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Peer-reviewedCC BY 4.0PLOS One

Comparative oligo-FISH validates genome assemblies and delivers a precise karyotype for Lens Mill. species

  • Alex Junior Aparecido Silvestrini1
  • Larissa Ramsay2
  • Eric Bishop von Wettberg
  • Kirstin E. Bett
  1. 1Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Canada
  2. 2Department of Agriculture and Life Sciences and Gund Institute for the Environment, University of Vermont, Burlington, United States of America
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Abstract

Chromosome structural rearrangements play a significant role in karyotype evolution and speciation. These rearrangements pose challenges for precise karyotyping and the assembly of a genus pan-genome for crops and their wild relatives. Lens culinaris, an important cool-season legume primarily grown in India and Canada, is a cultivated species with six wild relatives. All seven Lens species exhibit distinct chromosomal arrangements, which affect introgression and complicate the development of an accurate karyotype for the genus. Using gene synteny analysis between the cultivated Lens species and six wild relatives, we developed cross-species oligo-FISH (Fluorescent in situ hybridization) probes to in situ confirm genome assemblies and synteny. Chromosome spreads were used for oligo-FISH experiments, in which the DNA was denatured and a set of red and green oligo probes was hybridized to the metaphase chromosomes. The combination of both oligo sets/probes resulted in a distinct pattern for each Lens spp. chromosome, allowing the inference of a more robust karyotype for six Lens species. The karyotyping of Lens spp. confirmed the proper assignment of chromosomes in the genome assemblies and validated the rearrangements detected in the synteny analysis. The results attest to a higher sequence-level similarity among the closest related species despite the occurrence of several chromosomal structural changes among them. Oligo-FISH probes can be used in conjunction with plant genome assembly projects, supporting the delivery of a precise representation of the physical chromosomes of a species.

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Cite

BibTeXRIS
BibTeX
@article{silvestrini2026comparative,
  title = {{Comparative oligo-FISH validates genome assemblies and delivers a precise karyotype for Lens Mill. species}},
  author = {Alex Junior Aparecido Silvestrini and Larissa Ramsay and Eric Bishop von Wettberg and Kirstin E. Bett},
  journal = {PLOS One},
  year = {2026},
  month = sep,
  doi = {10.1371/journal.pone.0354141},
  url = {https://doi.org/10.1371/journal.pone.0354141},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Comparative oligo-FISH validates genome assemblies and delivers a precise karyotype for Lens Mill. species
AU  - Alex Junior Aparecido Silvestrini
AU  - Larissa Ramsay
AU  - Eric Bishop von Wettberg
AU  - Kirstin E. Bett
PY  - 2026
DA  - 2026/09/21
JO  - PLOS One
DO  - 10.1371/journal.pone.0354141
UR  - https://doi.org/10.1371/journal.pone.0354141
AB  - Chromosome structural rearrangements play a significant role in karyotype evolution and speciation. These rearrangements pose challenges for precise karyotyping and the assembly of a genus pan-genome for crops and their wild relatives. Lens culinaris, an important cool-season legume primarily grown in India and Canada, is a cultivated species with six wild relatives. All seven Lens species exhibit distinct chromosomal arrangements, which affect introgression and complicate the development of an accurate karyotype for the genus. Using gene synteny analysis between the cultivated Lens species and six wild relatives, we developed cross-species oligo-FISH (Fluorescent in situ hybridization) probes to in situ confirm genome assemblies and synteny. Chromosome spreads were used for oligo-FISH experiments, in which the DNA was denatured and a set of red and green oligo probes was hybridized to the metaphase chromosomes. The combination of both oligo sets/probes resulted in a distinct pattern for each Lens spp. chromosome, allowing the inference of a more robust karyotype for six Lens species. The karyotyping of Lens spp. confirmed the proper assignment of chromosomes in the genome assemblies and validated the rearrangements detected in the synteny analysis. The results attest to a higher sequence-level similarity among the closest related species despite the occurrence of several chromosomal structural changes among them. Oligo-FISH probes can be used in conjunction with plant genome assembly projects, supporting the delivery of a precise representation of the physical chromosomes of a species.
SN  - 1932-6203
ER  -