Search Results (256)

Chromosome rearrangements during plant evolution can lead to alterations in genome structure and gene function, thereby influencing species adaptation and evolutionary processes. Gymnosperms, as an ancient group of plants, offer valuable insights into the morphological, physiological, and ecological characteristics of early terrestrial flora. The reconstruction of ancestral karyotypes in gymnosperms may provide critical clues for understanding their evolutionary history. In this study, we inferred the ancestral gymnosperm karyotype (AGK), which comprises 12 chromosomes, and conducted a collinearity analysis with existing gymnosperm genomes. Our findings indicate that chromosome numbers have remained remarkably stable throughout the evolution of gymnosperms. For species with multiplied chromosome numbers, such as gnetophytes, weak collinearities with the AGK were observed. Comparisons between the AGK and gnetophyte genomes revealed a biased pattern regarding retained duplication blocks. Furthermore, our analysis of transposable elements in Welwitschia mirabilis identified enriched regions containing LINE-1 retrotransposons within the syntenic blocks. Syntenic analysis between the AGK and angiosperms also demonstrated a biased distribution across chromosomes. These results provide a fundamental resource for further characterization of chromosomal evolution in gymnosperms. Full article

To explore the dyeing technique and karyotype analysis of winter turnip rape (Brassica rape L.), the root tip of winter turnip rape Longyou 7 was used as the experimental material. Chromosome preparation technology was optimized, and karyotype analysis was carried out by changing the conditions of material collection time, pretreatment, fixation, and dissociation. The results showed that the optimal conditions for the preparation of dyeing winter turnip rape were as follows: the sampling time was 8:00–10:00, the ice–water mixture was pretreated at 4 °C for 20 h, the Carnot’s fixative solution I and 4 °C were fixed for 12 h, and the 1 mol/L HCl solution was bathed in a water bath at 60 °C for 10~15 min. Karyotype analysis showed that the number of chromosomes in winter turnip rape cells was 2n = 20, and the karyotype analysis formula was 2n = 2x = 20 = 16m + 4sm. The karyotype asymmetry coefficient was 58.85%, and the karyotype type belonged to type 2A, which may belong to the primitive type in terms of evolution. The results of this study provide a theoretical basis for further in-depth study of the phylogenetic evolution and genetic trend of Brassica rapa. Full article

Adansonia L. (1753) belongs to the family Malvaceae and is commonly known as the baobab tree. This species holds significant cultural and ecological value and is often referred to as the ‘tree of life.’ Although its nuclear genome has been reported, the mitogenome has not yet been studied. Mitogenome research is crucial for understanding the evolution of the entire genome. In this study, we assembled and analyzed the mitogenomes of four Adansonia species by integrating short-read and long-read data. The results showed that the mitogenomes of all four Adansonia species were resolved as single circular sequences. Their total genome lengths ranged from 507,138 to 607,344 bp and contained a large number of repetitive sequences. Despite extensive and complex rearrangements between the mitogenomes of Adansonia and other Malvaceae species, a phylogenetic tree constructed based on protein-coding genes clearly indicated that Adansonia is more closely related to the Bombax. Selection pressure analysis suggests that the rps4 gene in Adansonia may have undergone positive selection compared to other Malvaceae species, indicating that this gene may play a significant role in the evolution of Adansonia. Additionally, by analyzing intracellular gene transfer between the chloroplast, mitochondria, and nuclear genomes, we found that genes from the chloroplast and mitochondria can successfully transfer to each chromosome of the nuclear genome, and the psbJ gene from the chloroplast remains intact in both the mitochondrial and nuclear genomes. This study enriches the genetic information of Adansonia and provides important evidence for evolutionary research in the family Malvaceae. Full article

