Search

Since the framing of the Central Dogma, it has been speculated that physically distinct ribosomes within cells may influence gene expression and cellular physiology. While heterogeneity in ribosome composition has been reported in bacteria, protozoans, fungi, zebrafish, mice and humans, its functional implications remain actively debated. Here, we review recent evidence demonstrating that expression of conserved variant ribosomal DNA (rDNA) alleles in bacteria, mice and humans renders their actively translating ribosome pool intrinsically heterogeneous at the level of ribosomal RNA (rRNA). In this context, we discuss reports that nutrient limitation-induced stress in Escherichia coli leads to changes in variant rRNA allele expression, programmatically altering transcription and cellular phenotype. We highlight that cells expressing ribosomes from distinct operons exhibit distinct drug sensitivities, which can be recapitulated in vitro and potentially rationalized by subtle perturbations in ribosome structure or in their dynamic properties. Finally, we discuss evidence that differential expression of variant rDNA alleles results in different populations of ribosome subtypes within mammalian tissues. These findings motivate further research into the impacts of rRNA heterogeneities on ribosomal function and predict that strategies targeting distinct ribosome subtypes may hold therapeutic potential. This article is part of the discussion meeting issue 'Ribosome diversity and its impact on protein synthesis, development and disease'. [ABSTRACT FROM AUTHOR]

Genomes are organised into DNA loops by the Structural Maintenance of Chromosomes (SMC) proteins. SMCs establish functional chromosomal sub-domains for DNA repair, gene expression and chromosome segregation, but how SMC activity is specifically targeted is unclear. Here, we define the molecular mechanism targeting the condensin SMC complex to specific chromosomal regions in budding yeast. A conserved pocket on the condensin HAWK subunit Ycg1 binds to chromosomal receptors carrying a related motif, CR1. In early mitosis, CR1 motifs in receptors Sgo1 and Lrs4 recruit condensin to pericentromeres and rDNA, to facilitate sister kinetochore biorientation and rDNA condensation, respectively. We additionally find that chromosome arm condensation begins as sister kinetochores come under tension, in a manner dependent on the Ycg1 pocket. We propose that multiple CR1-containing proteins recruit condensin to chromosomes and identify several additional candidates based on their sequence. Overall, we uncover the molecular mechanism that targets condensin to functionalise chromosomal domains to achieve accurate chromosome segregation during mitosis. Synopsis: How the condensin complex is recruited to genomic domains to promote their condensation is incompletely understood. This study identifies a generalised molecular mechanism by which condensin is targeted to specific chromosomal loci. Budding yeast condensin is recruited to chromosomes via a conserved binding pocket on its Ycg1/CAP-G subunit. The Ycg1 pocket binds CR1 motifs in several chromosomal proteins. CR1 motifs in Sgo1 and Lrs4 recruit condensin to pericentromeres and rDNA, respectively. Condensin recruited to pericentromeres by Sgo1 promotes sister kinetochore biorientation in the absence of spindle tension. Chromosome arm and rDNA condensation is initiated by spindle tension, dependent on the Ycg1 binding pocket. A pocket in the CAP-G/Ycg1 subunit binds CR1 motifs in several chromosomal proteins to recruit condensin to specific chromosomal regions. [ABSTRACT FROM AUTHOR]

The current study aimed to produce an amyloglucosidase enzyme from the fungal consortium. The best amylolytic fungal consortia were identified as Alternaria alternata and Aspergillus niger through the 18S rDNA technique. Fermentation kinetics and various nutritional and cultural parameters were analyzed. Maximum production was obtained in M4 media, pH 5.5, 30 °C, and 4 mL inoculum at 150 rpm after 72 h of incubation. Along with that, sodium nitrate at 2.5%, maltose, beef extract 1%, zinc sulfate (0.1%), and Tween 80 (0.1%) supported the maximum amyloglucosidase production. Amyloglucosidase was partially purified up to 1.6 purification fold with a specific activity of 1.84 Umg−1 in a stepwise manner by ammonium sulfate purification, dialysis, and ion exchange chromatography. The AMG enzyme also revealed maximum activity at 50 °C with 5.0 pH. Upon the kinetic analysis, the specific yield coefficient Yp/x and volumetric rates Qp and Qx were also found to be significant in the above optimized conditions. The Km value 0.33 mg mL−1 and Vmax 26.31 U mL−1 were obtained at 1% soluble starch substrate. Thermodynamic parameters for soluble starch hydrolysis were as follows: ΔH = 48.78 kJ mol−1, (Ea) = − 46.0 kJ mol−1, and ΔS = − 43.10 J mol−1 K−1. This finding indicates the indigenously isolated fungal consortium can be the best candidate for industrial applications. [ABSTRACT FROM AUTHOR]

Pitaya (Hylocereus undatus ; 2n=22) is an important fruit crop from the Cactaceae family, originally domesticated in Mexico and the USA, and is now widely cultivated for its nutritional benefits. It is characterized by its distinctive triangular-shaped stems and large, showy flowers, thriving in arid and semi-arid environments, particularly in hot, dry climates. However, systematic chromosomal studies, including chromosomal mapping of cytogenetic markers in pitaya, are limited, presenting challenges for its cytogenetic improvement. To address this issue, we designed oligo-barcodes specific to thirty-three chromosome regions based on the pitaya reference genome and applied them to both pitaya and cactus (Selenicerus grandifloras ; 2n=22) for oligo-barcodes mapping, karyotyping, and chromosome identification. We utilized FISH technology, employing oligo, rDNA, and tandem repeat probes for chromosomal mapping, identification, and karyotyping of pitaya and related species. We successfully localized oligo-barcodes on eleven pairs of chromosomes in both pitaya and cactus, demonstrating the effectiveness of the synthesized oligo-barcodes. We used two ribosomal DNA (rDNA) probes (45S and 5S) and two tandem repeat probes (GTR11 and STR3) in pitaya (both diploid and tetraploid) and two other Cactaceae species (S. grandifloras and Opuntia humifusa ; 2n=40) for chromosomal mapping. The analysis of rDNA distribution and CMA (Chromomycin A3) banding across different chromosomes in pitaya and cacti highlights the concept of conserved rDNA. This study provides fundamental insights into cytogenetic markers and their localization across different chromosomes in pitaya and other Cactaceae species. [ABSTRACT FROM AUTHOR]

