Identification Of Chromosomes Research Articles

Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification.

This manuscript describes the identification, isolation and sequencing of a single chromosome containing high value resistance genes from a complex polyploid where sequencing the whole genome is too costly. The large complex genomes of many crops constrain the use of new technologies for genome-assisted selection and genetic improvement. One method to simplify a genome is to break it into individual chromosomes by flow cytometry; however, in many crop species most chromosomes cannot be isolated individually. Flow sorting of a single copy of a chromosome has been developed in wheat, and here we demonstrate its use to identify markers of interest in an Erianthus/Sacchurum hybrid. Erianthus/Saccharum hybrids are of interest because Erianthus is known to be highly resistant to soil borne diseases which cause extensive sugarcane yield losses in Australia. Sugarcane (Saccharum) cultivars are autopolyploids with a highly complex genome and over 100 chromosomes. Flow cytometry for sugarcane, as in most crops, does not resolve individual chromosomes to a karyotype peak for sorting. To isolate a single chromosome, we used genomic in situ hybridization (GISH) to identify the flow karyotype region containing the Erianthus chromosomes, flow sorted single chromosomes from this region, PCR screened for the Erianthus chromosomes and sequenced them. One Erianthus chromosome amplified and sequenced well, and from this data we could identify 57 resistant type genes and SNPs in nearly half of these genes. We developed KASP SNP assays and demonstrated that the identified SNP markers segregated as expected in a small introgression population. The pipeline we developed here to flow sort and sequence single chromosomes could be used in any crop with a large complex genome to rapidly discover and develop markers to important loci.

Disorders of sexual development in the cat: Current state of knowledge and diagnostic approach.

Practical relevance:Any congenital or developmental abnormality of any part of the male or female reproductive tract is a ‘disorder of sexual development’ (DSD). The tricolored male cat phenotype, cryptorchidism, gonadal hypoplasia and incidental abnormalities such as cystic remnants or embryonic ducts are well-known feline DSDs.Clinical challenges:Full characterization of DSDs requires sex chromosome determination and identification of genes related to development of the gonads, internal tubular genitalia and external genitalia. Fortunately, affected cats are seen sporadically and the clinical effects are usually minimal.Classification:The classification nomenclature has changed. In place of intersex, hermaphrodite, pseudohermaphrodite and sex reversal, the newer standard classification, based on sex chromosomes, designates sex chromosome DSD when there is an abnormality in the sex chromosomes, and XX (female) and XY (male) DSDs where there is not. Identification of the gonadal type (testes, ovaries, ovotestes or gonadal dysgenesis) and documentation of the internal and external genital components completes the classification.Evidence base:The original basis of the DSD classification was a consensus reached in humans. It was quickly accepted in veterinary pathology, courtesy of its logic and ease of application, and it has subsequently begun to appear in peer-reviewed papers and clinical reviews. This article reviewing the various disorders in cats is based on application of the classification and draws on the feline peer-reviewed literature encompassing chromosome analysis and definition of reproductive abnormalities, syndromes and diseases.

Rapid and visual monitoring of alien sequences using crop wild relatives specific oligo-painting: The case of cucumber chromosome engineering

Wild species related to domesticated crops (crop wild relatives, or CWRs) represent a high level of genetic diversity that provides a practical gene pool for crop pre-breeding employed to address climate change and food demand challenges globally. Nevertheless, rapid identifying and visual tracking of alien chromosomes and sequences derived from CWRs have been a technical challenge for crop chromosome engineering. Here, a species-specific oligonucleotide (oligo) pool was developed by using the reference genome of Cucumis hystrix (HH, 2n = 2x = 24), a wild species carrying many favorable traits and interspecific compatibility with cultivated cucumber (C. sativus, CC, 2n = 2x = 14). These synthetic double-stranded oligo probes were applied to validate the assembly and characterize the chromosome architectures of C. hystrix, as well as to rapidly identify C. hystrix-chromosomes in diverse C. sativus-hystrix chromosome-engineered germplasms, including interspecific hybrid F1 (HC), synthetic allopolyploids (HHCC, CHC, and HCH) and alien additional lines (CC-H). Moreover, a ∼2Mb of C. hystrix-specific sequences, introduced into cultivated cucumber, were visualized by CWR-specific oligo-painting. These results demonstrate that the CWR-specific oligo-painting technique holds broad applicability for chromosome engineering of numerous crops, as it allows rapid identification of alien chromosomes, reliable detection of homoeologous recombination, and visual tracking of the introgression process. It is promising to achieve directed and high-precision crop pre-breeding combined with other breeding techniques, such as CRISPR/Cas9-mediated chromosome engineering.

