. However, more than two sites were found in Hypsibarbus malcolmi, H. wetmorei, Mystacoleucus chilopterus, and M. ectypus. The number of chromosomes with 18S rDNA sites varied amongst their karyotypes from one to three; additionally, comparative genomic hybridization and microsatellite patterns varied among species. Our results reinforce the trend of chromosomal evolution in cyprinifom fishes, with major chromosomal rearrangements, while conserving their 2n.

A small RNA system ensures accurate homologous pairing and unpaired silencing of meiotic chromosomes.

During meiosis, chromosomes with homologous partners undergo synaptonemal complex (SC)-mediated pairing, while the remaining unpaired chromosomes are heterochromatinized through unpaired silencing. Mechanisms underlying homolog recognition during SC formation are still unclear. Here, we show that the Caenorhabditis elegans Argonaute proteins, CSR-1 and its paralog CSR-2, interacting with 22G-RNAs, are required for synaptonemal complex formation with accurate homology. CSR-1 in nuclei and meiotic cohesin, constituting the SC lateral elements, were associated with nonsimple DNA repeats, including minisatellites and transposons, and weakly associated with coding genes. CSR-1-associated CeRep55 minisatellites were expressing 22G-RNAs and long noncoding (lnc) RNAs that colocalized with synaptonemal complexes on paired chromosomes and with cohesin regions of unpaired chromosomes. CeRep55 multilocus deletions reduced the efficiencies of homologous pairing and unpaired silencing, which were supported by the csr-1 activity. Moreover, CSR-1 and CSR-2 were required for proper heterochromatinization of unpaired chromosomes. These findings suggest that CSR-1 and CSR-2 play crucial roles in homology recognition, achieving accurate SC formation between chromosome pairs and condensing unpaired chromosomes by targeting repeat-derived lncRNAs.

Heterozygous inversion breakpoints suppress meiotic crossovers by altering recombination repair outcomes.

Heterozygous chromosome inversions suppress meiotic crossover (CO) formation within an inversion, potentially because they lead to gross chromosome rearrangements that produce inviable gametes. Interestingly, COs are also severely reduced in regions nearby but outside of inversion breakpoints even though COs in these regions do not result in rearrangements. Our mechanistic understanding of why COs are suppressed outside of inversion breakpoints is limited by a lack of data on the frequency of noncrossover gene conversions (NCOGCs) in these regions. To address this critical gap, we mapped the location and frequency of rare CO and NCOGC events that occurred outside of the dl-49 chrX inversion in D. melanogaster. We created full-sibling wildtype and inversion stocks and recovered COs and NCOGCs in the syntenic regions of both stocks, allowing us to directly compare rates and distributions of recombination events. We show that COs outside of the proximal inversion breakpoint are distributed in a distance-dependent manner, with strongest suppression near the inversion breakpoint. We find that NCOGCs occur evenly throughout the chromosome and, importantly, are not suppressed near inversion breakpoints. We propose a model in which COs are suppressed by inversion breakpoints in a distance-dependent manner through mechanisms that influence DNA double-strand break repair outcome but not double-strand break formation. We suggest that subtle changes in the synaptonemal complex and chromosome pairing might lead to unstable interhomolog interactions during recombination that permits NCOGC formation but not CO formation.

Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks.

