Species-specific abundant retrotransposons elucidate the genomic composition of modern sugarcane cultivars

Huang, Yongji; Chen, Hong; Han, Jinlei; Zhang, Ya; Ma, Shulin; Yu, Guangrun; Wang, Zonghua; Wang, Kai

doi:10.1007/s00412-019-00729-1

Cited by 14 publications

(13 citation statements)

References 33 publications

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“…However, the low genome assembly coverage (382 Mb of ∼10 Gb; ∼3.8%) demonstrated the difficulty of dissecting the genome composition of sugarcane cultivars. Combined with the S. spontaneum-specific painting probe (Huang et al, 2020), we showed the possibility of uncovering the chromosomal composition in sugarcane cultivars. Here, chromosome 2 can be identified individually by the CP2 probe, and then S. spontaneum-derived chromosome 2 or fragments can be distinguished.…”

Section: Discussionmentioning

confidence: 98%

“…In sugarcane modern cultivars, recombination between S. spontaneum and S. officinarum frequently occurs, leading up to ∼40% of the chromosomes to be derived from interspecific recombinations (Huang et al, 2020). Determining how parental chromosome pairing and recombination produce such descent cultivars remains a fundamental and appealing pursuit for both crop breeders and researchers.…”

Section: Discussionmentioning

confidence: 99%

“…The purpose of this study was to identify the origin of each chromosome in sugarcane modern cultivars, which derived from interspecific hybridization of S. officinarum and S. spontaneum. To this end, we examined a dual-probe FISH strategy in which the chromosome 2 painting probe and a recently developed S. spontaneum-specific painting (SsP) probe (Huang et al, 2020) were applied to dissect the individual chromosome and its species origin. The SsP probe will generate chromosome painting signals in all chromosomes in S. spontaneum but not in S. officinarum.…”

Section: Tracing the S Spontaneum Chromosome 2-or Chromosome 2-derived Fragments In Modern Sugarcane Cultivarsmentioning

confidence: 99%

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

et al. 2021

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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.

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Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

Section: Tracing the S Spontaneum Chromosome 2-or Chromosome 2-derived Fragments In Modern Sugarcane Cultivarsmentioning

confidence: 99%

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

et al. 2021

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“…Retrotransposons, as mobile genetic elements, have attracted considerable attention. These elements can move, and occasionally spread, within the host genome through the reverse transcription of an RNA intermediate [14][15][16]. In many cases, genome-sized polymorphisms might re ect the activity of retrotransposons, particularly the copy number differences among long terminal repeat (LTR) retrotransposons, which can achieve exceptionally high copy numbers and often occupy over 50% of the nuclear DNA content, although these elements are typically transcriptionally silent [17].…”

Section: Introductionmentioning

confidence: 99%

An eruption of LTR retrotransposons in the autopolyploid genomes of Chrysanthemum nankingense (Asteraceae)

Wang¹,

He²,

Yu³

et al. 2021

Preprint

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Background Whole genome duplication, associated with the induction of widespread genetic changes, has played an important role in the evolution of many plant taxa. The majority of extant angiosperm species have undergone at least one polyploidization event, forming either an auto- or allopolyploid organism. Compared with allopolyploidization, however, few studies have examined autopolyploidization, and almost no studies have focused on the response of genetic changes to autopolyploidy. Results In the present study, newly synthesized C. nankingense autotetraploids (Asteraceae) were employed to characterize the genome shock following autopolyploidization. Available evidence suggested that the genetic changes primarily involved the loss of old fragments and the gain of novel fragments, and some novel sequences were potential long terminal repeat (LTR) retrotransposons. As Ty1-copia and Ty3-gypsy elements represent the two main superfamilies of LTR retrotransposons, the dynamics of Ty1-copia and Ty3-gypsy were evaluated using RT-PCR, transcriptome sequencing and LTR retrotransposon-based molecular marker techniques. These results suggest that autopolyploidization might also be accompanied by perturbations of LTR retrotransposons, and the emergence retrotransposon insertions might show more rapid homologue divergence, resulting in diploid-like behaviour, potentially accelerating the evolutionary process among progenies. Conclusions Our results strongly suggest a need to expand current evolutionary framework to encompass a genetic dimension when seeking to understand genomic shock following autopolyploidization in Asteraceae.

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“…However, identifying genetically mapped BACs with complete genome coverage is a challenge in most species; repetitive DNA sequences in the target DNA and BAC probes can cause non-specific hybridization. Development of repeat-free probes has proved difficult in some species (Bertioli et al, 2013), although in some cases repetitive DNA, particularly derived from repetitive DNA, may be valuable to identify different genomes in hybrids (Santos et al, 2015;Huang et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Identification of Chromosomes and Chromosome Rearrangements in Crop Brassicas and Raphanus sativus: A Cytogenetic Toolkit Using Synthesized Massive Oligonucleotide Libraries

et al. 2020

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Crop brassicas include three diploid [Brassica rapa (AA; 2n = 2x = 16), B. nigra (BB; 2n = 2x = 18), and B. oleracea (CC; 2n = 2x = 20)] and three derived allotetraploid species. It is difficult to distinguish Brassica chromosomes as they are small and morphologically similar. We aimed to develop a genome-sequence based cytogenetic toolkit for reproducible identification of Brassica chromosomes and their structural variations. A bioinformatic pipeline was used to extract repeat-free sequences from the whole genome assembly of B. rapa. Identified sequences were subsequently used to develop four c. 47-mer oligonucleotide libraries comprising 27,100, 11,084, 9,291, and 16,312 oligonucleotides. We selected these oligonucleotides after removing repeats from 18 identified sites (500–1,000 kb) with 1,997–5,420 oligonucleotides localized at each site in B. rapa. For one set of probes, a new method for amplification or immortalization of the library is described. oligonucleotide probes produced specific and reproducible in situ hybridization patterns for all chromosomes belonging to A, B, C, and R (Raphanus sativus) genomes. The probes were able to identify structural changes between the genomes, including translocations, fusions, and deletions. Furthermore, the probes were able to identify a structural translocation between a pak choi and turnip cultivar of B. rapa. Overall, the comparative chromosomal mapping helps understand the role of chromosome structural changes during genome evolution and speciation in the family Brassicaceae. The probes can also be used to identify chromosomes in aneuploids such as addition lines used for gene mapping, and to track transfer of chromosomes in hybridization and breeding programs.

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Species-specific abundant retrotransposons elucidate the genomic composition of modern sugarcane cultivars

Cited by 14 publications

References 33 publications

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

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

An eruption of LTR retrotransposons in the autopolyploid genomes of Chrysanthemum nankingense (Asteraceae)

Identification of Chromosomes and Chromosome Rearrangements in Crop Brassicas and Raphanus sativus: A Cytogenetic Toolkit Using Synthesized Massive Oligonucleotide Libraries

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