Nature, Journal Year: 2024, Volume and Issue: unknown
Published: May 31, 2024
Language: Английский
The Plant Genome, Journal Year: 2025, Volume and Issue: 18(1)
Published: Jan. 9, 2025
Abstract Repetitive DNA contributes significantly to plant genome size, adaptation, and evolution. However, little is understood about the transcription of repeats. This addressed here in green foxtail millet ( Setaria viridis ). First, we used RepeatExplorer2 calculate proportion (GP) all repeat types compared GP long terminal (LTR) retroelements against annotated complete incomplete LTR (Ty1/copia Ty3/gypsy) identified by DANTE a whole assembly. We show that DANTE‐identified can comprise ∼0.75% inflorescence poly‐A transcriptome ∼0.24% stem ribo‐depleted transcriptome. In RNA libraries from tissue, both transposons were highly abundant, where they may be taking advantage reduced epigenetic silencing germ line amplify. Typically, there was higher representation than RepeatExplorer2‐identified retroelements, potentially reflecting elements have insufficient genomic copy numbers detected RepeatExplorer2. contrast, for tissues, reverse observed, with retroelements. For repeats, most Ty1/copia Ty3/gypsy families positively correlated their transcript proportion. addition, guanine‐ cytosine‐rich repeats high sequence similarity also abundant transcriptome, these likely represent young are capable amplification due ability evade silencing.
Language: Английский
Citations
0
PROTOPLASMA, Journal Year: 2025, Volume and Issue: unknown
Published: Jan. 30, 2025
Language: Английский
Citations
0
Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 15 - 30
Published: Jan. 1, 2025
Language: Английский
Citations
0
Lecture notes in computer science, Journal Year: 2025, Volume and Issue: unknown, P. 180 - 195
Published: Jan. 1, 2025
Language: Английский
Citations
0
Biosystems, Journal Year: 2025, Volume and Issue: unknown, P. 105444 - 105444
Published: March 1, 2025
Language: Английский
Citations
0
Plant Cell & Environment, Journal Year: 2025, Volume and Issue: unknown
Published: March 27, 2025
Summary statement The relationship between genome size and cell is present in all land plants including mosses, stronger smaller cells. This depends on environmental pressures, affects differently depending their dominant photosynthetic phase.
Language: Английский
Citations
0
Tropical Plants, Journal Year: 2025, Volume and Issue: 4(1), P. 0 - 0
Published: Jan. 1, 2025
Language: Английский
Citations
0
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Jan. 23, 2024
ABSTRACT Although the mechanisms driving evolution of genome size are not yet fully understood, one potentially important factor is dynamics accumulation mobile selfish genetic elements called transposable (TEs). Since most these sequences neutral or slightly deleterious, a negative correlation between and selection efficacy expected. However, previous studies based on empirical data from closely related species with contrasting life history traits (thought to result in levels efficacy) have yielded inconsistent results, leaving this issue controversial. In study, we perform first large-scale analysis effect drift evolution, without any prior assumption about amount each sampled species. We reconstructed phylogeny whole-genome (2,242 genes) for 77 Drosophilid examine correlations size, TE content, measures (especially using dN/dS ratios non-synonymous synonymous divergence). highlight strong phylogenetic inertia confirm that TEs major components size. Using an integrative approach controls shared history, find genome-wide strongly positively correlated particularly GC-poor genes. This study highlights critical importance controlling heterogeneity base composition when testing controversial evolutionary rates Furthermore, our review reveals absence evidence association increased may be attributed secondary changes dynamics. conclusion, work provides proliferation fly genomes purifying reduced increases, shedding new light role architecture.
Language: Английский
Citations
3
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Aug. 27, 2024
Abstract Despite ferns being crucial to understanding plant evolution, their large and complex genomes has kept genetic landscape largely uncharted, with only a handful of sequenced sparse transcriptomic data. Addressing this gap, we generated extensive RNA-sequencing data for multiple organs across 22 representative species over the fern phylogeny, assembling high-quality transcriptomes. These facilitated construction time-calibrated phylogeny covering all major clades, revealing numerous whole-genome duplications highlighting uniqueness genetics, half uncovered gene families fern-specific. Our investigation into cell walls through biochemical immunological analyses identified occurrences lignin syringyl unit its independent evolution in ferns. Moreover, discovery an unusual sugar hints at divergent evolutionary path wall biochemistry, potentially driven by duplication sub-functionalization. We provide online database preloaded genomic other land plants, which used identify lignocellulosic modules framework unique that have navigated since they split from last common ancestor euphyllophytes more than 360 million years ago.
Language: Английский
Citations
3
Journal of Plant Research, Journal Year: 2025, Volume and Issue: unknown
Published: April 15, 2025
Language: Английский
Citations
0