The microscopic members of the genus Urodasys are easily recognizable due to their exceptionally long tail. There are 17 described species within this iconic genus, each distinguished by various sexual organ arrangements and reproduction modalities, including the sole known ovoviviparous gastrotrich species. The remarkable variety in reproductive characteristics has captured the interest of researchers aiming to illuminate its origin and evolution. The recent discovery of a species bearing a novel set of reproductive structures has challenged early hypotheses. However, all the evolutionary scenarios put forward need to be more convincing. To gain deeper insight into the evolutionary history of these iconic animals, we obtained the nucleotide sequence of two nuclear genes and one mitochondrial gene from species' representatives of the four known possible combinations of the reproductive apparatus and reproduction modalities. The multi-gene data matrix was analysed phylogenetically using three approaches. The analyses yielded phylogenetic trees with invariant topology. In all cases, the specimens appear organized in four robustly supported clades and subclades that reflect their reproductive system organization. Our results suggest that the sclerotized stylet evolved inside the copulatory organ before the loss of the left testis and offers a new scenario for the evolutionary history of genus Urodasys. [ABSTRACT FROM AUTHOR]

The genetic variabilities in internal transcribed spacers ITS1 and ITS2 of rDNA are explored to a limited extent in vertebrates including fish species. This study explores unique molecular signature in these spacers from multiple catfish species from the order siluriformes. Supporting the concerted evolution, both ITS1 and ITS2 were found prevalent with microsatellite and random repeats, with diverse distribution in each species in terms of nucleotide composition, their position and length, giving a species-specific impression in repeats. Their secondary structures too have shown distinct structural homology with variations in helix lengths, loops, and non-canonical base pairs, where ITS2 4-helix carries additional nine conserved motifs while that of ITS1 was found highly branched with multiple sub-branching unique to each species and a long tail helix common in all. This combination of secondary structures and repeats have formed unique molecular signatures distinguishing each catfish species. Since the evolutionary and maturation biology of rDNA is similar in vertebrates, these molecular signatures in internal spacers could effectively contribute to the molecular characterization across the diverse group of catfish species. [ABSTRACT FROM AUTHOR]

Panagrolaimidae members are bacterivorous with global distribution. There is no information on this species' morphology and molecular characterization in South Africa. During a survey of Molepo dam, Limpopo Province, a population of Propanagrolaimus nematodes belonging to the family Panagrolaimidae was recovered and determined utilizing conventional and molecular characters. Propanagrolaimus siweyae sp. n., was confirmed by morphological and molecular informations. Propanagrolaimus siweyae sp. n. is characterized by a body length 1026–1258 µm (a = 39.4–45.5, b = 5.4–6.5, c = 8.1–10.0, c' = 6.9–7.8, V = 53–57), post vulval uterine sac 25–53 µm, and tail length 108–158 µm long. The scan electron microscopy (SEM) photographs revealed a tessellated cuticle and six slightly separated lips. The discriminant analysis placed populations of P. siweyae sp. n. close to P. hygrophilus with clear separation from the mentioned species. Partial sequences of the 18S and 28S regions of the ribosomal DNA gene were amplified for P. siweyae sp. n. The phylogenetic analysis grouped P. siweyae sp. n. in a clade with 1.00 and 0.87 posterior probability values together with other Propanagrolaimus and Halicephalobus based on 18S and 28S rDNA, respectively. Principal component analysis revealed no correlation between Propanagrolaimus and water parameters. However, the result showed a high correlation with diatoms (r = 0.937) in Molepo dam (site MD-6). In contrast, The PCA showed salinity, pH, and temperature with no significant effect on nematodes in Molepo dam, Limpopo Province, South Africa. In conclusion, the usefulness of free-living nematodes as bioindicators is an advantage to studying pollution in aquatic systems. Limpopo Province is facing pollution in the river and dam systems. Therefore, finding a bioindicator is critical to examine the ecological role of free-living nematodes such as Propanagrolaimus. [ABSTRACT FROM AUTHOR]

Multicopy sequences evolve adaptations for increasing their copy number within nuclei. The activities of multicopy sequences under constraints imposed by cellular and organismal selection result in a rich intranuclear ecology in germline cells. Mitochondrial and ribosomal DNA are managed as domestic herds subject to selective breeding by the genes of the single-copy genome. Transposable elements lead a peripatetic existence in which they must continually move to new sites to keep ahead of inactivating mutations at old sites and undergo exponential outbreaks when the production of new copies exceeds the rate of inactivation of old copies. Centromeres become populated by repeats that do little harm. Organisms with late sequestration of germ cells tend to evolve more "junk" in their genomes than organisms with early sequestration of germ cells. [ABSTRACT FROM AUTHOR]

'Candidatus Phytoplasma ulmi' (16SrV-A) is the causal agent of elm yellows (EY), a lethal and/or decline disease of several Ulmus (elm) species and hybrids in North America and Europe. In this study, field observations and PCR assays were used to detect phytoplasma infections in diseased U. minor, U. pumila and U. glabra trees in southern Italy. Also, a multigene sequence analysis employing various less conserved genes was carried out to explore the genetic variation in detected strains. All the symptomatic elm trees tested were infected with 'Ca. Phytoplasma ulmi'. No other phytoplasmas or variants could be detected. Although 'Ca. Phytoplasma ulmi' was already known to occur in southern Italy on European field elm, the current work expands the information on the presence, disease incidence and severity, plant host range and molecular aspects of EY phytoplasma strains occurring in southern Italy. In addition, this is the first report from Italy on the molecular characterization of EY phytoplasma strains through map, imp and groEL gene sequence and phylogenetic analyses. Among the newly detected EY phytoplasma strains, some proved distantly related to each other and to other previously characterized EY phytoplasma strains within the genes examined. This implies the presence of distinct taxonomic entities within the material examined. The occurrence of different strains was not linked to the biological traits and geographical distribution. However, the data obtained may provide a basis for further studies aimed at elucidating several other unknown aspects of the EY agent, knowledge of which is essential for effective disease management and control strategies. The results of the current work also show that the EY phytoplasma is particularly widespread in southern Italy and is of considerable economic and ecological relevance. [ABSTRACT FROM AUTHOR]

During the assessment of coprophilous mucoralean diversity in northeastern areas of Brazil, a Lichtheimia-like specimen (URM 8358) was isolated from rabbit dung. It was characterized based on morphological, physiological, and molecular analyses of the internal transcribed spacer (ITS), large subunit ribosomal (LSU) and actin DNA sequences. These analyses revealed a novel Lichtheimia species, which is described herein. The novel species forms abundantly branched sporangiophores, with most branches arising near the main sporangia, various-shaped columellae, and irregularly shaped sporangiospores. Furthermore, this manuscript provides notes of all Lichtheimia species, and an identification key for the genus is provided. These findings contribute to the existing knowledge on the taxonomy and distribution of Lichtheimia. Because of the clinical relevance of other Lichtheimia species, we encourage future research to determine whether URM 8358 can be pathogenic to humans. [ABSTRACT FROM AUTHOR]