Features of Chromosome Introgression from Gossypium barbadense L. into G. hirsutum L. during the Development of Alien Substitution Lines.

The creation of G. barbadense L./G. hirsutum L. chromosome-substitution lines is an important method to transfer agronomically valuable traits from G. barbadense into G. hirsutum. In this study, 30 monosomic lines of G. hirsutum from the Cytogenetic Collection of Uzbekistan, created in the genotypic background of line L-458, were used in crosses with the G. barbadense line Pima 3-79 to create substitution lines. In the course of this work, new monosomic lines were identified for chromosome 12 and monotelodisome 6 of the Atsubgenome and for chromosomes 17, 21, and 22 of the Dtsubgenome using chromosome-specific SSR markers and a well-defined tester set of cotton translocation lines (USA). Compared to those in the F1 hybrids, a strong decrease in the crossing and setting rates was found in the BC1F1 backcross lines, with the substitution of chromosomes 2, 4, 6, 7, and 12 of the Atsubgenome and 17, 18, 21, and 22 of the Dtsubgenome. The F1 and BC1F1 offspring from interspecific crosses differed in their transmission of univalents. Despite the regular pairing of chromosomes and the high meiotic index, interspecific aneuploid hybrids were characterized by a decrease in pollen fertility, which may indicate hidden structural variability in these genomes that did not affect meiotic division. The identification of chromosomes using chromosome-specific SSR markers in the early stages of plant development has greatly accelerated the detection of monosomic plants. The analysis of morphobiological traits revealed that monosomic F1 hybrids were more similar to the donor line, while BC1F1 hybrids were more similar to the recurrent parent but also showed previously undetected traits.

Oligo-FISH Paints in Triticeae.

We developed seven oligonucleotide (oligo) pools based on single-copy sequences, targeting chromosomes 1 to 7 of barley (Hordeum vulgare L.) and wheat (Triticum aestivum) for chromosomal Oligo-FISH painting methods. The probes were applied to high-throughput karyotyping for the Triticeae tribe of over 350 species including 30 genera such as Triticum, Hordeum, Secale, Aegilops, Thinopyrum, and Dasypyrum, as well as several wheat alien-derived lines. In combination with other nondenaturing FISH (ND-FISH) procedures using tandem-repeat oligos, the newly developed Oligo-FISH painting technique provides an efficient tool for the identification of individual chromosomes with homologous linkage groups to establish standard karyotypes, particularly with any wild Triticeae species having nonsequenced genomes for chromosome evolutionary analysis. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Oligo-pool probe development Basic Protocol 2: Nondenaturing FISH Basic Protocol 3: Oligo-FISH painting.

Development and validation of a novel 26-plex system for prenatal diagnosis with forensic markers.

Short tandem repeat (STR) loci are commonly used in forensic casework, such as personal identification and paternity testing. In recent years, STR has also been widely used for rapid, accurate and automated prenatal diagnosis, known as quantitative fluorescent PCR (QF-PCR). Despite their usefulness, the current systems often lack the power to detect mosaicism for Turner syndrome. In this study, we developed a novel 26-plex system that combined the 22 STRs in chromosome 21/18/13/X, 3 sex loci and 1 quality control marker (TAF9L). The system was generated to achieve greater diagnostic power of trisomy 21/18/13 and sex chromosome abnormalities. Studies of the sensitivity, specificity, stability and accuracy were performed according to the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. Compared with the results of the chromosomal microarray analysis (CMA)/copy number variation sequencing (CNV-seq), the detection ratio of non-mosaic chromosome abnormalities of this system in the identification of chromosome 21/18/13/X/Y aneuploidies reached 100%, and the rate of negative results was consistently 100% based on 203 prenatal diagnosis sample analyses. In addition, our results suggested that this panel was a useful tool for mosaicism for Turner syndrome cases. Interestingly, we found one case with large segment loss of chromosome X, which indicated that we should be alert to this situation when the STR genotype of the parent-child is inconsistent in forensic genetics. In summary, this study demonstrated that our system is an accurate, cost-effective and rapid approach for the detection of chromosome numerical abnormalities in prenatal diagnosis.

