Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants

Li, Shu Fen; Su, Ting; Cheng, Guang Qian; Wang, Bing Xiao; Xu, Li; Deng, Chuan Liang; Gao, Wu‐Jun

doi:10.3390/genes8100290

Cited by 75 publications

(62 citation statements)

References 142 publications

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“…A vast majority of the genes in the A. setaceus genome were functionally annotated. Repetitive sequences, mainly consisting of TEs, constitute a major fraction of eukaryotic genomes and play vital roles in genome evolution 27,28 , chromosome rearrangement 29 , and gene regulation 30 . Repetitive sequences occupied 65.59% of the A. setaceus genome assembly; this percentage is very similar to that in the A. officinalis genome (69%).…”

Section: Discussionmentioning

confidence: 99%

Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus

Wang

Dong

et al. 2020

Hortic Res

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Asparagus setaceus is a popular ornamental plant cultivated in tropical and subtropical regions globally. Here, we constructed a chromosome-scale reference genome of A. setaceus to facilitate the investigation of its genome characteristics and evolution. Using a combination of Nanopore long reads, Illumina short reads, 10× Genomics linked reads, and Hi-C data, we generated a high-quality genome assembly of A. setaceus covering 710.15 Mb, accounting for 98.63% of the estimated genome size. A total of 96.85% of the sequences were anchored to ten superscaffolds corresponding to the ten chromosomes. The genome of A. setaceus was predicted to contain 28,410 genes, 25,649 (90.28%) of which were functionally annotated. A total of 65.59% of the genome was occupied by repetitive sequences, among which long terminal repeats were predominant (42.51% of the whole genome). Evolutionary analysis revealed an estimated divergence time of A. setaceus from its close relative A. officinalis of~9.66 million years ago, and A. setaceus underwent two rounds of whole-genome duplication. In addition, 762 specific gene families, 96 positively selected genes, and 76 resistance (R) genes were detected and functionally predicted in A. setaceus. These findings provide new knowledge about the characteristics and evolution of the A. setaceus genome, and will facilitate comparative genetic and genomic research on the genus Asparagus.

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Section: Discussionmentioning

confidence: 99%

Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus

Wang

Dong

et al. 2020

Hortic Res

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“…In C. nevadensis, the chromosomes were larger and with poorly defined morphology and heterochromatic bands, except for two CMA + blocks co-localized with 35S rDNA sites. Chromosome size variation among closely related species is commonly associated with genome size variation promoted by proliferation/elimination of repetitive sequences, mainly retroelements (Li et al 2017). The extra repetitive sequences may be more concentrated in the proximal region, as in C. nevadensis and other species (e.g., Gaeta et al 2010;Yuyama et al 2012).…”

Section: Discussionmentioning

confidence: 99%

Allopolyploid origin and genome differentiation of the parasitic speciesCuscuta veatchii(Convolvulaceae) revealed by genomic in situ hybridization

Ibiapino

García

Ferraz

et al. 2019

Genome

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Interspecific hybridization and genome duplication to form allopolyploids are major evolutionary events in angiosperms. In the parasitic genus Cuscuta (Convolvulaceae), molecular data suggested the existence of species of hybrid origin. One of them, C. veatchii, has been proposed as a hybrid between C. denticulata and C. nevadensis, both included in sect. Denticulatae. To test this hypothesis, a cytogenetic analysis was performed with CMA/DAPI staining and fluorescent in situ hybridization using 5S and 35S rDNA and genomic probes. Chromosomes of C. denticulata were small with a well-defined centromeric region, whereas C. nevadensis had larger, densely stained chromosomes, and less CMA+ heterochromatic bands. Cuscuta veatchii had 2n = 60 chromosomes, about 30 of them similar to those of C. denticulata and the remaining to C. nevadensis. GISH analysis confirmed the presence of both subgenomes in the allotetraploid C. veatchii. However, the number of rDNA sites and the haploid karyotype length in C. veatchii were not additive. The diploid parentals had already diverged in their chromosomes structure, whereas the reduction in the number of rDNA sites more probably occurred after hybridization. As phylogenetic data suggested a recent divergence of the progenitors, these species should have a high rate of karyotype evolution.

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“…Both mechanisms have been shown to occur in plants, especially in maize (Lister et al, 1993;Ziolkowski et al, 2003;Zhang and Peterson, 2004;Yu et al, 2011;Knoll et al, 2014). Epigenetic modification, given its role in transposable element de-activation and heterochromatin formation, may also play an important role in chromosome evolution in plants (Li et al, 2017). Given the high fraction of plant genomes occupied by transposable elements and other duplicated sequences, inversion mutation rates are likely to be high.…”

Section: Origin and Establishment Of Inversionsmentioning

confidence: 99%

Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants

2020

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Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of new genomic technologies has revealed that inversions are ubiquitous across much of the plant and animal kingdoms. Here we review the rapidly accumulating literature on inversions in the plant kingdom and discuss what we have learned about their establishment and likely evolutionary role. We show that inversions are prevalent across a wide range of plant groups. We find that inversions are often associated with locally favored traits, as well as with traits that contribute to assortative mating, suggesting that they may be key to adaptation and speciation in the face of gene flow. We also discuss the role of inversions in sex chromosome formation, and explore possible parallels with inversion establishment on autosomes. The identification of inversion origins, as well as the causal variants within them, will advance our understanding of chromosomal evolution in plants.

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Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants

Cited by 75 publications

References 142 publications

Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus

Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus

Allopolyploid origin and genome differentiation of the parasitic speciesCuscuta veatchii(Convolvulaceae) revealed by genomic in situ hybridization

Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants

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