The genus Vigna Savi (Leguminosae Juss.) comprises approximately 150 species, classified into five subgenera, most of which exhibit a diploid chromosome number of 2n = 22. However, the wild species Vigna lasiocarpa (Benth) Verdc. (V. subg. Lasiospron) is notable for its dysploid chromosome number of 2n = 20. This study aimed to elucidate the chromosomal events involved in the karyotype evolution of V. lasiocarpa (Vla). We used oligopainting probes from chromosomes 1, 2, 3, and 5 of Phaseolus vulgaris L. and two barcode probes from the genome of V. unguiculata (L.) Walp. Additionally, bacterial artificial chromosomes (BACs) from V. unguiculata and P. vulgaris, along with a telomeric probe from Arabidopsis thaliana (L.) Heynh., were hybridized to V. lasiocarpa metaphase chromosomes to characterize Vla3, Vla7/5, and Vla9. Our findings revealed conserved oligo-FISH patterns on chromosomes 2, 6, 8, 10, and 11 between V. unguiculata and V. lasiocarpa. Paracentric and pericentric inversions were identified for Vla3 and Vla9, respectively. Our integrative approach revealed that the dysploid chromosome originated from an “end-to-end fusion” of homoeologous chromosomes 5 and 7. This is the first report on the chromosomal mechanisms underlying descending dysploidy in Vigna, providing new insights into the evolutionary dynamics of the genus. Full article

Polyamine oxidase (PAO) is an important enzyme that functions in the catabolism of polyamines. While plant PAOs have been studied in several species, there is a lack of research on this gene family in soybean (Glycine max L.), one of the major food crops worldwide. Here, a genome-wide analysis identified 16 GmPAOs from the soybean genome, which were unevenly distributed in nine soybean chromosomes and were then phylogenetically classified into three groups. Collinearity analysis identified 17 duplicated gene pairs from the GmPAO family, and their Ka/Ks values were all less than one, indicating that the GmPAO family has undergone purifying selection during evolution. Analyses of the conserved motif and gene structure revealed the sequence differences among the GmPAOs of the three groups, suggestive of their functional differentiation. Additionally, the prediction of the secondary and tertiary structure of the GmPAOs provided a further basis for revealing their biological functions. A number of cis-acting elements relevant to development, phytohormone, and stress response were discovered in the promoter regions of the GmPAOs, which might be responsible for their functional diversities. Expression pattern analysis indicated that more than half of the GmPAOs showed preference in flower, two showed specificity in stem and shoot apical meristem, whereas four were barely expressed in all samples. Expression profiling of the GmPAOs also revealed that they were involved in the response to abiotic stresses, including cold, drought, and especially submergence stress. All these results lay an important foundation for further characterizing the functional roles of GmPAOs in soybean development and response to abiotic stresses. Full article

Tandem repeats in eukaryotic genomes exhibit intrinsic instability that drives rapid evolutionary diversification. However, their evolutionary dynamics in allopolyploid species such as the water hyacinth (Pontederia crassipes or Eichhornia crassipes) remain largely unexplored. Our study used integrated genomic and cytogenetic analyses of this allotetraploid species to characterize five representative tandem repeats, revealing distinct genomic distribution patterns and copy number polymorphisms. The highly abundant centromeric tandem repeat, putative CentEc, was co-localized with the centromeric retrotransposon CREc, indicating conserved centromeric architecture. Remarkably, putative CentEc sequences showed high sequence conservation (91–100%) despite subgenome divergence, indicative of active concerted evolution. Fluorescence in situ hybridization (FISH) analysis showed ubiquitous telomeric repeats across all chromosomes, while an interstitial chromosome region tandem repeat (ICREc) displayed chromosome-specific localization, both exhibiting copy number variation. Furthermore, differential rDNA organization was observed. 5S rDNA was detected on a single chromosome pair, whereas 35S rDNA exhibited multichromosomal distribution with varying intensities. A comparative analysis of subgenome-specific rDNA sequences revealed substantial heterogeneity in both 5S and 35S rDNA units, suggesting subgenome-biased evolutionary trajectories. Collectively, these findings elucidate the structural and evolutionary significance of tandem repeats in shaping the water hyacinth genome, highlighting mechanisms of concerted evolution and subgenome-biased adaptation in invasive polyploids. Full article