Sexual breeding at the tetraploid level is a promising strategy for rootstock breeding in citrus. Due to the interspecific origin of most of the conventional diploid citrus rootstocks that produced the tetraploid germplasm, the optimization of this strategy requires better knowledge of the meiotic behavior of the tetraploid parents. This work used Genotyping By Sequencing (GBS) data from 103 tetraploid hybrids to study the meiotic behavior and generate a high-density recombination landscape for their tetraploid intergenic Swingle citrumelo and interspecific Volkamer lemon progenitors. A genetic association study was performed with root architecture traits. For citrumelo, high preferential chromosome pairing was revealed and led to an intermediate inheritance with a disomic tendency. Meiosis in Volkamer lemon was more complex than that of citrumelo, with mixed segregation patterns from disomy to tetrasomy. The preferential pairing resulted in low interspecific recombination levels and high interspecific heterozygosity transmission by the diploid gametes. This meiotic behavior affected the efficiency of Quantitative Trait Loci (QTL) detection. Nevertheless, it enabled a high transmission of disease and pest resistance candidate genes from P. trifoliata that are heterozygous in the citrumelo progenitor. The tetrazyg strategy, using doubled diploids of interspecific origin as parents, appears to be efficient in transferring the dominant traits selected at the parental level to the tetraploid progenies.

The Control of the Crossover Localization in Allium.

Meiotic crossovers/chiasmata are not randomly distributed and strictly controlled. The mechanisms behind crossover (CO) patterning remain largely unknown. In Allium cepa, as in the vast majority of plants and animals, COs predominantly occur in the distal 2/3 of the chromosome arm, while in Allium fistulosum they are strictly localized in the proximal region. We investigated the factors that may contribute to the pattern of COs in A. cepa, A. fistulosum and their F1 diploid (2n = 2x = 8C + 8F) and F1 triploid (2n = 3x = 16F + 8C) hybrids. The genome structure of F1 hybrids was confirmed using genomic in situ hybridization (GISH). The analysis of bivalents in the pollen mother cells (PMCs) of the F1 triploid hybrid showed a significant shift in the localization of COs to the distal and interstitial regions. In F1 diploid hybrid, the COs localization was predominantly the same as that of the A. cepa parent. We found no differences in the assembly and disassembly of ASY1 and ZYP1 in PMCs between A. cepa and A. fistulosum, while F1 diploid hybrid showed a delay in chromosome pairing and a partial absence of synapsis in paired chromosomes. Immunolabeling of MLH1 (class I COs) and MUS81 (class II COs) proteins showed a significant difference in the class I/II CO ratio between A. fistulosum (50%:50%) and A. cepa (73%:27%). The MLH1:MUS81 ratio at the homeologous synapsis of F1 diploid hybrid (70%:30%) was the most similar to that of the A. cepa parent. F1 triploid hybrid at the A. fistulosum homologous synapsis showed a significant increase in MLH1:MUS81 ratio (60%:40%) compared to the A. fistulosum parent. The results suggest possible genetic control of CO localization. Other factors affecting the distribution of COs are discussed.

Molecular Cytological Analysis and Specific Marker Development in Wheat-Psathyrostachys huashanica Keng 3Ns Additional Line with Elongated Glume.

Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) is an excellent gene resource for wheat breeding, which is characterized by early maturity, low plant height, and disease resistance. The wheat-P. huashanica derivatives were created by the elite genes of P. huashanica and permeate into common wheat through hybridization. Among them, a long-glume material 20JH1155 was identified, with larger grains and longer spike than its parents. In the present study, the methods of cytological observation, GISH, and sequential FISH analysis showed that 20JH1155 contained 21 pairs of wheat chromosomes and a pair of P. huashanica. There were some differences in 5A and 7B chromosomes between 20JH1155 and parental wheat 7182. Molecular marker, FISH, and sequence cloning indicated 20JH1155 alien chromosomes were 3Ns of P. huashanica. In addition, differentially expressed genes during immature spikelet development of 20JH1155 and 7182 and predicted transcription factors were obtained by transcriptome sequencing. Moreover, a total of 7 makers derived from Ph#3Ns were developed from transcriptome data. Taken together, the wheat-P. huashanica derived line 20JH1155 provides a new horizon on distant hybridization of wheat and accelerates the utilization of genes of P. huashanica.

