Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2022.12.02.518695

Chloroplast DNA methylation in the kelp Saccharina latissima is determined by origin and influenced by cultivation

Scheschonk, L.·Nielsen, A. M.·Bischof, K.·Jueterbock, A. O.
View original source ↗Export metadata ↓

Abstract

DNA cytosine methylation is an important epigenetic mechanism in genomic DNA, but absent in the chloroplast DNA of most land plants. We detected methylation in the chloroplast DNA of the kelp Saccharina latissima, a non-model macroalgal species of high ecological (wild populations) and economic importance. Since the functional role of the chloroplast methylome is yet largely unknown, we compared for the first time the chloroplast DNA cytosine methylation between wild and cultured kelp from different climatic origins (High- Arctic (79 {degrees}N) and temperate (54 {degrees}N), laboratory samples at 5 {degrees}C, 10 {degrees}C and 15 {degrees}C). Our results suggest genome-wide differences in methylated sites, and methylation level, between the origins, and a strong effect of cultivation. Functions related to photosynthesis showed differential methylation only between origins. Significant differences in methylation between cultivated and wild samples of genes related to transcription and translation were unique to the high-arctic samples. Both findings indicate that origin and cultivation strongly, but differently affect the chloroplast methylome. Similar methylomes for samples from the same origin - independent from whether they grow in the wild or in the lab - suggest that origin- specific methylation marks on the chloroplast genome are inherited. Given that DNA- methylation affects gene expression, our study suggests that lab-cultivation alters epigenetically determined kelp chloroplast characteristics at least to the same degree as ecotypic differentiation does, but likely on a much shorter timescale. This indicates the capacity for rapid non-genetic adaptation in the kelp Saccharina latissima.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Scheschonk, L., Nielsen, A. M., Bischof, K., Jueterbock, A. O.. 2022-12-03. Chloroplast DNA methylation in the kelp Saccharina latissima is determined by origin and influenced by cultivation. https://doi.org/10.1101/2022.12.02.518695

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

Somatic mosaicism contributes to genomic variation, yet postzygotic structural variants remain under-characterized. We performed long- and short-read WGS from multiple individuals (n=47 normal tissues; n=168 samples) and identified mosaic structural variants in all individuals and germ layers, impacting a median 285.2 kb/genome. Nearly half of breakpoints were independently validated, with tissue distributions reflecting both early and late developmental origins. Most mosaic variants were repeat-mediated and 8.3% overlapped functional elements, an enrichment compared to germline variants. To extend these analyses in samples where long-read sequencing is infeasible, we measured repeat alterations from short-read sequencing, recapitulating mosaic tissue-specific differences. We characterized tumor- and tissue- specific variation in repeats across 15 cancer types and found tumor-related repeat variation to be similar in scale to that of normal mosaic variation. Tracking repeat changes in cell-free DNA provided a noninvasive approach for tumor monitoring. Our analyses revealed widespread repeat-driven structural variation in health and disease.

genomics↗
bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗
bioRxiv2026

Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes

Approximately 8% of the human genome is derived from ancient retroviral infections. The most recently integrated of these endogenous retroviruses is the HERV-K(HML-2) clade, whose expression has been associated with cancer, amyotrophic lateral sclerosis, and embryogenesis. Studies of HERV expression, particularly HML-2, have relied predominantly on short-read sequencing. However, the high similarity among HML-2 proviruses prevents many short reads from being assigned uniquely to individual loci. We therefore compared haplotype-resolved long-read genome assemblies from 292 donors to resolve variation in proviral structure and coding capacity. Several loci previously thought to be fixed were structurally polymorphic. Tandem arrays occurred at 13 loci and contained up to six proviral copies in a single array. At 8q11.23, we identified a previously undescribed full-length provirus in one haplotype. All 583 other haplotypes carried a solo-LTR. We found that standard reference genomes failed to represent the coding capacity retained in many individuals, whose proviruses contained intact open reading frames despite disruptive mutations in the reference sequences. Short-read genotypes left 32.5% of the tested donor-variant pairs unresolved at sites associated with viral reading frames. These findings show why HML-2 expression must be interpreted in the context of the structural and coding alleles each individual carries.

genomics↗