Karyotype Differentiation in Cultivated Chickpea Revealed by Oligopainting Fluorescence in situ Hybridization.

Chickpea (Cicer arietinum L.) is one of the main sources of plant proteins in the Indian subcontinent and West Asia, where two different morphotypes, desi and kabuli, are grown. Despite the progress in genome mapping and sequencing, the knowledge of the chickpea genome at the chromosomal level, including the long-range molecular chromosome organization, is limited. Earlier cytogenetic studies in chickpea suffered from a limited number of cytogenetic landmarks and did not permit to identify individual chromosomes in the metaphase spreads or to anchor pseudomolecules to chromosomes in situ. In this study, we developed a system for fast molecular karyotyping for both morphotypes of cultivated chickpea. We demonstrate that even draft genome sequences are adequate to develop oligo-fluorescence in situ hybridization (FISH) barcodes for the identification of chromosomes and comparative analysis among closely related chickpea genotypes. Our results show the potential of oligo-FISH barcoding for the identification of structural changes in chromosomes, which accompanied genome diversification among chickpea cultivars. Moreover, oligo-FISH barcoding in chickpea pointed out some problematic, most probably wrongly assembled regions of the pseudomolecules of both kabuli and desi reference genomes. Thus, oligo-FISH appears as a powerful tool not only for comparative karyotyping but also for the validation of genome assemblies.

Oligo-FISH Can Identify Chromosomes and Distinguish Hippophaë rhamnoides L. Taxa.

Oligo-fluorescence in situ hybridization (FISH) facilitates precise chromosome identification and comparative cytogenetic analysis. Detection of autosomal chromosomes of Hippophaë rhamnoides has not been achieved using oligonucleotide sequences. Here, the chromosomes of five H. rhamnoides taxa in the mitotic metaphase and mitotic metaphase to anaphase were detected using the oligo-FISH probes (AG3T3)3, 5S rDNA, and (TTG)6. In total, 24 small chromosomes were clearly observed in the mitotic metaphase (0.89–3.03 μm), whereas 24–48 small chromosomes were observed in the mitotic metaphase to anaphase (0.94–3.10 μm). The signal number and intensity of (AG3T3)3, 5S rDNA, and (TTG)6 in the mitotic metaphase to anaphase chromosomes were nearly consistent with those in the mitotic metaphase chromosomes when the two split chromosomes were integrated as one unit. Of note, 14 chromosomes (there is a high chance that sex chromosomes are included) were exclusively identified by (AG3T3)3, 5S rDNA, and (TTG)6. The other 10 also showed a terminal signal with (AG3T3)3. Moreover, these oligo-probes were able to distinguish one wild H. rhamnoides taxon from four H. rhamnoides taxa. These chromosome identification and taxa differentiation data will help in elucidating visual and elaborate physical mapping and guide breeders’ utilization of wild resources of H. rhamnoides.