Abstract 2117: Changes of the DNA methylation status in multiple myeloma patients experiencing chemotherapy induced peripheral neuropathy

Abstract Chemotherapy-Induced Peripheral Neuropathy (CIPN) is considered to be one of the most common side effects caused by anti-neoplastic agents (1) such as Bortezomib (BTZ), Cisplatin (CSP), Taxol (TAX), and Vincristine (VINC). Clinical manifestations of CIPN include deficits of varying intensities of sensory, motor, and autonomic functions. Growing evidence suggests that epigenetic alterations could strongly underlie the induction and maintenance of PN (Peripheral Neuropathy) caused by many factors, including chemotherapy. Recently, a few groups have reported epigenetic alterations as well as changes in the Gene Expression Profiles (GEP) using the DNA and RNA isolated from patients experiencing CIPN. Therefore, our goal was to determine epigenetic alterations that may serve as predictive biomarkers and/or diagnostic biomarkers in the DNA isolated from the Peripheral Blood Mononuclear Cells (PBMCs) of human patients who were exhibiting varying levels of CIPN. To obtain preliminary data, we analyzed the methylation status of the DNA isolated from 3 Multiple Myeloma (MM) patients who experienced different levels (grades 1-7) of CIPN. When the methylation status of the MM patients was analyzed, the DNA was differentially methylated in 12,230 regions, in comparison to a normal control. Out of the above-mentioned total, about 4,563 regions were hypermethylated and 7,667 regions were hypomethylated. These differentially methylated regions included CpG islands in the promoter, intronic, and exonic regions of various genes within the 23 pairs of chromosomes including X and Y. When the most enriched Gene Ontology (GO) terms were identified, about 20 of them exhibited DNA hyper-methylation with fold changes ranging from 1-4 with the highest significance of 2.0e-12. The ranking of the genes involved in the top 3 GO terms related to neuronal function revealed that a total of 112 were hypermethylated in all three patients compared to the control. Similarly, ranking of the genes in the top GO terms with the highest fold change of hypo-methylation revealed 176 genes. Though few other GO terms showed significant changes, they were excluded in our CIPN-related ranking analysis, because they appeared to be linked to cancer or cancer growth-related pathways. It appears that these 288 hyper or hypomethylated genes may be directly involved in the onset, progression, or maintenance of CIPN. Analysis of the functional significance of these genes would provide greater insight into the relevance of the methylation status and its impact on the functions of the neurons that might be involved in pre-disposing or causing CIPN. Our research outcomes are expected to facilitate the design of an assessment method to detect the onset and progression of CIPN in cancer patients. (This research was supported by the Community Foundation of Broward and the Royal Dames of Cancer Research Inc. of Ft. Lauderdale, Florida). Citation Format: Umamaheswari Natarajan, Sultan E. Ahmed, Steve Weinstein, Appu Rathinavelu. Changes of the DNA methylation status in multiple myeloma patients experiencing chemotherapy induced peripheral neuropathy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2117.

Meta-code Symbols Duplication in the Cultural Genes

In the educational process, cultural genes duplication and scientific knowledge learning are two main lines that go hand in hand. Scientific knowledge needs to be learned in verification, and cultural genes need to be copied. Compared with the chromosomes of biological genes and the double-helix structure of DNA, Chinese cultural genes have six pairs of “chromosomes”, of which five pairs are autosomes and one pair is sex chromosomes. The five pairs of autosomal chromosomes are composed of five tones, namely Gong, Shang, Jiao, Zheng and Yu. The sounds are arranged by four tonal symbols, the musical tones are arranged by twelve laws, and the sex chromosomes are arranged by the yin and yang symbols. “Book of Songs” and “Book of Changes” are the cultural gene symbols that Chinese people should try to duplicate most. The Book of Songs is a symbol of phonetic gene, and the Book of Changes is a symbol of text gene. The former reflects on the past, the latter plans for the future. The two types of symbols in the “Book of Songs” and the “Book of Changes” separate the past and the future, so that we can live in “Dasein” calmly without being constricted, as if we have God􀆳s help. Having “Book of Songs” and “Book of Changes” endorsed for us is like inheriting a rich heritage and having a strong spiritual backing to resist the violation of “false and ugly” symbols. Zhu Zaiyu, a great musician in the Ming Dynasty, believed that “Daya” was a palace tone, “Xiaoya” was a levy tone, and “Guofeng” was a corner tone. Sima Qian said, “Orthodox people all start with sound: if sound is right, behavior. is right. ” Voice comes from the mind. Only when the mind is correct can behaviors be correct. Correct education begins with voice.

