Heterochromatin evolution in Arachis investigated through genome-wide analysis of repetitive DNA

Samoluk, Sergio Sebastián; Chalup, Laura; Chavarro, Carolina; Robledo, Germán; Bertioli, David J.; Jackson, Scott A.; Seijo, Guillermo

doi:10.1007/s00425-019-03096-4

Cited by 15 publications

(6 citation statements)

References 76 publications

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“…Repetitive sequences, mainly consisting of TEs, are important drivers of genome evolution, chromosome rearrangement and gene regulation (Bennetzen & Wang, 2014; Li et al., 2017; Samoluk et al., 2019; Uzunović et al., 2019). In the C .…”

Section: Discussionmentioning

confidence: 99%

“…Repetitive sequences, mainly consisting of TEs, are important drivers of genome evolution, chromosome rearrangement and gene regulation (Bennetzen & Wang, 2014;Li et al, 2017;Samoluk et al, 2019;Uzunovi c et al, 2019). In the C. lanceoleosa genome, repetitive sequences occupied 80.63%, with high similarity to the genome of the 'Longjing 43' cultivar (80.06%) (Wang et al, 2020) but less than that of the genome of the 'Shuchazao' cultivar (86.87%) with chromosome-level genome assembly (CSS) (Xia et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

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Chromosome‐level genome of Camellia lanceoleosa provides a valuable resource for understanding genome evolution and self‐incompatibility

et al. 2022

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The section Oleifera (Theaceae) has attracted attention for the high levels of unsaturated fatty acids found in its seeds. Here, we report the chromosome-scale genome of the sect. Oleifera using diploid wild Camellia lanceoleosa with a final size of 3.00 Gb and an N50 scaffold size of 186.43 Mb. Repetitive sequences accounted for 80.63% and were distributed unevenly across the genome. Camellia lanceoleosa underwent a whole-genome duplication event approximately 65 million years ago (65 Mya), prior to the divergence of C. lanceoleosa and Camellia sinensis (approx. 6-7 Mya). Syntenic comparisons of these two species elucidated the genomic rearrangement, appearing to be driven in part by the activity of transposable elements. The expanded and positively selected genes in C. lanceoleosa were significantly enriched in oil biosynthesis, and the expansion of homomeric acetyl-coenzyme A carboxylase (ACCase) genes and the seed-biased expression of genes encoding heteromeric ACCase, diacylglycerol acyltransferase, glyceraldehyde-3phosphate dehydrogenase and stearoyl-ACP desaturase could be of primary importance for the high oil and oleic acid content found in C. lanceoleosa. Theanine and catechins were present in the leaves of C. lanceoleosa. However, caffeine can not be dectected in the leaves but was abundant in the seeds and roots. The functional and transcriptional divergence of genes encoding SAM-dependent N-methyltransferases may be associated with caffeine accumulation and distribution. Gene expression profiles, structural composition and chromosomal location suggest that the late-acting self-incompatibility of C. lanceoleosa is likely to have favoured a novel mechanism co-occurring with gametophytic self-incompatibility. This study provides valuable resources for quantitative and qualitative improvements and genome assembly of polyploid plants in sect. Oleifera.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Chromosome‐level genome of Camellia lanceoleosa provides a valuable resource for understanding genome evolution and self‐incompatibility

et al. 2022

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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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“…It is because of examples like these that proximal regions are considered hotspots of repetitive DNA families, although pericentromere residing sequences have diverged considerably in different plant clades [9]. In other plant groups, like Medicago [10] and Arachis [11], satellite repeats may also occur in interstitial and terminal regions.…”

Section: Introductionmentioning

confidence: 99%

Diversity of satDNA fraction in Cestrum, the Genus with the Largest Genomes within Solanaceae

Souza

Parteka

Assis

et al. 2021

Preprint

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Cestrum species present large genomes (~24 pg), a high occurrence of B chromosomes, and great diversity in heterochromatin bands. Despite this, there is maintenance of chromosome shape and karyotype symmetry. To deepen our knowledge on Cestrum genome composition, low coverage sequencing data of C. strigilatum and C. elegans were compared. Bioinformatics analyses showed retrotransposons comprising more than 70% of the repetitive fraction, followed by transposons (~18%). The four satDNA families that accumulated the most in the datasets were used as probes in FISH assays, and showed different distribution profiles along chromosomes. Most hybridization signals were located in the C-CMA/DAPI banding sites, including those related to AT-rich Cold-Sensitive Regions (CSRs) and heterochromatin. Although satellite probes hybridized in all tested species, a satDNA family named CsSat49 was highlighted as it predominates in centromeric regions. Data suggest that the satDNA fraction is still conserved in the genus, although there is variation in the number of FISH signals between karyotypes, as well as in the B chromosomes. This study brings an important advance in the knowledge on genome organization and heterochromatin composition in Cestrum, especially on the distribution and differentiation mechanisms of satellite fraction between species of a genus of Solanaceae with large genomes.

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Heterochromatin evolution in Arachis investigated through genome-wide analysis of repetitive DNA

Cited by 15 publications

References 76 publications

Chromosome‐level genome of Camellia lanceoleosa provides a valuable resource for understanding genome evolution and self‐incompatibility

Chromosome‐level genome of Camellia lanceoleosa provides a valuable resource for understanding genome evolution and self‐incompatibility

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

Diversity of satDNA fraction in Cestrum, the Genus with the Largest Genomes within Solanaceae

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