Optimum design of space structures using hybrid particle swarm optimization and genetic algorithm

Purpose This paper aims to present a new hybrid algorithm of Particle Swarm Optimization and the Genetic Algorithm (PSOGA) to optimize the space trusses with continuous design variables. The PSOGA is an efficient hybridized algorithm to solve optimization problems. Design/methodology/approach These algorithms have shown outstanding performance in solving optimization problems with continuous variables. The PSO conceptually models the social behavior of birds, in which individual birds exchange information about their position, velocity and fitness. The behavior of a flock is influencing the probability of migration to other regions with high fitness. The GAs procedure is based on the mechanism of natural selection. The present study uses mutation, random selection and reproduction to reach the best genetic algorithm by the operators of natural genetics. Thus, only identical chromosomes or particles can be converged. Findings In this research, using the idea of hybridization PSO and GA algorithms are hybridized and a new meta-heuristic algorithm is developed to minimize the space trusses with continuous design variables. To showing the efficiency and robustness of the new algorithm, several benchmark problems are solved and compared with other researchers. Originality/value The results indicate that the hybrid PSO algorithm improved in both exploration and exploitation. The PSO algorithm can be used to minimize the weight of structural problems under stress and displacement constraints.

Correction to: New molecular evidence on genome relationships and chromosome identification in fescue (Festuca) and ryegrass (Lolium)

Correction to: New molecular evidence on genome relationships and chromosome identification in fescue (Festuca) and ryegrass (Lolium)

Proportion and Pattern of Chromosomal Abnormalities in Primary Amenorrhea in Kerala- A Retrospective Study

Introduction: Primary amenorrhoea may be due to chromosomal abnormalities and identification of these abnormalities is important for counselling and management of these individuals. Aim: To identify the prevalence of chromosomal abnormalities in a cohort of primary amenorrhoea patients and to evaluate the various pattern of chromosomal abnormalities. Materials and Methods: This retrospective study was conducted at Government Medical College, Thiruvananthapuram, Kerala, India (serves as a referral centre for most of south Kerala and adjoining districts of Tamil Nadu), from January 2013 to December 2020. All phenotypically females, in the age group of 15-30 years, attending the Genetic Clinic with a diagnosis of primary amenorrhoea were evaluated with karyotype from peripheral blood as per the standard protocol. An abstraction proforma was used to collect the data from the master case sheet available in the genetic laboratory. Cytogenetic abnormalities were described as per the standard International System for Human Cytogenomic Nomenclature (ISCN). For statistical analysis, proportion of cases with chromosome abnormality in the cohort was described as percentage. Results: Chromosomal analysis revealed 25.5% (38 out of 149) with abnormal karyotype. Among the abnormalities, the most common abnormality was 45, X (12, 31.6%) Turners syndrome. Other abnormalities included sex reversal female (46, XY) in six (15.8%), isochromosome Turner syndrome in five (13.1%), partial deletion in X chromosome in three (7.8%) and various combination of mosaic pattern in nine (23.7%) cases. Hypergonadotropic hypogonadism was significantly associated with chromosomal abnormality. Conclusion: Cytogenetic abnormality is a cause for primary amenorrhoea in a significant proportion of cases and karyotype should be an integral part of evaluation in such cases. In resource limited settings, karyotype is having more clinical utility in cases with hypergonadotropic hypogonadism.

Classification of analyzable metaphase images using transfer learning and fine tuning.

Chromosomes are bodies that contain human genetic information. Chromosomal disorders can cause structural and functional disorders in individuals. Detecting the metaphase stages of the cells accurately is a crucial step to detect possible defects in chromosomes. Thus, it is vital at this stage to identify the identical chromosome of each chromosome, to perform the pairing process, and to identify problems arising from this process. In this study, it was investigated whether the analyzable metaphase images can be analyzed by using the transfer learning and fine tuning approaches of deep learning models. The weights of VGG16 and InceptionV3 models trained with ImageNet data set were transferred to this problem and the classification process was carried out. True positive ratio values are 99%(± 0.9) and 99%(± 0.9) for VGG and Inception networks, respectively. The classification performances obtained depending on the changing training set ratios are presented comparatively in figures. F-measure, precision, and recall values obtained for the VGG and Inception networks were observed as 99%(± 1.0) and 99%(± 1.0), respectively. F-measure, precision, and recall values of VGG and Inceptionv3 networks are also presented with respect to the ratio of training size. The obtained results have compared with the state-of-the-art methods in the literature and supported with the tables and graphics. The training phase was also accelerated by using transfer learning and fine tuning methods. Transfer learning and fine tuning processes have almost similar performance as the models used in the literature and trained from scratch in metaphase Graphical Abstract The Flowchart of the proposed system for classifying metaphase candidates detection.