The alternative transcription and expression characterization of Dmc1 in autotetraploid Carassius auratus.

Established autotetraploids often have a highly stable meiosis with high fertility compared with neo-autotetraploids. The autotetraploid Carassius auratus (4n = 200, RRRR) (4nRR), which stemmed from whole-genome duplication of Carassius auratus red var. (2n = 100, RR) (RCC), produces diploid gametes with an adopted diploid-like chromosome pairing in meiosis and maintains the formation of autotetraploid lineages. In this study, we focused on Dmc1, a meiosis-specific recombinase during the prophase of meiosis I, and elaborated on the genetic variation, alternative transcription, expression characterization, and epigenetic modification of Dmc1 in RCC and 4nRR. Two original Dmc1 from RCC were identified in 4nRR, and two duplicated Dmc1 differences in genetic composition were observed in 4nRR. Furthermore, we only noticed that one original and one duplicated Dmc1 were expressed in RCC and 4nRR, respectively. However, both possessed identical gene expression profiles, differential expression of sexual dimorphism, and hypomethylation levels. These results indicated that the specific expression of duplicated Dmc1 may be involve in the progression of meiosis of the diploid-like chromosome pairing in autotetraploid Carassius auratus. Herein, the findings significantly increase knowledge of meiosis of autopolyploid fish and provide meaningful insights into genetic breeding in polyploidy fish.

Karyomorphological Study in <i>Ledebouria botryoides</i> (Asparagaceae)

Cytogenetical studies were conducted on Ledebouria botryoides. We reported 2n=60 (15m+10sm+5st) chromosomes. The karyotype was asymmetrical and fell into the 4B category of Stebbins’ asymmetry classes. Two groups of chromosomes were observed, i.e. 15 pairs of long chromosomes (2.82–6.65 µm) and 15 pairs of short chromosomes (1.67–2.80 µm). Two chromosome pairs had a satellite on the short arms. The meiotic course was found to be normal with n=30 bivalents.

Karyomorphological Analysis and Genome Size Variation of Sixteen <i>Callicarpa</i> Taxa in China

Information on chromosomes and estimation of genome size could be applied to study the evolution and classification of a genus. In our study, the conventional pressing method was applied to prepare microscope slides for counting the chromosomes, and the chromosome numbers of all surveyed species were 2n=32, 34, 36, 38. The first-time determination of chromosome counts for 12 taxa and karyotypes for 16 taxa in Callicarpa were conducted. It exposed all the species with a higher ratio of m chromosomes and a lower ratio of sm chromosomes, and only C. macrophylla contained st chromosome pair. The minor differences between the karyotypes of all species revealed that the karyotype diversity of this genus evolved from a tiny variation of chromosome structure. Meanwhile, the genome size of 23 samples from 16 taxa of Callicarpa has been estimated by flow cytometry. The genome size ranged from 0.96 pg (C. pedunculata) to 1.26 pg (C. nudiflora), averaged out at 1.12 pg, and the variation of genome sizes was fine among the investigated species. Hence, it could also be referred from the viewpoints of cytology that Callicarpa was a group in Lamiaceae that evolved earlier and independently.

Identification PMS1 and PMS2 as potential meiotic substrates of CDK2 activity.

