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Conservation and divergence of small RNA pathways in vascular plants revealed by small RNA analyses in lycophytes and ferns

ABSTRACT: Conservation and divergence of small RNA pathways in vascular plants revealed by small RNA analyses in lycophytes and ferns

OTHER RELATED OMICS DATASETS IN: GSE98408

PROVIDER: PRJNA385013 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5490810.fastq.gz	Fastqsanger.gz
	SRR5490820.fastq.gz	Fastqsanger.gz
	SRR5490801.fastq.gz	Fastqsanger.gz
	SRR5490811.fastq.gz	Fastqsanger.gz
	SRR5490821.fastq.gz	Fastqsanger.gz

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Conservation and divergence of small RNA pathways in vascular plants revealed by small RNA analyses in lycophytes and ferns

Project description:Pathways underlying miRNA biogenesis, degradation, and activity were established early in land plant evolution, but the 24-nt siRNA pathway that guides DNA methylation was incomplete in early land plants, especially lycophytes. We show that the functional diversification of key gene families such as DICER-LIKE and ARGONAUTE (AGO) as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered an unexpected AGO family specific to lycophytes and ferns. Our phylogenetic analyses of miRNAs in lycophytes, bryophytes, ferns, and angiosperms refined the temporal origination of conserved miRNA families in land plants.

2017-07-20 | GSE98408 | GEO

Functional conservation and divergence of the helix-turn-helix motif of E2 ubiquitin-conjugating enzymes

Project description:Supporting .raw data for "Functional conservation and divergence of the helix-turn-helix motif of E2 ubiquitin-conjugating enzymes", DOI: 10.15252/embj.2021108823 Related to Figure 1E and EV1A.

2021-11-17 | MSV000088403 | MassIVE

Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes

Project description:Background The Lycophyta species are the extant taxa most similar to early vascular plants that were once abundant on Earth. However, their distribution has greatly diminished. So far, the absence of chromosome level assembled lycophyte genomes, has hindered our understanding of evolution and environmental adaption of lycophytes. Findings We present the reference genome of the tetraploid aquatic quillwort, Isoetes sinensis, a lycophyte. This genome represents the first chromosome-level assembled genome of a tetraploid seed-free plant. Comparison of genomes between I. sinensis and the diploid I. taiwanensis revealed of genomic features and polyploid of lycophytes. Comparison of the I. sinensis genome with those of other species representing the evolutionary lineages of green plants revealed the inherited genetic tools for transcriptional regulation and most phytohormones in I. sinensis. The presence and absence of key genes related to development and stress responses provides insights into environmental adaption of lycophytes. Conclusions The high-quality reference genome and genomic analysis presented in this study are crucial for future genetic research and the conservation of not only I. sinensis but also other lycophytes.

2023-08-21 | GSE198195 | GEO

Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes

2023-08-21 | GSE198193 | GEO

Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes

2023-08-21 | GSE198196 | GEO

Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes

2023-08-21 | GSE198194 | GEO

Conservation of small RNA pathways in platypus

Project description:Conservation of small RNA pathways in platypus

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Conservation and divergence of methylation patterning in plants and animals

Project description:Conservation and divergence of methylation patterning in plants and animals

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Conservation of small RNA pathways in platypus

Project description:Small RNA pathways play evolutionarily conserved roles in gene regulation and in defense from pathogenic and parasitic nucleic acids. The character and expression patterns of small RNAs show conservation throughout animal lineages, but specific animal clades also show variations on these recurring themes, including species-specific small RNAs. The monotremes, with only platypus and four species of echidna as extant members, represent the basal branch of the mammalian lineage. Here, we examine the small RNA pathways of monotremes by deep sequencing of six platypus and echidna tissues. We find that highly conserved microRNA species display their signature tissue-specific expression patterns. In addition, we find a large rapidly-evolving cluster of miRNAs on platypus chromosome X1 which is unique to monotremes. Platypus and echidna testes contain a robust piRNA system which appears to be participating in ongoing transposon defense. Keywords: piRNA Two size fractions of small RNAs (18-24nt and 25-33nt) were cloned and sequenced from platypus adult testis total RNA; one size fraction (28-24nt) was cloned and sequenced from echidna adult testis total RNA

2008-05-20 | E-GEOD-10571 | biostudies-arrayexpress

Conservation of small RNA pathways in platypus

2008-05-21 | GSE10571 | GEO