The origin of hexaploid sweetpotato [Ipomoea batatas (L.) Lam.] remains controversial. Comparative karyotype analysis is particularly useful in determining species relationships and the origin of polyploid species. In previous study, we developed a set of oligo probes and identified all chromosomes of Ipomoea nil, a model diploid Ipomoea species. Here, we found that this set of oligo probes could be used to identify all chromosomes of sweetpotato and its wild relatives with different ploidy. Karyotypes based on individually identified chromosomes were established and the number and position of 5S and 35S rDNA loci were determined for these Ipomoea species. Comparison of their karyotypes revealed distinct variations in the karyotypic parameters. Karyological relationships among these species were revealed by principal coordinate analysis (PCoA) based on six quantitative parameters (x, 2n, TCL, MCA, CVCL and CVCI). These results show that I. trifida is the most closely related diploid species to sweetpotato, and other diploid species could be excluded from consideration as its possible diploid ancestor. In addition, our study also provides cytogenetic evidence for the segmental allopolyploid hypothesis of sweetpotato origin. [ABSTRACT FROM AUTHOR]

The subgenus Stenocranius contains two cryptic species: Lasiopodomys gregalis (subdivided into three allopatrically distributed and genetically well‐isolated lineages A, B, and C) and Lasiopodomys raddei. To identify karyotype characteristics of this poorly studied cryptic species complex, we used comparative cytogenetic analysis of 138 individuals from 41 localities in South Siberia and Mongolia. A detailed description of the L. raddei karyotype and of the L. gregalis lineage С karyotype is presented for the first time. The A chromosome complement of all examined narrow‐headed voles consisted of 2n = 36 and a fundamental number of autosomal arms (FNa) of 50. Between species, patterns of differential staining were similar, though additional C‐heterochromatic blocks were found in L. gregalis lineages; Ag‐positive nucleolar organizers and ribosomal DNA (rDNA) clusters are located on eight and nine acrocentric pairs, respectively. No B chromosomes (Bs) were found in the Early Pleistocene relic L. raddei, while one to five small heterochromatic acrocentric Bs were detected in all L. gregalis lineages; the number and frequency of Bs varied considerably within lineages, but no intraindividual variation was observed. In both species, telomeric repeats were visualized at termini of all chromosomes, including Bs. The number and localization of rDNA clusters on Bs varied among B‐carriers. Immunodetection of several meiotic proteins indicated that meio‐Bs are transcriptionally inactive and have a pattern of meiotic behavior similar to that of sex chromosomes (some homology of Bs to sex chromosomes is supposed). The nature, mechanisms of inheritance and stability of Bs in L. gregalis require further investigation. [ABSTRACT FROM AUTHOR]

Clevelandellids are highly diversified and widespread unicellular eukaryotic organisms inhabiting the digestive tract of a broad spectrum of invertebrates and vertebrates. Time‐calibrated phylogeny of clevelandellids was built to reconstruct their ancestral hosts using stochastic mapping, investigate their coevolution with animal hosts using an event‐based tree reconciliation approach and examine the impact of hosts on their diversification dynamics and molecular evolution using the MuSSE method and phylogenetic regression. The progenitor of the analysed representatives of the order Clevelandellida colonized the hindgut of anurans in the Late Jurassic. Later on, clevelandellids switched from anuran to other terrestrial poikilotherm vertebrate and invertebrate hosts. Panesthiine cockroaches served as a source for at least four independent colonization waves into millipedes and non‐panesthiine cockroaches. Duplication events, duplications followed by host switching and inertia were recognized as the most relevant coevolutionary processes shaping the common history of clevelandellids and their animal hosts over geological time. Clevelandellids associated with panesthiine cockroaches were revealed to have significantly higher net‐diversification rates than ciliates living in millipedes, non‐panesthiine cockroaches and poikilotherm vertebrates. Clevelandellids show some interesting macroevolutionary trends, including clustering specific for higher taxa of their hosts, no backward transfers from invertebrate to vertebrate hosts and host‐dependent diversification dynamics. [ABSTRACT FROM AUTHOR]

Karyotype divergence may strongly affect the degree of hybridization between species. Western Palearctic slow worms (Anguis) are legless lizards forming different types of secondary contact zones. To identify the level of chromosomal variation in slow worms, we examined karyotype in multiple populations of all species except one and Pseudopus apodus as an outgroup. We applied conventional and molecular cytogenetic methods and whole-chromosome painting using macrochromosome probes from Varanus komodoensis to interpret results within the evolutionary framework of the common clade Anguiformes. All Anguis species and P. apodus have conserved karyotype structures composed of 44 chromosomes. Despite the conserved chromosome morphology, the phylogenetically oldest Anguis cephallonica living in partial sympatry with Anguis graeca , and parapatric Anguis colchica vs. Anguis fragilis exhibit distinct patterns of constitutive heterochromatin distribution and telomeric repeat accumulation. In contrast, the sister species A. colchica and A. graeca living in allopatry display highly similar karyotype features. Our findings thus indicate karyotype stasis in Anguis and Pseudopus for > 20 Myr, with fixed species-specific differences present in sympatric and parapatric species. These differences in repetitive DNA patterns may play a role as intrinsic factors co-maintaining species divergence. They may also be used as cytotaxonomic markers to identify slow worm species in practice. [ABSTRACT FROM AUTHOR]

Summary: A new genus and species of the Anguinidae, Turbiditylenchus corticeus n. gen., n. sp., was isolated from the bark of Eucalyptus macrorhyncha from southeastern Australia. Turbiditylenchus corticeus is readily differentiated from all recognised anguinid genera and is characterised primarily by a slender body, lateral field with six incisures, an anteriorly flattened lip region continuous with the body, delicate stylet 7.9-9.9 μ m long, muscular median bulb containing a strongly refractive valve, post-vulval uterine sac 1.87-4.4 times vulval body diam., conical tail with pointed tip, and males with leptoderan bursa and spicules 20.5-25.8 μ m in length. The phylogenetic relationships of the new species with other anguinid lineages were reconstructed using sequences of the small subunit ribosomal RNA (18S rRNA), the internal transcribed spacer region (ITS; comprising ITS1-5.8S-ITS2) and partial large subunit ribosomal RNA (28S rRNA D2-D3) genes based on Bayesian inference and maximum likelihood analyses. These analyses demonstrate the new species represents a lineage distinct from all other anguinids. Based on phylogenetic results we also transfer Ditylenchus parvicauda Gu, Ma, Castillo & Munawar, 2024 and Ditylenchus gracicauda Gu, Ma, Castillo & Munawar, 2024 to Ditylenchoides Subbotin & Ryss, 2024 as Ditylenchoides parvicauda n. comb. and Ditylenchoides gracicauda n. comb. [ABSTRACT FROM AUTHOR]

