Pre-labelled oligo probe-FISH karyotype analyses of four Araliaceae species using rDNA and telomeric repeat

Cytogenomic evaluation of regenerated Aralia elata using PLOP-FISH and flow cytometry

Aralia elata is closely related to Panax ginseng and contains high levels of saponins and other medicinal compounds. Successful A. elata micropropagation is commercially significant; however, the genomic stability of tissue culture-derived regenerants is unclear. In this study, callus-derived regenerated A. elata plants were obtained, and their cytogenomic constitutions were assessed. Using RepeatExplorer, pre-labeled oligonucleotide probes (PLOPs) were developed with newly mined tandem repeats from < 1× NGS whole-genome short reads, fluorescence in situ hybridization (FISH) was performed using six repeat probes, including three universal PLOPs, and genomic DNA content was estimated using flow cytometry. Regenerated A. elata plants (50) exhibited consistent ploidy, repeat distribution, and genome sizes compared with those exhibited by the mother plant. Six repeat probes were detected using FISH. Tandem repeat AeTR49 was identified as an excellent cytogenetic marker for homologous chromosomes, and AeTR161 and AeTR178 were localized in the centromeric and telomeric sections, respectively. Genomic DNA content (2C) was estimated at 2.46 ± 0.04 pg in the mother plant and 2.41 ± 0.05 pg in regenerated plants, with no significant variations in genome size or chromosome length. These results demonstrate that cytogenomics can be used to effectively evaluate chromosome-level genomic stability in regenerated A. elata plants.

Fluorescence in situ Hybridization Analysis of Oligonucleotide 5S Ribosomal DNA, 45S Ribosomal DNA, and (TTTAGGG)3 Locations in Gloriosa superba L

INTRODUCTION

Gloriosa superba L. is a horticulturally and medicinally important plant native to Africa. However, the few cytogenetic studies of the species are mainly focused on chromosome counting and chromosome morphology-based karyotyping. Fluorescence in situ hybridization (FISH) is a powerful tool for the detection of DNA repetitive elements in a specific region of a chromosome.

METHODS

Here, detailed karyotypes of G. superba were constructed by FISH using 5S and 45S rDNAs, and telomeric repeat (TTTAGGG)3 oligonucleotides.

RESULTS AND CONCLUSION

Twenty-two chromosomes were observed. Two 5S rDNA hybridization signals were detected in the proximal regions of the short arms of one pair of chromosomes, which were adjacent to the (TTTAGGG)3 terminal signals. Four 45S rDNA signals were detected near the centromere region of the short arm of the four chromosomes, but one of these was very weak and almost undetectable compared to the others. Telomeric repeat hybridization signals were distributed at the terminal region of each chromosome. The chromosomes displayed were intact, and the chromosome counts were accurate. Chromosome length ranged from 3.46 to 9.31 μm. These results will facilitate the cytogenetic mapping of other major repeats, thus contributing to an improved understanding of the G. superba genome structure and evolutionary history.

INTRODUCTION

Gloriosa superba L. is a horticulturally and medicinally important plant native to Africa. However, the few cytogenetic studies of the species are mainly focused on chromosome counting and chromosome morphology-based karyotyping. Fluorescence in situ hybridization (FISH) is a powerful tool for the detection of DNA repetitive elements in a specific region of a chromosome.

METHODS

Here, detailed karyotypes of G. superba were constructed by FISH using 5S and 45S rDNAs, and telomeric repeat (TTTAGGG)3 oligonucleotides.

RESULTS AND CONCLUSION

Twenty-two chromosomes were observed. Two 5S rDNA hybridization signals were detected in the proximal regions of the short arms of one pair of chromosomes, which were adjacent to the (TTTAGGG)3 terminal signals. Four 45S rDNA signals were detected near the centromere region of the short arm of the four chromosomes, but one of these was very weak and almost undetectable compared to the others. Telomeric repeat hybridization signals were distributed at the terminal region of each chromosome. The chromosomes displayed were intact, and the chromosome counts were accurate. Chromosome length ranged from 3.46 to 9.31 μm. These results will facilitate the cytogenetic mapping of other major repeats, thus contributing to an improved understanding of the G. superba genome structure and evolutionary history.

Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants

Fluorescence in situ hybridization (FISH) is an indispensable technique for studying chromosomes in plants. However, traditional FISH methods, such as BAC, rDNA, tandem repeats, and distributed repetitive sequence probe-based FISH, have certain limitations, including difficulties in probe synthesis, low sensitivity, cross-hybridization, and limited resolution. In contrast, oligo-based FISH represents a more efficient method for chromosomal studies in plants. Oligo probes are computationally designed and synthesized for any plant species with a sequenced genome and are suitable for single and repetitive DNA sequences, entire chromosomes, or chromosomal segments. Furthermore, oligo probes used in the FISH experiment provide high specificity, resolution, and multiplexing. Moreover, oligo probes made from one species are applicable for studying other genetically and taxonomically related species whose genome has not been sequenced yet, facilitating molecular cytogenetic studies of non-model plants. However, there are some limitations of oligo probes that should be considered, such as requiring prior knowledge of the probe design process and FISH signal issues with shorter probes of background noises during oligo-FISH experiments. This review comprehensively discusses de novo oligo probe synthesis with more focus on single-copy DNA sequences, preparation, improvement, and factors that affect oligo-FISH efficiency. Furthermore, this review highlights recent applications of oligo-FISH in a wide range of plant chromosomal studies.

Karyotype and Phylogenetic Relationship Analysis of Five Varieties and Cultivars of Zanthoxylum armatum Based on Oligo-FISH

Green prickly ash (Zanthoxylum armatum) has edible and medicinal value and is an economically significant plant in many countries. Z. armatum has many cultivars and varieties with similar phenotypes that are difficult to distinguish via traditional methods. In this study, we utilized oligo-FISH to distinguish five varieties and cultivars of Z. armatum on the basis of three oligonucleotide probes of 5S rDNA, (AG₃T₃)₃, and (GAA)₆. Karyotype analysis of the five varieties and cultivars of Z. armatum showed that the Z. armatum 'Tengjiao' karyotype formula was 2n = 2x = 98m with karyotype type 1C and an arm ratio of 4.3237, including two pairs of 5S rDNA signals and five pairs of (GAA)₆ signals. The karyotype formula of Z. armatum 'Youkangtengjiao' was 2n = 2x = 128m + 8sm with karyotype type 2B and an arm ratio of 3.5336, including three pairs of 5S rDNA signals and 17 pairs of (GAA)₆ signals. The karyotype formula of Z. armatum var. novemfolius was 2n = 2x = 134m + 2sm with karyotype type 1C and an arm ratio of 5.5224, including two pairs of 5S rDNA signals and eight pairs of (GAA)₆ signals. The karyotype formula of Z. armatum 'YT-03' was 2n = 2x = 2M + 128m + 4sm + 2st with karyotype type 2C and an arm ratio of 4.1829, including three pairs of 5S rDNA signals and nine pairs of (GAA)₆ signals. The karyotype formula of Z. armatum 'YT-06' was 2n = 2x = 126m + 10sm with cytotype 2B and an arm ratio of 3.3011, including three pairs of 5S rDNA signals and two pairs of (GAA)₆ signals. The five varieties and cultivars of Z. armatum had (AG₃T₃)₃ signals on all chromosomes. The chromosomal symmetry of Z. armatum 'Tengjiao' was high, whereas the chromosomal symmetry of Z. armatum 'YT-03' was low, with the karyotypes of the five materials showing a trend toward polyploid evolution. The phylogenetic relationship between Z. armatum 'Tengjiao' and Z. armatum var. novemfolius was the closest, while that between Z. armatum 'YT-03' and Z. armatum 'YT-06' was closer than with Z. armatum 'Youkangtengjiao' according to oligo-FISH. The results provided a karyotype profile and a physical map that contributes to the distinction of varieties and cultivars of Z. armatum and provides strategies for distinguishing other cultivated species.

