Chromosome painting in meiosis reveals pairing of specific chromosomes in polyploid Solanum species

He, Li; Braz, Guilherme Tomaz; Torres, Giovana Augusta; Jiang, Jiming

doi:10.1007/s00412-018-0682-9

Cited by 51 publications

(38 citation statements)

References 52 publications

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“…Thus, for allotetraploids we would expect a high proportion of aabb and a low proportion of aaab since preferential pairing would ensure that two homologues from the first subgenome and two homologues from the second subgenome are present after recombination. Conversely, it is known in potato that during meiosis the majority of cells contain quadrivalents (He et al 2018). In this case, after recombination an individual might have 0, 1, 2 or 3 homologues from a given subgenome.…”

Section: Allotetraploid Vs Autotetraploidmentioning

confidence: 99%

GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes

Ranallo-Benavidez

Jaroň

Schatz

2019

Preprint

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An important assessment prior to genome assembly and related analyses is genome profiling, where the k-mer frequencies within raw sequencing reads are analyzed to estimate major genome characteristics such as genome size, heterozygosity, and repetitiveness. Here we introduce GenomeScope 2.0 (https://github.com/tbenavi1/genomescope2.0), which applies combinatorial theory to establish a detailed mathematical model of how k-mer frequencies are distributed in heterozygous and polyploid genomes. We describe and evaluate a practical implementation of the polyploid-aware mixture model that, within seconds, accurately infers genome properties across thousands of simulated and eleven real datasets spanning a broad range of complexity. We also present a new method called Smudgeplots (https://github.com/KamilSJaron/smudgeplot) to visualize and infer the ploidy and genome structure of a genome by analyzing heterozygous k-mer pairs. We successfully apply the approach to systems of known variable ploidy levels in the Meloidogyne genus and also the extreme case of octoploid Fragaria x ananassa.

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Section: Allotetraploid Vs Autotetraploidmentioning

confidence: 99%

GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes

Ranallo-Benavidez

Jaroň

Schatz

2019

Preprint

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“…A modified pattern would indicate a potential chromosomal rearrangement associated with a cultivar. In addition, barcode probes can also be used for chromosome identification in genetically related species (Braz et al 2018;Liu et al 2020) (Figure 2). Most importantly, barcode FISH probes can be developed readily in any plant species with a sequenced genome.…”

Section: Discussionmentioning

confidence: 99%

“…Such oligo-FISH probes generate specific hybridization patterns on individual chromosomes, which resemble distinct barcodes on different chromosomes. This chromosome identification strategy has been successfully demonstrated in potato (Braz et al 2018), rice (Liu et al 2020) and sugarcane (Meng et al 2020). Here, we report the development of similar barcode FISH probe in maize.…”

Section: Introductionmentioning

confidence: 96%

“…If the genomic sequence is available from a target species, oligos, typically 40-50 bp long, specific to a chromosomal region or to an entire chromosome can be synthesized in parallel and labeled as a FISH probe (Han et al 2015). Oligo-FISH probes have been successfully developed in several plant species for various types of cytogenetic studies (Albert et al 2019;Bi et al 2020;He et al 2018;Hou et al 2018;Martins et al 2019;Meng et al 2018;Qu et al 2017;Simonikova et al 2019;Song et al 2020;Xin et al 2018;Xin et al 2020).…”

Section: Introductionmentioning

confidence: 99%

“…A FISH probe can include oligos derived from multiple regions from multiple chromosomes (Braz et al 2018). Such oligo-FISH probes generate specific hybridization patterns on individual chromosomes, which resemble distinct barcodes on different chromosomes.…”

Section: Introductionmentioning

confidence: 99%

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A universal chromosome identification system for maize and wildZeaspecies

Braz

Martins

Zhang

et al. 2020

Preprint

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Maize was one of the first eukaryotic species in which individual chromosomes can be identified cytologically, which made maize one of the oldest models for genetics and cytogenetics research. Nevertheless, consistent identification of all 10 chromosomes from different maize lines as well as from wild Zea species remains a challenge. We developed a new technique for maize chromosome identification based on fluorescence in situ hybridization (FISH). We developed two oligonucleotide-based probes that hybridize to 24 chromosomal regions. Individual maize chromosomes show distinct FISH signal patterns, which allow universal identification of all chromosomes from different Zea species. We developed karyotypes from three Zea mays subspecies and two additional wild Zea species based on individually identified chromosomes. A paracentric inversion was discovered on the long arm of chromosome 4 in Z. nicaraguensis and Z. luxurians based on modifications of the FISH signal patterns. Chromosomes from these two species also showed distinct distribution patterns of terminal knobs compared to other Zea species. These results support that Z. nicaraguensis and Z. luxurians are closely related species. ReferencesAdawy SSM, Stupar RM, Jiang J (2004) Fluorescence in situ hybridization of knob-associated DNA elements analysis reveals multiple loci in one-knob and knobless maize lines. J (2019) Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships. P Natl Acad Sci USA 116:1679-1685 Amarillo FIE, Bass HW (2007) A transgenomic cytogenetic sorghum (Sorghum propinquum) bacterial artificial chromosome fluorescence in situ hybridization map of maize (Zea mays L.) pachytene chromosome 9, evidence for regions of genome hyperexpansion.

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