Zoraptera (also called "angel insects") is one of the most unexplored insect orders. However, it holds promise for understanding the evolution of insect karyotypes and genome organization given its status as an early branching group of Polyneoptera and Pterygota (winged insects) during the Paleozoic. Here, we provide karyotype descriptions of three Zorapteran species: Brazilozoros huxleyi (2n♂; ♀ = 42; 42), B. kukalovae (2n♂; ♀ = 43; 44) and Latinozoros cacaoensis (2n♂; ♀ = 36; 36). These species represent two of the four recently recognized Zorapteran subfamilies. Contrary to an earlier suggestion that Zoraptera has holocentric chromosomes, we found karyotypes that were always monocentric. Interestingly, we detected both X0 (B. kukalovae) and XY (B. huxleyi, L. cacaoensis) sex chromosome systems. In addition to conventional karyotype descriptions, we applied fluorescent in situ hybridization for the first time in Zoraptera to map karyotype distributions of 18S rDNA, histone H3 genes, telomeres and (CAG)n and (GATA)n microsatellites. This study provides a foundation for cytogenetic research in Zoraptera. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Henan Agricultural Sciences is the property of Editorial Board of Journal of Henan Agricultural Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract The ribosomal DNA (rDNA) constitutes a remarkably conserved DNA sequence within species, located in the area of the nucleolus, and responsible for coding three major types of rRNAs (18S, 5.8S and 28S). While historical investigations into rDNA focused on its structure and coding capabilities, recent research has turned to explore its functional roles in various biological processes. In this review, we summarize the main findings of rDNA methylation with embryonic development, aging and diseases in multiple species, including epigenetic alterations, related biological processes and potential applications of rDNA methylation. We present an overview of current related research and identify gaps in this field.

Gene expression patterns are very sensitive to external influences and are reflected in phenotypic changes. It was previously described that transferring melanoma cells from a plastic surface to Matrigel led to formation of de novo vascular networks—vasculogenic mimicry—that are characteristic to a stemness phenotype in aggressive tumors. Up to now there was no detailed data about the gene signature accompanying this process. Here, we show that this transfer shortly led to extremely strong epigenetic changes in gene expression in the melanoma cells. We observed that on Matrigel numerous genes controlling ribosome biogenesis were upregulated. However, most of the activated genes were inhibitors of the differentiation genes (ID1, ID2, and ID3). At the same time, the genes that control differentiation were downregulated. Both the upregulated and the downregulated genes are simultaneously targeted by different transcription factors shaping sets of co-expressed genes. The specific group of downregulated genes shaping contacts with rDNA genes are also associated with the H3K27me3 mark and with numerous lincRNAs and miRNAs. We conclude that the stemness phenotype of melanoma cells is due to the downregulation of developmental genes and formation of dedifferentiated cells. [ABSTRACT FROM AUTHOR]

Ribosomal DNA (rDNA) copies exist across multiple chromosomes, and interindividual variation in copy number is speculated to influence the hypertrophic response to resistance training. Thus, we examined if rDNA copy number was associated with resistance training-induced skeletal muscle hypertrophy. Participants (n = 53 male, 21 ± 1 yr old; n = 29 female, 21 ± 2 yr old) performed 10–12 wk of full-body resistance training. Hypertrophy outcomes were determined, as was relative rDNA copy number from preintervention vastus lateralis (VL) biopsies. Pre- and postintervention VL biopsy total RNA was assayed in all participants, and mRNA/rRNA markers of ribosome content and biogenesis were also assayed in the 29 female participants before training, 24 h following training bout 1, and in the basal state after 10 wk of training. Across all participants, no significant associations were evident between relative rDNA copy number and training-induced changes in whole body lean mass (r = −0.034, P = 0.764), vastus lateralis thickness (r = 0.093, P = 0.408), mean myofiber cross-sectional area (r = −0.128, P = 0.259), or changes in muscle RNA concentrations (r = 0.026, P = 0.818), and these trends were similar when examining each gender. However, all Pol-I regulon mRNAs as well as 45S pre-rRNA, 28S rRNA, and 18S rRNA increased 24 h following the first training bout in female participants. Follow-up studies using LHCN-M2 myotubes demonstrated that a reduction in relative rDNA copy number induced by bisphenol A did not significantly affect insulin-like-growth factor-induced myotube hypertrophy. These findings suggest that relative rDNA copy number is not associated with myofiber hypertrophy. NEW & NOTEWORTHY: We examined ribosomal DNA (rDNA) copy numbers in men and women who resistance trained for 10–12 wk and found no significant associations with skeletal muscle hypertrophy outcomes. These data, along with in vitro data in immortalized human myotubes whereby rDNA copy number was reduced, provide strong evidence that relative rDNA copy number is not associated with anabolism. [ABSTRACT FROM AUTHOR]

The genes encoding ribosomal RNA are highly conserved across life and in almost all eukaryotes are present in large tandem repeat arrays called the rDNA. rDNA repeat unit size is conserved across most eukaryotes but has expanded dramatically in mammals, principally through the expansion of the intergenic spacer region that separates adjacent rRNA coding regions. Here, we used long-read sequence data from representatives of the major amniote lineages to determine where in amniote evolution rDNA unit size increased. We find that amniote rDNA unit sizes fall into two narrow size classes: "normal" (∼11–20 kb) in all amniotes except monotreme, marsupial, and eutherian mammals, which have "large" (∼35–45 kb) sizes. We confirm that increases in intergenic spacer length explain much of this mammalian size increase. However, in stark contrast to the uniformity of mammalian rDNA unit size, mammalian intergenic spacers differ greatly in sequence. These results suggest a large increase in intergenic spacer size occurred in a mammalian ancestor and has been maintained despite substantial sequence changes over the course of mammalian evolution. This points to a previously unrecognized constraint on the length of the intergenic spacer, a region that was thought to be largely neutral. We finish by speculating on possible causes of this constraint. [ABSTRACT FROM AUTHOR]

