Chromosome‐specific painting unveils chromosomal fusions and distinct allopolyploid species in the Saccharum complex

Abstract

Karyotypes provide key cytogenetic information on the phylogenetic relationships and evolutionary origins in related eukaryotic species. Despite our knowledge of the chromosome numbers of sugarcane and its wild relatives, the chromosome composition and evolution among the species in the Saccharum complex have been elusive owing to the complex polyploidy and the large numbers of chromosomes of these species.Oligonucleotide-based chromosome painting has become a powerful tool of cytogenetic studies especially for plant species with large numbers of chromosomes. We developed oligobased chromosome painting probes for all 10 chromosomes in Saccharum officinarum (2n = 8x = 80). The 10 painting probes generated robust fluorescence in situ hybridization signals in all plant species within the Saccharum complex, including species in the genera Saccharum, Miscanthus, Narenga and Erianthus.We conducted comparative chromosome analysis using the same set of probes among species from four different genera within the Saccharum complex. Excitingly, we discovered several novel cytotypes and chromosome rearrangements in these species.We discovered that fusion from two different chromosomes is a common type of chromosome rearrangement associated with the species in the Saccharum complex. Such fusion events changed the basic chromosome number and resulted in distinct allopolyploids in the Saccharum complex.

Chromosome-scale genome assembly of the diploid oat Avena longiglumis reveals the landscape of repetitive sequences, genes and chromosome evolution in grasses

“…Poales grasses [86], and to use as baits (cf. https://treeoflife.kew.org/methods and Johnson et al [87]) to identify the variation of all AGK01 genes across the group.…”

“…Most notably, the conservation of large syntenic blocks and the orthologous relationships of the seven extant ALO chromosomes to the 12 chromosomes of OSA and AGK was evident, with defined fusion and translocation events but limited major duplications or deletions. Apart from the long-term evolutionary conservation, such regions harbour conserved sequence regions that might be synthesized as oligonucleotides for in situ hybridization to label linkage group 1 across all Poales grasses [86], and to use as baits (cf. https://treeoflife.kew.org/methods and Johnson et al [87]) to identify the variation of all AGK01 genes across the group.…”

Chromosome painting reveals inter‐chromosomal rearrangements and evolution of subgenome D of wheat

“…umbellulata, respectively (Parisod & Badaeva, 2020). Oligo-based FISH probes have recently been reported in plant species with large and complex genomes, including sugarcane (Yu et al, 2022) and wheat (Song et al, 2020a). Li et al (2021) applied FISH with oligo-based probes to study representative Aegilops species with the N, U, and C genomes and reported rearrangements involved in Aegilops chromosomes 2, 4, 6, and 7.…”

“…umbellulata , respectively (Parisod & Badaeva, 2020). Oligo‐based FISH probes have recently been reported in plant species with large and complex genomes, including sugarcane (Yu et al., 2022) and wheat (Song et al., 2020a). Li et al.…”

“…(Šimoníková et al., 2019), strawberry ( Fragaria vesca ) (Qu et al., 2017), potato ( Solanum tuberosum ) (Braz et al., 2018), poplar ( Populus spp.) (Xin et al., 2020), sugarcane ( Saccharum officinarum ) (Meng et al., 2018; Yu et al., 2022), maize ( Zea mays ) (Albert et al., 2019; do Vale Martins et al., 2019; Braz et al., 2021), and citrus ( Citrus spp.) (He et al., 2020), as well as wheat and related wild species (Li et al., 2021; Song et al., 2020a).…”