Classification of fluorescent R-Band metaphase chromosomes using a convolutional neural network is precise and fast in generating karyograms of hematologic neoplastic cells

Karyotype analysis has a great impact on the diagnosis, treatment and prognosis in hematologic neoplasms. The identification and characterization of chromosomes is a challenging process and needs experienced personal. Artificial intelligence provides novel support tools. However, their safe and reliable application in diagnostics needs to be evaluated. Here, we present a novel laboratory approach to identify chromosomes in cancer cells using a convolutional neural network (CNN). The CNN identified the correct chromosome class for 98.8% of chromosomes, which led to a time saving of 42% for the karyotyping workflow. These results demonstrate that the CNN has potential application value in chromosome classification of hematologic neoplasms. This study contributes to the development of an automatic karyotyping platform.

Localization of ITS and 5S rDNA on the chromosomes of Ulva prolifera using fluorescence in situ hybridization

ABSTRACT Ulva prolifera has been identified as the dominant species of the world’s largest green tides occurring in the Yellow Sea, China, using the molecular markers of internal transcribed spacer (ITS) and 5S ribosomal DNA (5S rDNA). In this study, these two markers were successfully located on the chromosomes of U. prolifera using the fluorescence in situ hybridization (FISH) technique. The ITS rDNA probe was localized on chromosome number 1 of gametophytes and the 5S rDNA probe appeared on chromosome number 6. Dual-colour FISH was also performed, and the locations of the two markers were consistent with single-colour localization, indicating a precise gene location. The localization of these rDNAs using the FISH technique facilitated the identification of individual chromosomes and a karyotype analysis of Ulva, which is beneficial for understanding the blooming mechanism of green tides in the Yellow Sea.

Effects of carbon dioxide purities on mitotic index in lymphocyte culture and metaphase chromosome quality

Abstract. Purnami S, Wibisari IP, Suvifan VA, Nurhayati S, Ramadhani D. 2021. Effects of carbon dioxide purities on mitotic index in lymphocyte culture and metaphase chromosome quality. Nusantara Bioscience 13: 171-176. The metaphase chromosome spread quality is necessary for a faster individual dose prediction following radiological accidents using dicentric chromosome assay. It is well known that the low-quality metaphase chromosome spreads can lead to false positives of dicentric chromosome identification. Thus, evaluation of the main variable that influences the preparation of high-quality metaphase chromosome spreads is important to perform. Until now, no studies have assessed the effects of CO2 purities on metaphase chromosome spread quality. This study aimed to evaluate the effects of carbon dioxide (CO2) purities on lymphocyte proliferation, and the quality of metaphase chromosome spreads to improve the chromosome aberration assay for cytogenetic biodosimetry purposes. Whole blood samples from three different subjects were cultured and incubated for 48 hours with two different grades of CO2 (high purity and food grades) and without CO2. The mitotic index (MI) from each subject was assessed, and the quality of metaphase chromosome spreads was evaluated by comparing the lengths of chromosomes 1, 2, and 21. Statistical analysis revealed that the difference between manual and automatic MI under three different conditions of CO2 purity was not statistically significant (p = 0.162; p = 0.901). Comparative analysis of the lengths of chromosomes 1, 2, and 21 from 145 metaphases also showed a difference that was not statistically significant (p = 0.745; p = 0.915; p = 0.399). Overall, our findings suggest that CO2 purities do not impair lymphocyte proliferation or metaphase quality. Further investigation should include other technical improvements such as drop-slide optimization.

Chromosome identification in oil palm (Elaeis guineensis) using in situ hybridization with massive pools of single copy oligonucleotides and transferability across Arecaceae species.