Globally, the poultry industry is seriously threatened by coccidiosis caused by various species of Eimeria. This protozoan parasite inhabits the epithelial lining of the gastrointestinal tract of poultry globally and can cause serious clinical disease. The present study was carried out on poultry farms located in various regions of Kashmir, India, to investigate the prevalence and phylogenetic relationships of Eimeria species affecting broiler chickens. Over a period of one year, fecal samples were collected from 60 poultry farms in Kashmir and morphological and molecular techniques were employed for Eimeria species identification. Results revealed a high prevalence of coccidiosis, with 58.3% (35/60) of farms positive for Eimeria. The most prevalent species were E. tenella (31/35, 88.6%) followed by E. acervulina (25/35, 71.4%), E. maxima (19/35, 54.3%), E. mitis (18/35, 51.4%), and E. necatrix (9/35, 25.7%). Seasonal variation in prevalence was also observed, with the highest rates in autumn (86.7%) and summer (66.7%). Additionally, younger birds (3–4 weeks) exhibited higher infection rates (85.7%) compared to older birds (57.9%) (5–6 weeks). Mixed infection was found in 94.2% (33/35) of positive farms. Phylogenetic analysis using ITS1 sequences confirmed species clustering and revealed evolutionary relationships among Eimeria species. E. tenella and E. necatrix formed a distinct clade, while E. acervulina formed another. The study underscores the importance of molecular techniques in accurate species identification and provides valuable insights into the epidemiology of coccidiosis in poultry in Kashmir. Effective control strategies, including vaccination and improved management practices, are necessary to mitigate the economic losses associated with this widespread poultry disease. [ABSTRACT FROM AUTHOR]

Simple Summary: The genus Rineloricaria of Neotropical armored catfish has several species with chromosomal polymorphism, which is where individuals of the same population have different numbers of chromosomes and chromosome structures. This characteristic affects how these fish reproduce and adapt, but we do not fully understand its role in the evolution of this fish group. This study looks at Rineloricaria lanceolata, a species known for its chromosome polymorphism. It aims to understand how these different karyotypes arise and how individuals with different karyotypes can still produce offspring even when there is an imbalance in gamete generation. We used one individual as a model to find out how the karyotype was created. It turned out that two chromosomes from different pairs fused together to form a third larger chromosome. This resulted in an odd number of chromosomes, which led to different combinations of gametes being formed in meiosis because of how the chromosomes paired. Chromosomal polymorphism is a significant aspect of population genetics, influencing the adaptation and evolution of species. In Rineloricaria lanceolata, a Neotropical fish species, chromosomal polymorphism has been observed, yet the underlying mechanisms and evolutionary implications remain poorly understood. This article aims to investigate the chromosomal polymorphism in Rineloricaria lanceolata, focusing on elucidating the meiotic behavior of karyotypic variants and tracing the phylogenetic origins of this polymorphism within the genus. By employing molecular markers and cytogenetic techniques, we aim to uncover the mechanisms driving chromosomal rearrangements and their potential role in speciation and adaptation. Understanding the genetic basis of chromosomal polymorphism in R. lanceolata not only contributes to our knowledge of species evolution but also holds implications for the conservation of genetic diversity within this vulnerable group of Neotropical fishes. [ABSTRACT FROM AUTHOR]

Background & Objectives: Genotypic identification of the etiologic agents of vaginal candidiasis (VC) is of significance in epidemiologic studies and in the establishment of adequate treatment protocol. The aim of this study was to determine the antifungal susceptibility and gene diversity of C. albicans isolated from a group of Jordanian women with VC. Methods: A total of 312 isolates of candida species, recovered from women with vaginal candidiasis who attended gynecology clinics affiliated to three major private hospitals in Amman over a period of five months (July 2020 to December 2020) were included in this study. The isolated Candida were characterized by phenotypic and genotypic means. Genotypic studies were performed using specific PCR primers of the rDNA and RPS genes. Susceptibility testing of all C. albicans isolates was conducted following the National Committee for Clinical Laboratory Standards and E-test strips. Results: Candida albicans was the most dominant Candida spp. that caused VC among the studied population. C. albicans isolates were found to be of three different subtypes at the 25S rDNA gene. All isolates belonged to genotypes A, B and C while genotypes D and E were not detected. The diversity of C. albicans was higher on the basis of RPS region where the use of two markers (P-I and P-II) resulted in the identification of nine distinct C. albicans subtypes. The sensitivity testing revealed variations in the susceptibility of various genotypes to different antifungal drugs. Genotype A isolates were more susceptible to fluconazole, flucytosine and ketoconazole than genotypes B and C. Conclusion: Candida albicans incriminated as etiologic agents of vaginitis among Jordanian women exhibited relationship between various genotypes and antifungal drugs. [ABSTRACT FROM AUTHOR]

Freshwater crabs (Potamiscus manipuriensis), commonly consumed as local delicacies by the native people in the state of Manipur, were found to harbour metacercariae of Microphallus sp. (Family Microphyllidae), which were morphologically different from metacercariae of Microphallus spp reported earlier from different regions. So, PCR-based molecular characterization of this metacercaria was done utilizing rDNA marker regions: larger subunit (LSU) or 28S (D1-D3 region) and inter-transcribed spacer 2 (ITS2). Sequence and phylogenetic analyses confirmed that the taxon under study belonged to family Microphyllidae of genus Microphallus. [ABSTRACT FROM AUTHOR]

Nucleoli form interchromosomal contacts with genes controlling differentiation and carcinogenesis. DUX4 genes specify transcription factor possessing two homeodomains. Previously, using Circular Chromosome Conformation Capture (4С) approach on population of cells, it was demonstrated that DUX4 gene clusters form frequent contacts with nucleoli. It was found also that these contacts are almost completely abolished after heat shock treatment. 4C approach as all ligation-mediated methods is capable to detect rather close interactions between chromatin loops in nuclei. In order to independently confirm the formation and the frequency of the contacts in single cells we used FISH approach. Here, we show that DUX genes in single cells form stable contacts in all tested HEK293T cells. During heat shock, DUX4 genes reversibly move 1–3 µm away from the nuclei. We conclude that interchromosomal contacts formed by nucleoli are strong, dynamic, and reversible, providing both the initiation and maintenance of a differentiated state. [ABSTRACT FROM AUTHOR]

In order to analyze the types, abundance, chromosomal distribution patterns, and interspecific differences of repetitive sequences in three common species of coastal Suaeda, the sequence similarity-based clustering analysis and fluorescence in situ hybridization techniques were used for the comparative analysis of their repetitive sequences. The results revealed that there were tandem repeats and transposable elements in all the three species. Among them, the telomeric sequences, 5S rDNA, and 35S rDNA were identified as the conserved tandem repeats across the three species, while the other two tandem repeats were identified as being specific to Suaeda glauca. These tandem repeats tended to be enriched in the chromosome telomeres, subtelomeres, and chromosomal arms. Furthermore, the transposable elements in the three Suaeda species were mainly composed of retrotransposons and DNA transposons. Notably, the genome of Ty3/gypsy retrotransposons were found to have a higher genomic proportion, while the Ty1/copia retrotransposons and DNA transposons were relatively less abundant. Except for the CRM lineage, which was mainly clustered in the centromeric region, most of transposable elements exhibited a dispersed distribution across the chromosomes, while some transposable elements with lower genomic abundance were not detected. According to the analysis results of repetitive sequence and chromosomal distribution, the genomic relationship between Suaeda australis and Suaeda salsa was closer than that of Suaeda glauca. These findings would provide a basis for understanding the characteristics of repetitive sequences and the evolutionary relationships among the three species of coastal Suaeda. [ABSTRACT FROM AUTHOR]