Cyclin dependent-kinase 2 (CDK2) plays important functions during the mitotic cell cycle and also facilitates several key events during germ cell development. The majority of CDK2's known meiotic functions occur during prophase of the first meiotic division. Here, CDK2 is involved in the regulation of meiotic transcription, the pairing of homologous chromosomes, and the maturation of meiotic crossover sites. Despite that some of the CDK2 substrates are known, few of them display functions in meiosis. Here, we investigate potential meiotic CDK2 substrates using in silico and in vitro approaches. We find that CDK2 phosphorylates PMS2 at Thr337, PMS1 at Thr331, and MLH1 in vitro. Phosphorylation of PMS2 affects its interaction with MLH1 to some degree. In testis extracts from mice lacking Cdk2, there are changes in expression of PMS2, MSH2, and HEI10, which may be reflective of the loss of CDK2 phosphorylation. Our work has uncovered a few CDK2 substrates with meiotic functions, which will have to be verified in vivo. A better understanding of the CDK2 substrates will help us to gain deeper insight into the functions of this universal kinase.

Ovarian dysfunction in women with Turner syndrome.

Ovarian dysfunction is one of the most common features of women with Turner syndrome. In these women, oocyte apoptosis is markedly accelerated from the early stage of fetal life. Reduction in the number of germ cells disturbs primordial follicle development and thereby leads to the formation of streak gonads. There are three possible causes of accelerated germ cell loss in 45,X ovaries. First, chromosomal pairing failure due to X chromosomal aneuploidy is believed to induce meiotic arrest. Indeed, it has been suggested that the dosage of the X chromosome is more critical for the survival of the oocytes than for other cells in the ovary. Second, impaired coupling between oocytes and granulosa cells may also contribute to germ cell apoptosis. Previous studies have shown that 45,X ovaries may tend to lose tight junctions which are essential for intercellular interactions. Lastly, ovarian dysfunction in women with Turner syndrome is partly attributable to the reduced dosage of several genes on the X chromosome. Specifically, BMP15, PGRMC1, and some other genes on the X chromosome have been implicated in ovarian function. Further studies on the mechanisms of ovarian dysfunction are necessary to improve the reproductive outcomes of women with Turner syndrome.

High-density linkage maps detail sex-specific regions of suppressed recombination near fusions of polymorphic chromosomes in purebred and hybrid North American Atlantic salmon (Salmo salar L.).

The North American (NA) Atlantic salmon typically has 27 pairs of chromosomes, whereas the European (EU) subspecies typically has 29. We investigated within-family recombination within three previously identified chromosome rearrangements (Ssa01p/23, Ssa08/29, and Ssa26/28) in NA Atlantic salmon by creating high-density linkage maps using a custom 50K SNP chip developed for the Saint John River aquaculture strain. Linkage maps created for individual purebred and EU hybrid parents in 10 full-sibling families averaged 14 337 SNPs per cross, covering 43 033 SNPs from the 50K SNP chip. Chromosomal translocation Ssa01p/23 was fixed except in one hybrid female map. In contrast, fusion Ssa08/29 was present in maps in 4 out of 10 females and 8 out of 10 males, whereas fusion Ssa26/28 was present in maps in 6 out of 10 females and 8 out of 10 males. The orientation of Ssa08/29 differed from the previous map; the short arm of the metacentric Ssa08 was fused to the centromere of the acrocentric Ssa29. We detected large regions of recombination suppression in female maps at the fusion of Ssa08 to Ssa29. This suppression may reduce the impacts of aneuploidy resulting from pairing of fused and unfused chromosomes, thereby allowing the persistence of chromosomal polymorphisms in this population.

Genomes of two Extinct-in-the-Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights.

