Biggest genome ever found belongs to this odd little plant DOI

Max Kozlov

Nature, Journal Year: 2024, Volume and Issue: unknown

Published: May 31, 2024

Language: Английский

Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis DOI Creative Commons
Ana Luiza Franco, Wenjia Gu, Petr Novák

et al.

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

Influence of Ty3/gypsy and Ty1/copia LTR-retrotransposons on the large genomes of Alstroemeriaceae: genome landscape of Bomarea edulis (Tussac) Herb DOI
J. I. B. do Nascimento, Mariela Sader, Tiago Ribeiro

et al.

PROTOPLASMA, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 30, 2025

Language: Английский

Citations

0

Introduction to genomics DOI
Vilnis Šķipars, Dainis Ruņģis

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 15 - 30

Published: Jan. 1, 2025

Language: Английский

Citations

0

An Efficient Implementation of Cosine Distance on Minimal Absent Word Sets Using Suffix Automata DOI

M. Ehsan,

Sk. Sabit Bin Mosaddek,

Mohammad Saifur Rahman

et al.

Lecture notes in computer science, Journal Year: 2025, Volume and Issue: unknown, P. 180 - 195

Published: Jan. 1, 2025

Language: Английский

Citations

0

Progressive evolution of plants: a critical review DOI
Alexey V. Melkikh

Biosystems, Journal Year: 2025, Volume and Issue: unknown, P. 105444 - 105444

Published: March 1, 2025

Language: Английский

Citations

0

Mosses Reveal a Universal Genome‐Cell Size Relationship Across Land Plants Shaped by Shared Evolutionary Pressures DOI
Pere Miquel Mir-Rosselló, Jaume Flexas, Marc Carriquí

et al.

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

Artificial intelligence-driven plant bio-genomics research: a new era DOI
Yang Lin, Hao Wang, Meiling Zou

et al.

Tropical Plants, Journal Year: 2025, Volume and Issue: 4(1), P. 0 - 0

Published: Jan. 1, 2025

Language: Английский

Citations

0

Relaxed purifying selection is associated with an accumulation of transposable elements in flies DOI Creative Commons
Vincent Mérel, Théo Tricou, Nelly Burlet

et al.

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

Comparative transcriptomics in ferns reveals key innovations and divergent evolution of secondary cell wall DOI Creative Commons

Zahin Mohd Ali,

Qiao Wen Tan, Peng Ken Lim

et al.

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

Dynamic changes in chromatin structure and transcriptional activity in the generative cells of Lilium longiflorum DOI
Mio K. Shibuta,

Tomoko Aso,

Yutaka Okawa

et al.

Journal of Plant Research, Journal Year: 2025, Volume and Issue: unknown

Published: April 15, 2025

Language: Английский

Citations

0