Oxidative stress and aging are known to alter the satellite III repeat (1q12) (SatIII(1q)) and telomere repeat (TR) copy numbers (CNs) in DNA of human cells. Extreme conditions of Antarctica could potentially affect the CNs of the repeats in human blood cells, the effect being possibly associated with inhibition of the antioxidant system and activation of apoptosis. The ribosomal DNA (rDNA), SatIII(1q), and TR repeat CNs were studied in leukocytes of 11 men who participated in an expedition to the Vostok Station from 2019 to 2020. To observe the dynamic changes in repeat CNs and the degree of repeat oxidation, six blood samples were taken: before the arrival in Antarctica and after 27, 85, 160, 270, and 315 days of wintering. To analyze the adaptive changes, expression levels were measured for the genes coding for BAX, BCL2, NOX4, NRF2, SOD1, and HIF1. A decrease in SatIII(1q) CN and an increase in TR CN were detected, while the rDNA CN remained stable in human blood cells during wintering. The changes, along with a decrease in the oxidation marker 8-oxodG in DNA, were associated with an increase in NOX4 activity, a decrease in NRF2 activity, and an increase in expression of the proapoptotic protein BAX. Wintering in Antarctica was therefore assumed to stimulate the adaptive response in the human body, including higher elimination of "ballast" cells with a higher level of DNA oxidation, a higher SatIII(1q) content, and a lower TR content from the bloodstream. An increase in ROS due to chronic NOX4 activation and a NRF2 blockage might play a significant role in the response. [ABSTRACT FROM AUTHOR]

Aporcelaimellus obtusicaudatus was recovered from mustard and sugarcane fields of Uttar Pradesh and Uttarakhand, India. The present species was identified through morphology, molecular and phylogenetic analysis. The Indian populations are characterized by having females with a body length (1.7–3.4 mm), lip region (4.9–8.8 µm), Amphids 6–9 µm, odontostyle length (15.7–26.4 µm), neck length (374.6–745.1 µm), pharyngeal expansion occupying 45–60% of neck length, simple uterus (67.4–124.3 µm), V = 49.1–58.7, female tail (32–44.9 µm, c = 41.1–105, c' = 0.5–1.3) with short, conoid, rounded terminus to convex conical. The molecular phylogenetic analysis based on 18S and 28S rDNA revealed A. obtusicaudatus as a paraphyly. The present populations of Indian A. obtusicaudatus (OM269524; OP020675) placed close to deposited Indian sequence (OP048816; OP048823) and Slovakian populations of A. obtusicaudatus (MH206119). The result of 28S rDNA phylogeny showed that the present population (OM258706) placed close to other populations of the same species from India (OM418794) with 0.55 posterior probability supports. The haplotype analysis based on 28S rDNA revealed 6 haplotypes, which displayed low nucleotide (π = 0.013) diversity. In contrast, haplotype diversity (Hd) was 1.00, and the number of segregating sites (S) was 14. The phylogenetic analysis grouped the various populations into two clades, and the result showed German populations placed into two clades, which showed high variability in haplotype supported by the haplotype network. Tajima (D) and Fu's Fs were found to be negative (P > 0.05), whereas the overall FST value was 0.31040 (P = 0.118). In conclusion, genetic analysis revealed 31.04% variation among groups/populations and 68.95 within populations, indicating a low genetic variation between the same populations of A. obtusicaudatus belonging to the same country. [ABSTRACT FROM AUTHOR]

The ribosomal DNA (rDNA) constitutes a remarkably conserved DNA sequence within species, located in the area of the nucleolus, and responsible for coding three major types of rRNAs (18S, 5.8S and 28S). While historical investigations into rDNA focused on its structure and coding capabilities, recent research has turned to explore its functional roles in various biological processes. In this review, we summarize the main findings of rDNA methylation with embryonic development, aging and diseases in multiple species, including epigenetic alterations, related biological processes and potential applications of rDNA methylation. We present an overview of current related research and identify gaps in this field. [ABSTRACT FROM AUTHOR]

The major loci for the large primary ribosomal RNA (rRNA) genes (35S rRNAs) exist as hundreds to thousands of tandem repeats in all organisms and dozens to hundreds in Drosophila. The highly repetitive nature of the ribosomal DNA (rDNA) makes it intrinsically unstable, and many conditions arise from the reduction in or magnification of copy number, but the conditions under which it does so remain unknown. By targeted DNA damage to the rDNA of the Y chromosome, we created and investigated a series of rDNA alleles. We found that complete loss of rDNA leads to lethality after the completion of embryogenesis, blocking larval molting and metamorphosis. We find that the resident retrotransposons— R1 and R2 —are regulated by active rDNA such that reduction in copy number derepresses these elements. Their expression is highest during the early first instar, when loss of rDNA is lethal. Regulation of R1 and R2 may be related to their structural arrangement within the rDNA , as we find they are clustered in the flanks of the nucleolus organizing region (NOR ; the cytological appearance of the rDNA). We assessed the complex nucleolar dominance relationship between X - and Y -linked rDNA using a histone H3.3–GFP reporter construct and incorporation at the NOR and found that dominance is controlled by rDNA copy number as at high multiplicity the Y -linked array is dominant, but at low multiplicity the X -linked array becomes derepressed. Finally, we found that multiple conditions that disrupt nucleolar dominance lead to increased rDNA magnification, suggesting that the phenomena of dominance and magnification are related, and a single mechanism may underlie and unify these two longstanding observations in Drosophila. [ABSTRACT FROM AUTHOR]

Fecal analysis is a useful tool for studying the species identity of rare mammals. The possibility of using non-invasive biological materials in molecular genetic studies of rare bovids is shown, using the example of the markhor and Siberian ibex of Uzbekistan. Field work including noninvasive genetic sampling collection was carried out in the study area in spring and autumn 2022-2023 in the Hissar, Surkhan State Reserves and Ugam-Chatkal State National Natural Park and Termez zoo in Uzbekistan. We used species-specific 16S rRNA mitochondrial gene fragments for polymerase chain reaction amplification for species identification. The results of the molecular analysis with the 16S rRNA mitochondrial gene allowed the identification of Capra sibirica, C. falconeri and C. hircus belonging to the subfamily Caprinae using a noninvasive genetic sampling method. This method is quite easy to use, while avoiding direct contact with the animal, which minimizes the degree of impact on the object being studied and does not require significant material and labor costs for researchers. We believe that noninvasive genetic sampling is emerging as one of the most effective and accurate methods for estimating the population size of animals, and we recommend considering this approach for endangered and rare species. The protocol developed could be a valuable tool in the management and conservation of the Capra species occurring on the Uzbekistan.