Genomics can play important roles in biodiversity conservation, especially for Extinct-in-the-Wild species where genetic factors greatly influence risk of total extinction and probability of successful reintroductions. The Christmas Island blue-tailed skink (Cryptoblepharus egeriae) and Lister's gecko (Lepidodactylus listeri) are two endemic reptile species that went extinct in the wild shortly after the introduction of a predatory snake. After a decade of management, captive populations have expanded from 66 skinks and 43 geckos to several thousand individuals; however, little is known about patterns of genetic variation in these species. Here, we use PacBio HiFi long-read and Hi-C sequencing to generate highly contiguous reference genomes for both reptiles, including the XY chromosome pair in the skink. We then analyse patterns of genetic diversity to infer ancient demography and more recent histories of inbreeding. We observe high genome-wide heterozygosity in the skink (0.007 heterozygous sites per base-pair) and gecko (0.005), consistent with large historical population sizes. However, nearly 10% of the blue-tailed skink reference genome falls within long (>1Mb) runs of homozygosity (ROH), resulting in homozygosity at all major histocompatibility complex (MHC) loci. In contrast, we detect a single ROH in Lister's gecko. We infer from the ROH lengths that related skinks may have established the captive populations. Despite a shared recent extinction in the wild, our results suggest important differences in these species' histories and implications for management. We show how reference genomes can contribute evolutionary and conservation insights, and we provide resources for future population-level and comparative genomic studies in reptiles.

A cytological revisit on parthenogenetic Artemia and the deficiency of a meiosis-specific recombinase DMC1 in the possible transition from bisexuality to parthenogenesis.

Although parthenogenesis is widespread in nature and known to have close relationships with bisexuality, the transitional mechanism is poorly understood. Artemia is an ideal model to address this issue because bisexuality and "contagious" obligate parthenogenesis independently exist in its congeneric members. In the present study, we first performed chromosome spreading and immunofluorescence to compare meiotic processes of Artemia adopting two distinct reproductive ways. The results showed that, unlike conventional meiosis in bisexual Artemia, meiosis II in parthenogenic Artemia is entirely absent and anaphase I is followed by a single mitosis-like equational division. Interspecific comparative transcriptomics showed that two central molecules in homologous recombination (HR), Dmc1 and Rad51, exhibited significantly higher expression in bisexual versus parthenogenetic Artemia. qRT-PCR indicated that the expression of both genes peaked at the early oogenesis and gradually decreased afterward. Knocking-down by RNAi of Dmc1 in unfertilized females of bisexual Artemia resulted in a severe deficiency of homologous chromosome pairing and produced univalents at the middle oogenesis stage, which was similar to that of parthenogenic Artemia, while in contrast, silencing Rad51 led to no significant chromosome morphological change. Our results indicated that Dmc1 is vital for HR in bisexual Artemia, and the deficiency of Dmc1 may be correlated with or even possibly one of core factors in the transition from bisexuality to parthenogenesis.

Characterization of meiotic chromosome behavior in the autopolyploid Saccharum spontaneum reveals preferential chromosome pairing without distinct DNA sequence variation

Autopolyploidy and allopolyploidy may represent an evolutionary advantage and are more common in plants than assumed. However, less attention has been paid to autopolyploidy than to allopolyploidy, and its evolutionary consequences are largely unclear, especially for plants with high ploidy levels. In this study, we developed oligonucleotide (oligo)-based chromosome painting probes to identify individual chromosomes in S. spontaneum. Using fluorescence in situ hybridization (FISH), we investigated chromosome behavior during pachytene, metaphase, anaphase, and telophase of meiosis I (MI) in autotetraploid, autooctoploid, and autodecaploid S. spontaneum clones. All autopolyploid clones showed stable diploidized chromosome behavior; so that homologous chromosomes formed almost exclusively bivalents during MI. Two copies of homologous chromosome 8 with similar sizes in the autotetraploid clone showed preferential pairing with each other with respect to the other copies. However, sequence variation analysis showed no apparent differences among homologs of chromosome 8 and all other chromosomes. We suggest that either the stable diploidized pairing or the preferential pairing between homologous copies of chromosome 8 in the studied autopolyploid sugarcane are accounted for by unknown mechanisms other than DNA sequence similarity. Our results reveal evolutionary consequences of stable meiotic behavior in autopolyploid plants.

