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ABSTRACT: Analysis of Klebsormidium nitens NIES-2285 (NIES-2285 strain was taxonomically reclassified from K. flaccidum)

PROVIDER: PRJDB4956 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	DRR064061.fastq.gz	Fastqsanger.gz
	DRR064062.fastq.gz	Fastqsanger.gz
	DRR064063.fastq.gz	Fastqsanger.gz
	DRR064064.fastq.gz	Fastqsanger.gz

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Klebsormidium nitens strain:NIES-2285

Project description:genome sequence project of a filamentous terrestrial alga Klebsormidium nitens NIES-2285 (NIES-2285 strain was taxonomically reclassified from K. flaccidum)

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Project description:RNA-seq of Klebsormidium nitens NIES-2285 in the presence of IAA (NIES-2285 strain was taxonomically reclassified from K. flaccidum)

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Co-option of transcriptional hub expanded triangular functional interactions among nutrients during plant terrestrialzation

Project description:Plant nitrate, phosphate, and sucrose responses create a complex molecular network fine-tuned for growth and survival. This triangular interplay, crucial for the adaptability of terrestrial plants, allows the availability of one nutrient to influence plant responses to others. However, the origins and functional repurposing of this complex network for plant terrestrialization remain scarcely understood. By delving into the time-series transcriptome responses to nitrate, phosphate, and sucrose in the bryophyte Marchantia polymorpha and its streptophycean algal relatives Klebsormidium nitens, we observed convergent yet largely species-specific regulatory circuits in nutrient response. A key gene regulatory network (GRN) module centered on MpCSD, MpERF20, and MpHD9 was found to govern the hierarchical responses and crosstalk among the three nutrients in M. polymorpha. In K. nitens, these transcription factors were involved in nutrient responses but were co-opted during phytoterrestrialization to serve additional functions. Further network perturbation experiments validated the extensive evolution of transcriptional targets of these regulatory circuits, with cytokinin responsive genes being recruited exclusively into macronutritional GRNs in M. polymorpha thus optimizing nutrient response. Our findings illuminate the evolutionary strategies employed to redeploy the triad of nutrient interactions during the adaptation of ancestral green plants to terrestrial habitats.

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Transcriptomic Response to High Light in the Charophyte Klebsormidium nitens

Project description:Transcriptomic Response to High Light in the Charophyte Klebsormidium nitens

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Project description:Transposable elements are entangled in a constant evolutionary arms race with their host genomes, constantly evolving ways to evade host silencing mechanisms. One silencing mechanism used by many distantly related eukaryotes is dependent on cytosine methylation, an epigenetic mark deposited by C5 cytosine methyltransferases (CMTs). Therefore, it is expected transposable elements would acquire mechanisms to escape from being targeted by cytosine methylation. Here we report how two distantly related eukaryotic lineages have incorporated CMTs into the coding regions of distinct retrotransposon classes. Three of these events have occurred in the dinoflagellates of the genus Symbiodinium, where these CMT-encoding retrotransposons show hundreds of insertions. In a case of convergent evolution, the charophyte Klebsormidium nitens shows an independent expansion of CMT encoding retrotransposons. Concomitantly, we find that Symbiodinium genomes show cytosine methylation patterns unlike any other eukaryote with most of the genome hypermethylated in CpGs, while targeted CH methylation accumulates on transposable elements. Similarly, K. nitens shows CHH and CHG targeted methylation on repressed transposable elements, while CpG methylation is concentrated in gene bodies and transposable elements. Furthermore, we demonstrate the ability of retrotransposon CMTs to de novo methylate CpGs, indicating a putative role in mimicking retrotranscribed DNA as host active genomic DNA. Our results show an unprecedented example of how retrotransposons incorporate host-derived genes involved in DNA methylation as a source of adaptation to their host epigenomic environments.

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Project description:Purpose: To understand the dynamic heat-sress response in M. polymorpha and K. nitens

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