Pitaya (Hylocereus undatus; 2n=22) is an important fruit crop from the Cactaceae family, originally domesticated in Mexico and the USA, and is now widely cultivated for its nutritional benefits. It is characterized by its distinctive triangular-shaped stems and large, showy flowers, thriving in arid and semi-arid environments, particularly in hot, dry climates. However, systematic chromosomal studies, including chromosomal mapping of cytogenetic markers in pitaya, are limited, presenting challenges for its cytogenetic improvement. To address this issue, we designed oligo-barcodes specific to thirty-three chromosome regions based on the pitaya reference genome and applied them to both pitaya and cactus (Selenicerus grandifloras; 2n=22) for oligo-barcodes mapping, karyotyping, and chromosome identification. We utilized FISH technology, employing oligo, rDNA, and tandem repeat probes for chromosomal mapping, identification, and karyotyping of pitaya and related species. We successfully localized oligo-barcodes on eleven pairs of chromosomes in both pitaya and cactus, demonstrating the effectiveness of the synthesized oligo-barcodes. We used two ribosomal DNA (rDNA) probes (45S and 5S) and two tandem repeat probes (GTR11 and STR3) in pitaya (both diploid and tetraploid) and two other Cactaceae species (S. grandifloras and Opuntia humifusa; 2n=40) for chromosomal mapping. The analysis of rDNA distribution and CMA (Chromomycin A3) banding across different chromosomes in pitaya and cacti highlights the concept of conserved rDNA. This study provides fundamental insights into cytogenetic markers and their localization across different chromosomes in pitaya and other Cactaceae species.

Zoraptera (also called “angel insects”) is one of the most unexplored insect orders. However, it holds promise for understanding the evolution of insect karyotypes and genome organization given its status as an early branching group of Polyneoptera and Pterygota (winged insects) during the Paleozoic. Here, we provide karyotype descriptions of three Zorapteran species: Brazilozoros huxleyi (2n♂; ♀ = 42; 42), B. kukalovae (2n♂; ♀ = 43; 44) and Latinozoros cacaoensis (2n♂; ♀ = 36; 36). These species represent two of the four recently recognized Zorapteran subfamilies. Contrary to an earlier suggestion that Zoraptera has holocentric chromosomes, we found karyotypes that were always monocentric. Interestingly, we detected both X0 (B. kukalovae) and XY (B. huxleyi, L. cacaoensis) sex chromosome systems. In addition to conventional karyotype descriptions, we applied fluorescent in situ hybridization for the first time in Zoraptera to map karyotype distributions of 18S rDNA, histone H3 genes, telomeres and (CAG)n and (GATA)n microsatellites. This study provides a foundation for cytogenetic research in Zoraptera.

Abstract Presenting new molecular and scanning electron microscope (SEM) features, this study gives additional data to the better knowledge of Thaparocleidus vistulensis (Siwak, 1932) (Monopisthocotyla, Ancylodiscoididae), a parasite of the European catfish Silurus glanis Linnaeus, 1758 (Siluriformes, Siluridae) cultured in a commercial fish farm in Hungary. In addition, notes on the early development of sclerotized anchors are also provided. The main morphological difference of T. vistulensis compared to other congeneric species is associated with the male copulatory organ, which exhibits 5–7 loops in the middle of the penis length and a long open V-shaped sclerotized accessory piece, dividing terminally into two parts, securing the terminal part of the penis tube. The present study provides for the first time molecular characterization data based on the 2694 bp long nucleotide sequence of rDNA (ITS1, 5.8S, ITS2, and flanked with partial 18S and partial 28S) submitted in GenBank with the accession number OR916383. A phylogenetic tree based on ITS1 sequences supports a well-defined clade including T. vistulensis, forming a sister group with T. siluri, a species-specific monopisthocotylan parasite to S. glanis. The morphological characterization of T. vistulensis, especially for the male copulatory organ, together with the molecular data in the present study, extends knowledge about this monopisthocotylan species and provides new information for future phylogeny studies.

During a survey of soil nematodes in South Africa, a species of predatory nematodes, namely Mylonchulus hawaiiensis was recovered from soil in the Magoebaskloof mountain of Limpopo Province, South Africa. The morphology of the material studied fit well with the previous populations of the same species. A molecular study of 18S rDNA region of M. hawaiiensis indicated a 100% similarity between the South African population and the Japanese population of M. hawaiiensis (AB361438; AB361439; AB361440; AB361442). In addition, phylogenetic analysis placed all M. hawaiiensis in a group with 0.97 posterior probability. Additionally, ITS rDNA of M. hawaiiensis amplified for the first time. However, Principal component analysis (PCA) showed a morphological variation among the different populations of M. hawaiiensis. In addition, haplotype analysis also revealed that the South African population is close to the Japanese population. In conclusion, 18S rDNA was a good marker for detecting M. hawaiiensis. Measurement, photographs, and phylogenetic position of South African M. hawaiinesis are given.

Background: A number of association studies have linked ribosomal DNA gene copy number (rDNA CN) to aging and pathology. Data from these studies are contradictory and depend on the quantitative method. Methods: The hybridization technique was used for rDNA quantification in human cells. We determined the rDNA CN from healthy controls (HCs) and patients with schizophrenia (SZ) or cystic fibrosis (CF) (total number of subjects N = 1124). For the first time, rDNA CN was quantified in 105 long livers (90–101 years old). In addition, we conducted a joint analysis of the data obtained in this work and previously published by our group (total, N = 3264). Results: We found increased rDNA CN in the SZ group (534 ± 108, N = 1489) and CF group (567 ± 100, N = 322) and reduced rDNA CN in patients with mild cognitive impairment (330 ± 60, N = 93) compared with the HC group (422 ± 104, N = 1360). For the SZ, CF, and HC groups, there was a decreased range of rDNA CN variation in older age subgroups compared to child subgroups. For 311 patients with SZ or CF, rDNA CN was determined two or three times, with an interval of months to several years. Only 1.2% of patients demonstrated a decrease in rDNA CN over time. We did not find significant rDNA CN variation in eight different organs of the same patient or in cells of the same fibroblast population. Conclusions: The results suggest that rDNA CN is a relatively stable quantitative genetic trait statistically associated with some diseases, which however, can change in rare cases under conditions of chronic oxidative stress. We believe that age- and disease-related differences between the groups in mean rDNA CN and its variance are caused by the biased elimination of carriers of marginal (predominantly low) rDNA CN values.

