Chromosome Painting Provides Insights Into the Genome Structure and Evolution of Sugarcane

Abstract

The genus Saccharum is composed of species with high polyploidy and highly varied chromosome numbers, laying a challenge for uncovering its genomic structure and evolution. We developed a chromosome 2 painting (CP2) probe by designing oligonucleotides covering chromosome 2 of Saccharum spontaneum (2n = 8x = 64). Fluorescence in situ hybridization (FISH) using this CP2 probe revealed six types of ploidies from twenty S. spontaneum clones, including 6x, 8x, 10x, 11x, 12x, and 13x clones. The finding of S. spontaneum clones with uneven of ploid suggested that certain S. spontaneum clones come from hybridization. It renews our knowledge that S. spontaneum is derived from autopolyploidization. Combined with a S. spontaneum-specific probe, chromosome 2-derived chromosome or fragments from either S. spontaneum or Saccharum officinarum can be identified in sugarcane modern cultivars. We revealed unexpected high level of interspecific recombination from introgressive S. spontaneum chromosomes (>50.0%) in cultivars ROC22 and ZZ1, indicating frequent chromosome exchange in cultivars. Intriguingly, we observed interspecific recombination recurring among either homoeologous or non-homoeologous chromosomes in sugarcane cultivars. These results demonstrated that chromosome painting FISH is a powerful tool in the genome dissection of sugarcane and provide new insights into the genome structure and evolution of the complex genus Saccharum.

Characterization of Repetitive DNA in Saccharum officinarum and Saccharum spontaneum by Genome Sequencing and Cytological Assays

“…The obtained results lead to a hypothesized that this was an assembly error in the current genome assembly. To confirm this hypothesis, we conducted dual-probe FISH using the chromosome 7-specific probe Ss7 ( Meng et al, 2021 ) and the Se1C692 probe. FISH results showed clear monospot signals from the centromeres of all eight chr7 homologous chromosomes ( Supplementary Figure 3 ), indicating that the Se1C692 copies were concentrated in a region.…”

“…Saccharum spontaneum shows the highest level of genetic diversity in the Saccharum genus ( Panje and Babu, 1960 ; Irvine, 1999 ; Mary et al, 2006 ) with ploidies from 6x to 13x ( Meng et al, 2021 ). In order to study how centromeric repeats evolved along with genomic ploidy change in S. spontaneum .…”

“…We revealed highly similar compositions of TEs ( Figure 1 ) in the two polyploids S. spontaneum and S. officinarum. Recent studies based on cytological and genomic comparisons revealed that S. spontaneum and S. officinarum have a close genetic relationship and may have diverged less than one million years ago ( D’Hont, 2005 ; Zhang et al, 2019 ; Meng et al, 2021 ). Therefore, there are two possibilities to explain the high similarity of TE compositions in the two species: TEs in both genomes may have remained steady or TES may have evolved under a relatively similar dynamic after divergence from their common ancestor.…”

Plant Cytogenetics in the Micronuclei Investigation—The Past, Current Status, and Perspectives

“…The most advanced FISH-based approach in plants is chromosome painting (CP), which permits the selective visualization of entire chromosomes or their specific segments during mitosis as well the interphase [49][50][51][52][53][54]. The wide use of this technique for humans and mammals to determine the involvement of specific chromosomes in the formation of micronuclei showed that they preferentially comprise particular chromosomes that are related to the chromatin organization [55].…”

Remnant of Unrelated Amniote Sex Chromosomal Linkage Sharing on the Same Chromosome in House Gecko Lizards, Providing a Better Understanding of the Ancestral Super-Sex Chromosome

“…Nevertheless, technical issues still exist and contigs cannot be assembled across centromeres or large heterochromatic blocks [ 8 , 9 , 10 ]. The fluorescence in situ hybridization (FISH) technique should therefore be applied to build a physical chromosome map in several map-poor species before starting the genome project, in order to investigate biological evolutionary constraints in genome structure [ 11 , 12 , 13 ]. It is also necessary to integrate technologies for whole-sequence data with molecular cytogenetics in so-called ‘chromosomics’ [ 14 ].…”