Development of a set of chromosome-specific oligonucleotide markers and karyotype analysis in the Japanese morning glory Ipomoea nil

Feng

et al. 2022

IJMS

A precise, rapid and straightforward approach to chromosome identification is fundamental for cytogenetics studies. However, the identification of individual chromosomes was not previously possible for Chinese cherry or other Prunus species due to the small size and similar morphology of their chromosomes. To address this issue, we designed a pool of oligonucleotides distributed across specific pseudochromosome regions of Chinese cherry. This oligonucleotide pool was amplified through multiplex PCR with specific internal primers to produce probes that could recognize specific chromosomes. External primers modified with red and green fluorescence tags could produce unique signal barcoding patterns to identify each chromosome concomitantly. The same oligonucleotide pool could also discriminate all chromosomes in other Prunus species. Additionally, the 5S/45S rDNA probes and the oligo pool were applied in two sequential rounds of fluorescence in situ hybridization (FISH) localized to chromosomes and showed different distribution patterns among Prunus species. At the same time, comparative karyotype analysis revealed high conservation among P. pseudocerasus, P. avium, and P. persica. Together, these findings establish this oligonucleotide pool as the most effective tool for chromosome identification and the analysis of genome organization and evolution in the genus Prunus.

Section: Discussionmentioning

confidence: 57%

Section: Introductionmentioning

confidence: 99%

Accurate Chromosome Identification in the Prunus Subgenus Cerasus (Prunus pseudocerasus) and its Relatives by Oligo-FISH

Feng

et al. 2022

IJMS

“…The recent development of oligopainting FISH provided an opportunity to establish cytogenetic barcoding systems for rapid characterization of plant karyotypes ( Braz et al, 2018 , 2020 ; Chen et al, 2020 ; Liu et al, 2020 ). In this study, we developed an oligo-FISH barcode system for kabuli-type chickpea, CDC Frontier ( Varshney et al, 2013 ).…”

Section: Discussionmentioning

confidence: 99%

“…The oligopainting probes can be designed to cover entire chromosomes or only chromosome arms to label multiple regions of multiple chromosomes and obtain a chromosome-specific FISH pattern. The latter approach was termed the oligo-FISH barcode system ( Braz et al, 2018 ) and is based on the production of two different oligomer libraries, which facilitate unambiguous identification of all chromosomes of a species (e.g., Braz et al, 2020 ; Chen et al, 2020 ; Liu et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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

“…In the bird family Rhynchocyclidae, chromosome mapping using BACs across different genera has helped clarify phylogenetic incongruences(Kretschmer et al 2021). In plants, comparative cytogenomics in Ipomoea L., based on oligo-and rDNA-FISH results, suggested a different topology(Chen et al 2020). Similarly, the discovery of a chromosomal fusion responsible for a change in the basic chromosome number in distinct allopolyploids helped elucidating the Saccharum complex (Yu et al 2022).Macroptilium followed the general Phaseoleae trend of karyotype evolution, characterized by limited genome reshu ing with the maintenance of chromosome number, as evidenced in most Phaseolus(Schmutz et al.…”

mentioning

confidence: 99%

Cytogenomic and phylogenomic evidence for new infrageneric relationships in Macroptilium (Benth.) beans

Montenegro,

Ibiapino,

Nascimento

et al. 2024

Preprint

Macroptilium (Benth.) Urb. is a forage genus native to regions from North to South America. Phylogenetic analyses place it close to Phaseolus L., but its infrageneric division into two sections is not well supported. Despite its chromosomal number stability (2n = 22), interspecific rDNA loci variation enabled species differentiation, suggesting that a cytogenomic approach might be valuable for inferring species relationships and genome evolution. Here, we (1) characterized nine Macroptilium species through oligonucleotide-based chromosome painting and barcoding (Oligo-FISH); (2) generated genome skimming data for six species and used it to investigate their repeatome dynamics, and (3) performed phylogenomic reconstruction using complete plastomes. Oligo-FISH data unveiled de novotranslocations between chromosomes 2 and 6, and 3 and 11 in species from proposed groups II and III, respectively, in disagreement with the currently proposed phylogenetic hypothesis. Our phylogenomic (plastid) and repeatome (nuclear) analyses supported groups II and III as clades, with shared satDNA families. Group I was paraphyletic and resembled the Ancestral Phaseolinae Karyotype. We demonstrated the efficiency of different cytogenomic approaches to characterize Macroptilium species, providing insights into its genomic evolution and indicating the need for a systematic re-evaluation of the genus. These findings also support the power of these approaches to solve phylogenetic relationships even in groups with chromosome number stability and recent diversification.