FISH Mapping of Telomeric and Non-Telomeric (AG3T3)3 Reveal the Chromosome Numbers and Chromosome Rearrangements of 41 Woody Plants

Data for the chromosomal FISH mapping localization of (AG₃T₃)₃ are compiled for 37 species belonging 27 families; for 24 species and 14 families, this is the first such report. The chromosome number and length ranged from 14–136 and 0.56–14.48 μm, respectively. A total of 23 woody plants presented chromosome length less than 3 μm, thus belonging to the small chromosome group. Telomeric signals were observed at each chromosome terminus in 38 plants (90.5%) and were absent at several chromosome termini in only four woody plants (9.5%). Non-telomeric signals were observed in the chromosomes of 23 plants (54.8%); in particular, abundant non-telomeric (AG₃T₃)₃ was obviously observed in Chimonanthus campanulatus. Telomeric signals outside of the chromosome were observed in 11 woody plants (26.2%). Overall, ten (AG₃T₃)₃ signal pattern types were determined, indicating the complex genome architecture of the 37 considered species. The variation in signal pattern was likely due to chromosome deletion, duplication, inversion, and translocation. In addition, large primary constriction was observed in some species, probably due to or leading to chromosome breakage and the formation of new chromosomes. The presented results will guide further research focused on determining the chromosome number and disclosing chromosome rearrangements of woody plants.

Five Fabaceae Karyotype and Phylogenetic Relationship Analysis Based on Oligo-FISH for 5S rDNA and (AG3T3)3

Most Fabaceae have nitrogen fixation abilities and are valuable forage and medicinal resources. However, cytogenetic data of many Fabaceae species are unclear. Karyotypes reveal cytological characteristics and are crucial to understanding the organization and evolution of chromosomes in species. Oligo-FISH can reveal genetic composition and karyotype variation patterns with rapid and efficient results. Karyotype analysis of five Fabaceae species by oligonucleotide probes showed that: Robinia pseudoacacia, karyotype formula 2n = 2x = 20m + 2sm, cytotype 2B, arm ratio 3.4821, eight chromosomes distributed 5S rDNA signal. The karyotype formula of Robinia pseudoacacia ‘idaho’ was 2n = 2x = 20m + 2sm, cytotype 1A, arm ratio 1.8997, and 5S rDNA signal was distributed on six chromosomes. Karyotype of Robinia pseudoacacia f. decaisneana 2n = 2x = 20m + 2sm, cytotype 1B, arm ratio 2.0787, the distribution of eight chromosomes with 5S rDNA signal. Karyotype formula of Styphnolobium japonicum 2n = 2x = 14m + 12sm + 2st, cytotype 2B, arm ratio 2.6847, two chromosomes have 5S rDNA signal. Amorpha fruticose karyotype 2n = 2x = 38m + 2sm, cytotype 1B, arm ratio 3.2058, four chromosomes possessed 5S rDNA signal. Both ends of all species’ chromosomes have (AG₃T₃)₃ signals. The results of this study provide chromosome numbers and a physical map, contributing to the construction of the Oligo-FISH barcode and providing molecular cytogenetics data for Fabaceae.

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.

Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review

The discovery of telomeric repeats in interstitial regions of plant chromosomes (ITRs) through molecular cytogenetic techniques was achieved several decades ago. However, the information is scattered and has not been critically evaluated from an evolutionary perspective. Based on the analysis of currently available data, it is shown that ITRs are widespread in major evolutionary lineages sampled. However, their presence has been detected in only 45.6% of the analysed families, 26.7% of the sampled genera, and in 23.8% of the studied species. The number of ITR sites greatly varies among congeneric species and higher taxonomic units, and range from one to 72 signals. ITR signals mostly occurs as homozygous loci in most species, however, odd numbers of ITR sites reflecting a hemizygous state have been reported in both gymnosperm and angiosperm groups. Overall, the presence of ITRs appears to be poor predictors of phylogenetic and taxonomic relatedness at most hierarchical levels. The presence of ITRs and the number of sites are not significantly associated to the number of chromosomes. The longitudinal distribution of ITR sites along the chromosome arms indicates that more than half of the ITR presences are between proximal and terminal locations (49.5%), followed by proximal (29.0%) and centromeric (21.5%) arm regions. Intraspecific variation concerning ITR site number, chromosomal locations, and the differential presence on homologous chromosome pairs has been reported in unrelated groups, even at the population level. This hypervariability and dynamism may have likely been overlooked in many lineages due to the very low sample sizes often used in cytogenetic studies.

Chromosomal Characterization of Tripidium arundinaceum Revealed by Oligo-FISH

Sugarcane is of important economic value for producing sugar and bioethanol. Tripidium arundinaceum (old name: Erianthus arundinaceum) is an intergeneric wild species of sugarcane that has desirable resistance traits for improving sugarcane varieties. However, the scarcity of chromosome markers has hindered the cytogenetic study of T. arundinaceum. Here we applied maize chromosome painting probes (MCPs) to identify chromosomes in sorghum and T. arundinaceum using a repeated fluorescence in situ hybridization (FISH) system. Sequential FISH revealed that these MCPs can be used as reliable chromosome markers for T. arundinaceum, even though T. arundinaceum has diverged from maize over 18 MYs (million years). Using these MCPs, we identified T. arundinaceum chromosomes based on their sequence similarity compared to sorghum and labeled them 1 through 10. Then, the karyotype of T. arundinaceum was established by multiple oligo-FISH. Furthermore, FISH results revealed that 5S rDNA and 35S rDNA are localized on chromosomes 5 and 6, respectively, in T. arundinaceum. Altogether, these results represent an essential step for further cytogenetic research of T. arundinaceum in sugarcane breeding.

Cytogenetic analysis of Bienertia sinuspersici Akhani as the first step in genome sequencing

BACKGROUND

C₄ plants are efficient in suppressing photorespiration and enhancing carbon gain as compared to C₃ plants. Bienertia sinuspersici Akhani is one of the few species in the family Amaranthaceae that can perform C₄ photosynthesis within individual chlorenchyma cells, without the conventional Kranz anatomy in its leaf. This plant is salt-tolerant and is well-adapted to thrive in hot and humid climates. To date, there have been no reported cytogenetic analyses yet on this species.

OBJECTIVE

This study aims to provide a cytogenetic analysis of B. sinuspersici as the first step in genome sequencing.

METHODS

Fluorescence in situ hybridization (FISH) karyotype analysis was conducted using the metaphase chromosomes of B. sinuspersici probed with 5S and 45S rDNA and Arabidopsis-type telomeric repeats.

RESULTS

Results of the cytogenetic analysis confirmed that B. sinuspersici has 2n = 2x = 18 consisting of nine pairs of metacentric chromosomes. Two loci of 45S rDNA were found on the distal regions of the short arm of chromosome 7. Nine loci of 5S rDNA were found in the pericentromeric regions of chromosomes 1, 3, 4, 6, and 8, which also colocalized with Arabidopsis-type telomeric repeats; while four loci in the interstitial regions of chromosome 5 and 8 can be observed. The single locus of 5S rDNA that was found in chromosome 8 appears to be hemizygous.

CONCLUSION

The FISH karyotype analysis, based on the combination of rDNAs, telomeric tandem repeat markers and C₀t DNA chromosome landmarks, allowed efficient chromosome identification and provided useful information in characterizing the genome of B. sinuspersici.