Chromosome identification is essential for linking sequence and chromosomal maps, verifying sequence assemblies, showing structural variations and tracking inheritance or recombination of chromosomes and chromosomal segments during evolution and breeding programs. Unfortunately, identification of individual chromosomes and chromosome arms has been a major challenge for some economically important crop species with a near-continuous chromosome size range and similar morphology. Here, we developed oligonucleotide-based chromosome-specific probes that enabled us to establish a reference chromosome identification system for oil palm (Elaeis guineensis Jacq., 2n = 32). Massive oligonucleotide sequence pools were anchored to individual chromosome arms using dual and triple fluorescent in situ hybridization (EgOligoFISH). Three fluorescently tagged probe libraries were developed to contain, in total 52,506 gene-rich single-copy 47-mer oligonucleotides spanning each 0.2-0.5Mb across strategically placed chromosome regions. They generated 19 distinct FISH signals and together with rDNA probes enabled identification of all 32 E. guineensis chromosome arms. The probes were able to identify individual homoeologous chromosome regions in the related Arecaceae palm species: American oil palm (Elaeis oleifera), date palm (Phoenix dactylifera) and coconut (Cocos nucifera) showing the comparative organization and concerted evolution of genomes in the Arecaceae. The oligonucleotide probes developed here provide a valuable approach to chromosome arm identification and allow tracking chromosome transfer in hybridization and breeding programs in oil palm, as well as comparative studies within Arecaceae.

P-053: BoBafit: a Copy Number-clustering tool to refit and recalibrate the diploid region of Multiple Myeloma genomic profiles

<h3>Background</h3> The genetic architecture of Multiple Myeloma(MM) is very complex and heterogeneous and includes a huge variety of copy number alterations(CNAs). CNAs affect almost all chromosomes and, based on their presence, patients can be stratified into several, prognostically meaningful subgroups: in particular, the presence of particular CNAs clearly identify high-risk patients, thus underlining the importance of a precise detection of these chromosomal aberrations. FISH is considered the gold standard to detect CNAs in MM, even though the recent implementation of molecular technologies has highlighted the advantage to simultaneously detect the whole landscape of genomic CNAs. Molecular methods require the use of computational algorithms to estimate CNAs, based on the correct identification of the so-called "diploid region", which need to be defined according to the overall genomic characteristics of the patient analyzed. This topic is crucial in genomically complex diseases, since the employed algorithms might fail the diploid region estimation, leading to a possible incorrect CNAs call and therefore to an incorrect patients' stratification. <h3>Aim</h3> To design a bio-informatic method able to check and re-calculate the diploid region starting from genomic data obtained by molecular technologies. <h3>Methods</h3> To this aim, two MM genomic databases have been used, including 595 and 1044 profiles, collected at the "Seràgnoli" Institute of Hematology (SNPs array data) and downloaded from the CoMMpass study (NGS data), respectively; results have been validated on a Breast Cancer(BC) database, including 2133 profiles, downloaded from the TCGA-BRCA project (SNPs array data). R software was used. <h3>Results</h3> An original R package, named "BoBafit", was designed, aimed at check and recalculate the diploid region with a tumor specific approach. The package included several functions: the main one, DRrefit, refits and recalibrates the wrong diploid regions, using a clustering method and a chromosome list; these tools allow a disease-specific correction, based on the identification of chromosomes commonly not carrying disease-specific CNAs, as defined by the Compute Normal Chromosome function. By applying BoBafit, we showed that 1-3% of CNAs calls needed a diploid region correction and a redefinition of the calls; the package can perform a disease-specific refit, independently from the molecular technique employed (e.g., NGS or SNPs array). <h3>Conclusions</h3> The use of the BoBafit allowed the correction of inaccurate CNAs calls. The package, based on MM data, has been validated on BC data, thus both confirming the method's robustness and highlighting the importance of diploid region's refit in complex genomic profiles. We propose BoBafit as final step in the CNAs' analysis pipeline, in order to avoid the inaccurate estimate of whole-chromosome either arm-level or focal alterations, finally supporting the correct patient's clinical stratification. <h3>Acknowledgment</h3> AIRC IG2018-22059.