Rice (Oryza sativa) is one of the key staple crops, providing food for nearly half of the world’s population. The past twenty years have seen significant advances in understanding Oryza species through genome sequencing efforts. However, the stability of Oryza genomes during their divergence has not been well characterized. Here, by performing gene collinearity and comparative genomics analysis, we selected ten Oryza species and three other Poaceae species to check their genome stability, with Leersia perrieri as the reference. Intra- and intergenomic analysis showed a ~30% difference in homologous block numbers and a 35.7% difference in collinear gene numbers per block, indicating that Oryza genomes have undergone extensive DNA permutations. Notably, we found that Oryza chromosomes with smaller ordinal numbers have often preserved larger percentages of genes, while those with bigger numbers have undergone more gene losses. This unique observation may be explained by elevated gene losses incurred by illegitimate or homoeologous recombination between homoeologous chromosomes produced by the grass-common tetraploidization (GCT) ~100 million years ago (Mya), e.g., Chro. 11 and 12. However, the lowered gene loss rates in Chro. 1–3 could be explained by earlier restriction of illegitimate recombination after the GCT due to there often being (larger) neo-chromosomes produced by the fusion of ancestral chromosomes. The enriched NBS-LRR (nucleotide-binding site and leucine-rich repeat) genes in chromosomes 11 and 12 are another explanation for the above observation. Further evidence was obtained from other Poaceae plants. Moreover, we revealed around twice as many differences in tandem genes and their densities among Oryza plants, further showing their divergent levels of genome stability. The present efforts may contribute to the understanding of the stability of the Oryza genome and its formation, evolution, and functional innovation. Full article

Snakes are cytogenetically dynamic, characterized by largely conserved diploid chromosome numbers although displaying varied variable evolutionary stages of their sex chromosomes. This study examined four snakes, with a special focus on the genus Ptyas, to provide evolutionary insights into the evolution of ZW sex chromosomes. We performed an extensive karyotype characterization using conventional and molecular cytogenetic approaches, described for the first time the karyotype of Ptyas korros, and revisited the karyotype descriptions of P. mucosa, Chrysopelea ornata, and Fowlea flavipunctatus. We found that all species except F. flavipunctatus have highly heterochromatic W chromosomes enriched in satDNAs or microsatellite repeats. Repetitive sequences accumulate with the heterochromatinization of the W chromosome but are not necessarily associated with this process, demonstrating the dynamic makeup of snake sex chromosomes. Autosomal locus-specific and sex chromosome probes from Pogona vitticeps and Varanus acanthurus did not show hybridization signals in Ptyas snakes, suggesting divergent evolutionary pathways. This finding highlighted the dynamic nature of sex chromosome evolution in snakes, which occurred independently in lizards. Full article

Chromosomes are essential carriers of human genetic material, and karyotype diagnosis plays a crucial role in prenatal diagnostics, genetic disease identification, and medical research. Physicians rely heavily on karyotype images to diagnose potential abnormalities in chromosome numbers and structure. However, the process is tedious and challenging. To improve diagnostic efficiency and accuracy, artificial intelligence (AI) researchers have developed convolutional neural networks (CNNs) for chromosome image classification. Despite this progress, the gap between cytogeneticists and AI experts results in a time-consuming workflow. In this study, we propose a framework based on improved Differentiable Architecture Search (DARTS) to automatically design convolutional architectures for the classification task. The improvement strategies based on DARTS are implemented in two stages. First, a procedural approach was designed to comprehensively analyze the evolution of architectural parameters. Based on this analysis, the search space of the DARTS algorithm was refined, resulting in an optimized search space. Next, an entropy-based regularization term was incorporated into the supernetwork’s objective function to guide the algorithm in searching for a more effective architecture. Then, extensive experiments were conducted on CIFAR-10, ImageNet, and the Copenhagen datasets to evaluate the performance of the searched architecture in comparison with related works. The network composed of the searched architecture achieved accuracies of 97.27 $\pm$ 0.05%, 75.40%, and 98.64% on the three datasets, respectively. These results demonstrate that the architecture is high-performing and the proposed framework for designing networks for chromosome classification is effective. Full article

