Extraordinarily conserved chromosomal synteny ofCitrusspecies revealed by chromosome‐specific painting

Abstract

Summary Reliable identification of individual chromosomes in eukaryotic species is the foundation for comparative chromosome synteny and evolutionary studies. Unfortunately, chromosome identification has been a major challenge for plants with small chromosomes, such as the Citrus species. We developed oligonucleotide‐based chromosome painting probes for all nine chromosomes in Citrus maxima (Pummelo). We were able to identify all C. maxima chromosomes in the same metaphase cells using multiple rounds of sequential fluorescence in situ hybridization with the painting probes. We conducted comparative chromosome painting analysis in six different Citrus and related species. We found that each painting probe hybridized to only a single chromosome in all other five species, suggesting that the six species have maintained a complete chromosomal synteny after more than 9 million years of divergence. No interchromosomal rearrangement was identified in any species. These results support the hypothesis that karyotypes of woody species are more stable than herbaceous plants because woody plants need a longer period to fix chromosome structural variants in natural populations.

Shaping the biology of citrus: I. Genomic determinants of evolution

“…citrus (He et al, 2020), and we followed a mapping approach as a proxy of orthology. DNA HiSeq Illumina reads from whole genome sequencing projects deposited on repositories (Supplemental Table S7) were filtered (Phred quality base >30, length 100 bp) and mapped on the clementine reference genome (v1.0, Phytozome) (Goodstein et al, 2012) with bwa-mem (v0.7.15-r1140) to generate Binary Alignment/Map (BAM) files, setting -r 1.2 option.…”

A genomic approach to the evolution, diversification and domestication of the genus Citrus

“…Synteny analyses based on these reference genomes highlighted a generally well-conserved genomic structure in citrus and their relatives, with a small number of inversions or translocations affecting large portions of the genome. Similar results were obtained recently by chromosome-specific FISH in six different Citrus species, suggesting that synteny in this genus is extremely conserved (He et al, 2020).…”

“…The phylogeny of this genus was clearly marked by the radiation event, but the genomic determinants driving their evolution have not been yet explored. Indeed, Citrus genomes display a well-conserved synteny (He et al, 2020), despite some specific gene families being expanded in the genome of some species of this genus (Gonzalez-Ibeas et al, 2021a,b, in press). However, other factors may have also played a role during the speciation and diversification of the Citrus species.…”

Chorus2: design of genome‐scale oligonucleotide‐based probes for fluorescence in situ hybridization

“…For many years the 5S and 45S ribosomal RNA genes have been the most commonly used FISH probes because the rDNA generate strong FISH signals and can be used universally in all plant species (Fukui et al., 1994 ; Jiang and Gill, 1994 ; Leitch and Heslop‐Harrison, 1992 ; Maluszynska and Heslop‐Harrison, 1991 ; Schmidt et al., 1994 ). However, the number of rDNA loci as well as their chromosomal locations often vary among closely related species in some plant lineages (Badaeva et al., 1996 ; Datson and Murray, 2006 ; Fukui et al., 1994 ; He et al., 2020 ; Schubert and Wobus, 1985 ). Thus, the rDNA probes are not reliable markers for chromosome identification or comparative cytogenetic studies.…”