Localization of 5S rDNA analysis of homologous pairing in tetraploid hybrids of red crucian carp (♀) × common carp (♂)

AbstractInterspecies crossing and allopolyploidization increase the opportunity for generating new breeding resources for fish farming. Allotetraploid hybrid fish (4nAT) were created by crossing red crucian carp (RCC, Carassius auratus red var., ♀) with common carp (CC, Cyprinus carpio L., ♂). However, the genetic pattern of the heterogeneous genomes during gametogenesis in 4nAT is still unclear, which hinders the understanding of the mechanism of generation of new phenotypes during allopolyploidization in fish breeding. In the present study, fluorescence in situ hybridization of 5S rDNA was employed to track homologous pairing, and the characteristics of bivalents were observed using air‐drying preparation technology and electron microscopy. The results showed two strong signals of 5S rDNA localization from the RCC genome, paired in the pachytene stage and metaphase stage of meiosis I cells in 4nAT, suggesting pairing of homologous chromosomes in 4nAT occurred between identical chromosomes. Furthermore, all bivalent pairs possessed one monochiasmate and were neatly arranged in the equatorial plate during meiosis I, which ensured normal separation of homologous chromosomes in 4nAT. This study elucidated the genetic pattern of heterogeneous genomes in 4nAT, providing important evidence for the genetic stability of 4nAT. These findings are of great significance for aquatic breeding.

Karyotype structure and cytogenetic markers of Amoimyrmex bruchi and Amoimyrmex silvestrii: contribution to understanding leaf-cutting ant relationships.

Leaf-cutting ants are considered the most important herbivores in terrestrial environments throughout the Neotropics. Amoimyrmex Cristiano, Cardoso, & Sandoval, 2020 is the sister clade of the remaining leaf-cutting ants from the genera Atta and Acromyrmex. Amoimyrmex striatus was the only species cytogenetically studied within the genus and shares the same chromosomal number as Atta, bearing 22 chromosomes, whereas Acromyrmex bears 38 chromosomes, with the exception of the social parasite Acromyrmex ameliae (2n = 36). Our objective here was to cytogenetically analyze the species of Amoimyrmex bruchi and Amoimyrmex silvestrii, as well as to describe the karyotype of these sister species, using an integrative approach using classical and molecular cytogenetics. We aimed to characterize the cytogenetic markers that contribute to the systematics and taxonomy of the genus. Our results showed that the karyotypes of these two species are very similar, with an identical chromosome number (2n = 22), chromosome morphology (2K = 20m + 2sm), and location of 18S rDNA and telomeric repeat TTAGG on the chromosomes. However, the microsatellite probe GA(15) showed variation across the species and populations studied. We suggest that both species diverged relatively recently and are unmistakably sisters because of the many shared characteristics, including the highly conserved karyotypes.

Chromosome Identification and Cytogenetic Map Construction of Zhikong Scallop (Chlamys farreri) Based on Fluorescence in situ Hybridization

Zhikong scallop (Chlamys farreri) is a bivalve species with broad economic and biological value, and an essential species of aquaculture in North China. Recently, efforts have been made to improve knowledge of genome, genetics, and cytogenetics, which is devoted to develop the molecular breeding project for the scallop. In this study, we constructed a cytogenetic map and identified all chromosomes of C. farreri using fluorescence in situ hybridization (FISH). A total of 100 Bacterial Artificial Chromosome (BAC) clones and 27 fosmid clones, including 58 microsatellite marker-anchored BAC clones, 4 genes-anchored BAC clones, 38 random BAC clones, 22 repetitive sequences-anchored fosmid clones, and 5 gene-anchored fosmid clones, were tested as probes, and 69 of them produced specific and stable signal on one pair of chromosomes. Then, multiple co-hybridizations were conducted to distinguish all the submetacentric and subtelocentric chromosomes with similar morphology by the abovementioned chromosome-specific markers. On this basis, a cytogenetic map of C. farreri containing 69 clones was constructed by co-hybridization and karyotype analysis. The markers covered all 19 pairs of chromosomes, and the average number of markers on each chromosome was 3.6. The cytogenetic map provides a platform for genetic and genomic analysis of C. farreri, which facilitates the molecular breeding project of C. farreri and promotes the comparative studies of chromosome evolution in scallops and even bivalves.