Background: Cisplatin resistance is a major cause of tumor recurrence and mortality in high-grade serous ovarian cancer (HGSOC). Extrachromosomal circular DNA (eccDNA) has emerged as a critical factor in tumor evolution and drug resistance. However, the specific contribution of eccDNA to cisplatin resistance in HGSOC remains unclear. Methods: We performed whole-genome sequencing, Circle-Seq, and RNA-Seq in four pairs of primary and cisplatin-resistant (cisR) HGSOC cell lines to characterize genome-wide eccDNA distribution and features. Functional enrichment analyses were subsequently conducted on differentially expressed eccDNA-related genes. Results: In the SKOV3 cisR cell line, we identified a large extrachromosomal circular DNA (ecDNA) carrying the HIF1A gene, which regulates DNA repair, drug efflux, and epithelial–mesenchymal transition, contributing to cisplatin resistance. Using Circle-Seq, we detected a total of 161,062 eccDNAs, most of which were less than 1000 bp and distributed across all chromosomes. Notably, the number of eccDNAs on chromosome 21 differed significantly between the primary and cisR cell lines. Additionally, eccDNAs were predominantly located in non-coding repetitive elements. Functional analysis of eccDNA-related differentially expressed genes revealed that, compared to primary cell lines, cisR cell lines were associated with mitotic spindle assembly, regulation of vascular permeability, and cell differentiation. eccDNA-related genes involved in these pathways include MISP, WIPF1, RHOD, KRT80, and PLVAP. Conclusions: Our findings suggest that eccDNAs, particularly ecDNA amplifications like HIF1A, contribute significantly to cisplatin resistance mechanisms in HGSOC. These insights highlight eccDNA as a potential target for overcoming therapeutic resistance and improving treatment outcomes in ovarian cancer. Full article

Transcription factors play an important regulatory role in tomato fruit ripening. We identified and analyzed eight transcription factor families (TF families) associated with fruit ripening in the genomes of seven tomato species and two outgroup species, revealing the impact of whole-genome duplication (WGD) events on the structure and functional characteristics of these TF families. The results indicate that the Solanaceae Common Hexaploidization (SCH) event is the primary driver for the increase in the number of members within these TF families, leading to a more concentrated chromosomal distribution of family members. Compared with the two outgroup species, the tomato fruit-ripening-related TF families exhibit stronger codon usage bias, which may have been enhanced by WGD. Phylogenetic analysis found that family members generated by SCH show faster evolutionary rates, suggesting that SCH events significantly contribute to the evolution of these families. Additionally, our research uncovered that WGD events might maintain expression activity during fruit ripening by generating duplicate TF family members. Our study not only deepens our understanding of the mechanisms underlying tomato fruit ripening but also provides a theoretical foundation for future breeding improvements. Full article

Chromoplexy is a phenomenon of complex genome rearrangement, occurring during a single cell event and characterized by the formation of chain rearrangements affecting multiple chromosomes. Unlike other genomic rearrangements such as chromothripsis, which involves a single chromosome, chromoplexy affects several chromosomes at once, creating patterns of complex, balanced translocations, and leading to the formation of fusion genes and the simultaneous disruption of several genes. Chromoplexy was first identified in prostate cancers, but it is now observed in various cancers where gene fusions take place. The precise mechanisms behind chromoplexy remain under investigation. The occurrence of these rearrangements follows multiple double-stranded breaks that appear to occur in certain regions or during particular genome configurations (open chromatin, active transcription area), and which lead to an intricate series of inter- and intra-chromosomal translocations and deletions without significant alterations in the number of copies. Although chromoplexy is considered a very early event in oncogenesis, the phenomenon can be repeated and can constitute a mechanism of clonal tumor progression. The occurrence of chromoplexy supports the equilibrium model punctuated by tumor evolution, characterized by periods of relative stability punctuated by sudden and rapid periods of radical genomic changes. Full article