There are thousands of Narcissus cultivars, however; their genome compositions are not so clear, except that their ploidy levels are extensively investigated. The present study analyzed eight popular cultivars using GISH or/and FISH. The present results clearly revealed their genome compositions: 'Bridal Crown' was diploid (2n = 2x = 17 = 10 + 7 = AE) rather than aneuploid, 'Jinzhanyintai' was autotriploid (2n = 3x = 30 = 10 + 10 + 10 = AAA) rather than allotetraploid or hexaploid, 'Tête-à-Tête' was allotriploid (2n = 3x = 24 + B = 10 + 7 + 7 + B = AEE), 'Cultivar X' was also allotriploid (2n = 3x = 24 = 10 + 7 + 7 = AEX), and 'Dutch Master', 'Replete' and 'Queen's Day' were all autotetraploid (2n = 4x = 28 = 7 + 7 + 7 + 7 = EEEE). Together with other reports, we concluded that 'Tête-à-Tête' contained one genome of Narcissus tazetta, one genome of Narcissus cyclamineus, and one genome of Narcissus pseudonarcissus, and that 'Pink Parasol' was aneu-autotetraploid (2n = 4x + 2 = 30 = 7 + 7 + 7 + 7 + 2 = EEEE+2) rather allotetraploid (2n = 4x = 10 + 10 + 5 + 5 = CCDD). Based on the cultivar's genome composition and origin, it is concluded that distant hybridization, sexual polyploidization and chromosome doubling play different roles in breeding modern Narcissus cultivars. [ABSTRACT FROM AUTHOR]

Introduction: Passeriformes has the greatest species diversity among Neoaves, and the Tyrannidae is the richest in this order with about 600 valid species. The diploid number of this family remains constant, ranging from 2n = 76 to 84, but the chromosomal morphology varies, indicating the occurrence of different chromosomal rearrangements. Cytogenetic studies of the Tyrannidae remain limited, with approximately 20 species having been karyotyped thus far. This study aimed to describe the karyotypes of two species from this family, Myiopagis viridicata and Sirystes sibilator. Methods: Skin biopsies were taken from each individual to establish fibroblast cell cultures and to obtain chromosomal preparations using the standard methodology. The chromosomal distribution of constitutive heterochromatin was investigated by C-banding, while the location of simple repetitive sequences (SSRs), 18S rDNA, and telomeric sequences was found through fluorescence in situ hybridization. Results: The karyotypes of both species are composed of 2n = 80. The 18S rDNA probes hybridized into two pairs of microchromosomes in M. viridicata, but only a single pair in S. sibilator. Only the telomeric portions of each chromosome in both species were hybridized by the telomere sequence probes. Most of the SSRs were found accumulated in the centromeric and telomeric regions of several macro- and microchromosomes in both species, which likely correspond to the heterochromatin-rich regions. Conclusion: Although both species analyzed showed a conserved karyotype organization (2n = 80), our study revealed significant differences in their chromosomal architecture, rDNA distribution, and SSR accumulation. These findings were discussed in the context of the evolution of Tyrannidae karyotypes. [ABSTRACT FROM AUTHOR]

The ribosomal DNA locus (rDNA) is central for the functioning of cells because it encodes ribosomal RNAs, key components of ribosomes, and also because of its links to fundamental metabolic processes, with significant impact on genome integrity and aging. The repetitive nature of the rDNA gene units forces the locus to maintain sequence homogeneity through recombination processes that are closely related to genomic stability. The co-presence of basic DNA transactions, such as replication, transcription by major RNA polymerases, and recombination, in a defined and restricted area of the genome is of particular relevance as it affects the stability of the rDNA locus by both direct and indirect mechanisms. This condition is well exemplified by the rDNA of Saccharomyces cerevisiae. In this review we summarize essential knowledge on how the complexity and overlap of different processes contribute to the control of rDNA and genomic stability in this model organism. [ABSTRACT FROM AUTHOR]

In this study, the ability of the Quick-DNA™ Tissue/Insect Miniprep Kit and Chelex® methods to extract DNA from O. niloticus skin, muscle, and gill tissue was compared. The quantity and purity of the DNA were measured with a NanoDrop spectrophotometer. Based on the results obtained, it appears that the DNA extracted using the Kit has good quality based on A260/280 (1.67–1.98), and the Chelex method (1.52-1.81) was acceptable. ANOVA for the amount of nucleic acid revealed a significant difference between muscle and skin with gill tissue (P < 0.05). However, the skin of O. niloticus subjected to both methods was the best at extracting DNA (1.89-1.81). The extracted DNA was also studied by 28S ribosomal DNA and COI of mitochondrial DNA genes. Phylogenetic analysis based on 28S rDNA and COI of mtDNA placed the South African population of O. niloticus in a clade with other related species with a posterior probability value of 1.00. Finally, the molecular results showed that 28S ribosomal DNA is a suitable marker for the identification of O. niloticus. In conclusion, precise identification of O. niloticus is critical for breeding for farmers and commercial sectors. [ABSTRACT FROM AUTHOR]

Introduction: The Pacific abalone, Haliotis discus hannai, is one of the most commercially important marine shellfish in China. Cell engineering breeding is an important tool in abalone genetic breeding, and the triploids obtained through this method have high commercial value. However, current research mainly focuses on establishing induction methods and evaluating the growth traits of triploids, while there is a lack of basic research on triploid cytogenetics. Method: In this study, Cytogenetic analysis of triploid Haliotis discus hannai larvae (produced by chemical treatment) and diploid larvae was performed. Result: The results showed that triploid H. discus hannai had a chromosome number of 3n = 54, consisting of 30 metacentric (m) and 24 submetacentric (sm) chromosomes, while the diploids had a chromosome number of 2n = 36, consisting of 20 metacentric (m) and 16 submetacentric (sm) chromosomes. Notably, both triploids and diploids displayed variation in the number of NORs and/or their diameter. The average number of NORs in triploid was significantly higher than that in diploids (p <0.05), but the average diameter of NORs of triploid was no significant different from that of diploid (p> 0.05). Additionally, 5S rDNA localization to 3 submetacentric chromosomes was observed in triploids, compared to 2 submetacentric chromosomes in diploids. The number of 18S rDNA sites displayed positional conservancy and quantitative variability in both diploids and triploids. Specifically, 18S rDNA was found at the end of the chromosome in both groups, with triploids exhibiting a significantly higher number of loci than diploids (p <0.01). Conclusion: This study provides valuable insights into the cytogenetic characteristics of triploid H. discus hannai, which could facilitate further research on the stability of the chromosome set in this species. [ABSTRACT FROM AUTHOR]