Cytogenetic and Molecular Characterization of Eigenmannia aff. desantanai (Gymnotiformes: Sternopygidae): A First Report of System of Sex Chromosomes ZW1W2/ZZ in Gymnotiformes.

Gymnotiformes a monophyletic group of fish endemic to the Neotropics, represent an important component of the freshwater ichthyofauna that presents relevant taxonomic problems. Thus, in view of the morphological complexity involving Eigenmannia (Gymnotiformes) fish species, this study aimed to characterize Eigenmannia aff. desantanai of the upper Paraguay River basin through cytogenetic and molecular analyses, to help in the correct identification and delimitation of species. This study reports a multiple sex system of the type ZW1W2/ZZ, with 2n = 31 for females and 2n = 30 for males. A single pair of chromosomes carrying the nucleolar organizing regions (NORs) was detected. The heterochromatin was colocated in NOR sites and mainly located in the centromeric regions of chromosomes. Besides that, individual sequences COI from the specimens of E. aff. desantanai were obtained, totalizing three haplotypes. The distance p between the haplotypes in E. aff. desantanai, ranged from 0.2% to 7.1%. Species delimitation tests indicated the existence of two possible operational taxonomic units of E. aff. desantanai. Thus, this study reports a new multiple sex system in Gymnotiformes and these specimens previously identified as E. aff. desantanai may belong to two distinct species.

Karasu ırmağında (Erzurum) yayılış gösteren Chondrostoma regium'un (Teleostei: Leuciscidae) karyotipik analizleri

In this study, the karyotypic characteristics of Chondrostoma regium (Heckel, 1843) have been investigated. Fish samples were caught from the Karasu River (Euphrates River Basin) with fishing net. The live fish were transported to the laboratory and kept in aerated aquaria before the analyses. The karyotype analysis was performed in fish kidney and gill epithelium cells. It was determined that C. regium had 2n=50 chromosomes. In detail, the karyotype formula of C. regium was determined as 9 metacentric, 7 submetacentric, 1 subtelocentric and 8 telocentric chromosome pairs (18M+14SM+2ST+16T), and fundamental arm number was calculated as 82. Constitutive heterochromatin regions were determined on telomeres of the chromosomes. Nuclear orgnizer regions were detected on 21st chromosome. Karyotype symmetry/asymmetry index was calculated as 2.32. The karyotypes of gill and kidney cells were the same. No sex chromosomes were cytologically detected.

Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture

The detection of structural chromosomal abnormalities (SCA) is crucial for diagnosis, prognosis and management of many genetic diseases and cancers. This detection, done by highly qualified medical experts, is tedious and time-consuming. We propose a highly performing and intelligent method to assist cytogeneticists to screen for SCA. Each chromosome is present in two copies that make up a pair of chromosomes. Usually, SCA are present in only one copy of the pair. Convolutional neural networks (CNN) with Siamese architecture are particularly relevant for evaluating similarities between two images, which is why we used this method to detect abnormalities between both chromosomes of a given pair. As a proof-of-concept, we first focused on a deletion occurring on chromosome 5 (del(5q)) observed in hematological malignancies. Using our dataset, we conducted several experiments without and with data augmentation on seven popular CNN models. Overall, performances obtained were very relevant for detecting deletions, particularly with Xception and InceptionResNetV2 models achieving 97.50% and 97.01% of F1-score, respectively. We additionally demonstrated that these models successfully recognized another SCA, inversion inv(3), which is one of the most difficult SCA to detect. The performance improved when the training was applied on inversion inv(3) dataset, achieving 94.82% of F1-score. The technique that we propose in this paper is the first highly performing method based on Siamese architecture that allows the detection of SCA. Our code is publicly available at: https://github.com/MEABECHAR/ChromosomeSiameseAD.