MADS-box transcription factors play a crucial role in plant growth and development. Although previous genome-wide analyses have investigated the MADS-box family in cucumber, this study provides the first comprehensive reannotation of the MADS-box gene family in Cucumis sativus using updated Cucurbitaceae genome data, offering novel insights into the gene family’s evolution and functional diversity. The results show that a total of 48 CsMADS-box genes were identified in the V3 version of cucumber, while 3 of the 43 genes identified in the V1 version were duplicated. The V1 version actually has only 40 genes. Additionally, we analyzed the variability in protein sequences and found that the amino acid sequences of 14 genes showed no differences between the two versions of the database, while the amino acid sequences of 29 genes exhibited significant differences. The further analysis of conserved motifs revealed that although the amino acid lengths of 15 genes had changed, their conserved motifs remained unchanged; however, the conserved motifs of 12 genes had altered. Furthermore we found that motif1 and motif2 were present in most proteins, indicating that they are highly conserved. Gene structure analysis revealed that most type I (Mα, Mβ) MADS-box genes lack introns, whereas type II (MIKC) genes exhibit a similar structure with a higher number of introns. Chromosomal localization analysis indicated that CsMADS-box genes are unevenly distributed across the seven chromosomes of cucumber. Promoter region analysis showed that the promoter regions of CsMADS-box genes contain response elements related to plant growth and development, suggesting that CsMADS-box genes may be extensively involved in plant growth and development. Different CsMADS-box genes exhibit specific high expression in roots, stems, leaves, tendrils, male flowers, female flowers, and ovaries, suggesting that these genes play crucial roles in the growth, development, reproduction and morphogenesis of cucumber. Moreover, 26, 18, 8, and 10 CsMADS-box genes were differentially expressed under high temperature, NaCl and/or silicon, downy mildew, and powdery mildew treatments, respectively. Interestingly, CsMADS07 and CsMADS16 responded to all tested stress conditions. These findings provide a reference and basis for further investigation into the function and mechanisms of the MADS-box genes for resistance breeding in cucumber. Full article

Anseriformes represent a basal order in the phylogeny of neognath birds and are of particular interest in cytogenetic research due to their distinctive chromosomal features. However, aspects of their chromosomal evolution, such as the distribution and organization of microsatellite sequences, remain poorly understood. Given the role of these dynamic repetitive sequences in chromosome organization, differentiation, and evolution, we analyzed microsatellite distribution in three Anatidae species, each representing a different subfamily: Amazonetta brasiliensis-Brazilian Teal (Anatinae), Coscoroba coscoroba-Coscoroba Swan (Anserinae), and Dendrocygna viduata-White-faced Whistling Duck (Dendrocygninae). This is the first karyotypic description for White-faced Whistling Duck (2n = 78) and Brazilian Teal (2n = 80), whereas Coscoroba Swan, previously analyzed, exhibits a notably high diploid number (2n = 98). Despite sharing a similar macrochromosome morphology, the three showed differences in diploid numbers and microsatellite distribution. Extensive microsatellite accumulation was found in both autosomal and sex chromosomes (Z and W) of Brazilian Teal and Coscoroba Swan, while White-faced Whistling Duck displays minimal hybridization signals and an absence of microsatellites on the sex chromosomes. The accumulation of specific microsatellites, such as (CAC)₁₀ and (GAG)₁₀, in centromeric and pericentromeric regions suggests an association with transposable elements, potentially driving chromosomal evolution. Notably, the substantial accumulation of these sequences on the Z and W chromosomes of Brazilian Teal and Coscoroba Swan, but not White-faced Whistling Duck, supports the hypothesis that repetitive sequence expansion occurs in a species-specific manner, contributing to sex chromosome differentiation. These findings highlight microsatellite mapping as a valuable tool for understanding chromosomal evolution and genomic differentiation in Anseriformes. Full article

The DEAD-box RNA helicase family, acting as a critical regulator in RNA metabolism, plays a vital role in plant growth, development, and adaptation to various stresses. Although a number of DEAD proteins have been reported to participate in heat stress response in several species, the response of DEAD-box RNA helicases to heat stress has not been comprehensively analyzed in tomato. In this study, 42 SlDEAD genes were identified from the tomato genome. Evolutionary analysis of DEAD family genes across different plant species reveals that DEAD family genes can be segregated into five groups. A comprehensive analysis of their physicochemical properties, gene structure, chromosome location, and conserved motifs unveils diversity among the members of the SlDEAD family. An investigation into the subcellular localization of seven SlDEAD proteins indicates that SlDEAD7, SlDEAD14, and SlDEAD26 are located in the endoplasmic reticulum, and SlDEAD40 is located in the endoplasmic reticulum and nucleus, whereas SlDEAD17, SlDEAD25, and SlDEAD35 are located in the chloroplast. The expression of 37 out of 42 SlDEAD genes was responsive to heat stress induction. During the early stage of high-temperature treatment, they exhibited five distinct expression patterns. These findings contribute to a deeper comprehension of the evolution, expansion complexity, and function of SlDEAD genes and provide insights into the potential role of SlDEAD genes in tomato tolerance to heat stress. Full article