Biology subjects

Andren, E.

Publications and source records attributed to Andren, E..

3 recordsLinked to original sources

bioRxiv2026

A High-Quality Genome Assembly of Chaetoceros muelleri Reveals Extensive Gene Duplication, Functional Diversification, and Unique Lineage-Specific Innovation

Diatoms are major contributors to marine primary production, yet high-quality nuclear genome resources remain scarce for ecologically dominant lineages such as Chaetoceros. Here, we present the first high-quality nuclear genome assembly of Chaetoceros muelleri, generated from living cells resurrected from resting spores preserved in Baltic Sea sediments and sequenced using PacBio HiFi long-read technology. The assembly is compact (43{square}Mb), highly contiguous (N50{square}={square}1.40{square}Mb), and highly complete (93% BUSCO). Comparative analyses across 14 diatom genomes revealed extensive lineage-specific and expanded gene families in C. muelleri, alongside a small, conserved core genome, reflecting rapid evolutionary turnover. Functional enrichment highlighted diversification of polysaccharide biosynthesis, vesicle-mediated trafficking, membrane remodelling, and transcriptional regulation, consistent with adaptations linked to frustule formation and environmental responsiveness. Transposable elements (TEs) strongly shape the genome, accounting for [~]18% of the assembly, with dominant LTR retrotransposons and a large fraction of unclassified repeats suggesting novel or highly diverged TE lineages. Enrichment of DNA replication, recombination, and repair functions further indicates compensatory genome maintenance associated with TE-driven structural dynamics. Direct comparison with C. tenuissimus revealed contrasting patterns of gene family expansion and regulatory innovation, underscoring divergent evolutionary strategies within Chaetoceros. By integrating resurrection ecology with long-read genomics, this study provides a foundational genomic resource for C. muelleri and highlights the role of TE-mediated genome plasticity in diatom evolution.

genomics↗

bioRxiv2024

Decoding the Baltic Sea's Past and Present: A simple Molecular Index for Ecosystem Assessment

Marginal sea ecosystems, such as the Baltic Sea, are severely affected by anthropogenic pressures, such as climate warming, pollution, and eutrophication, which increased in the course of the past century. Biodiversity monitoring data and assessment of environmental status in such systems have typically been carried out only for the past few decades, if at all, and knowledge on pre-impact stability and good ecological status is limited. An extension of monitoring time series can potentially be achieved through analyses of paleoecological records, e.g. for phytoplankton, which form the base of the food web and are highly susceptible to environmental changes. Within the phytoplankton community, dinoflagellates and diatoms play a significant role as primary producers, and their relative dominance in the spring bloom, calculated as Dia/Dino index, is used as an indicator for the environmental status of the Baltic Sea. To extend time series on the dominance patterns and include non-fossilized dinoflagellates, we here establish a simple droplet digital PCR (ddPCR) reaction on ancient DNA from sediment cores that decodes phytoplankton dynamics. We focus on two common spring bloom species, the diatom Skeletonema marinoi and the dinoflagellate Apocalathium malmogiense, for which we evaluate a DNA based dominance index. It performs very well in comparison to DNA metabarcoding and modern monitoring and can elucidate past species dominance across the past century in three basins of the Baltic and across millennia in two of these basins. For the past century, we see a dominance shift already starting before the mid-20th century in two of the Baltic Sea basins, thus substantially predating current monitoring programs. Shifts are only partly coeval among the cores and the index shows different degrees of stability. This pattern is confirmed across millennia, where a long-term stable relationship between the diatom and the dinoflagellate is observed in the Eastern Gotland Basin, while data from the Gulf of Finland bear testimony to a much more unstable relationship. This confirms that good ecological status based on the dominance pattern of diatoms and dinoflagellates must be established locally and exemplifies how sediment core DNA can be employed to extend monitoring data.

ecology↗

bioRxiv2018

Holocene DNA sequences -- a dream come true

Microscopic marine planktons have played a major role in the Earths ecosystem and accounts for half the globes primary production. Predicting the fate of marine planktons is imperative to understanding how ocean life will change in future centuries and how organisms have adapted to changes in the past over long timescales (over thousands of years). Studies of revived resting spores of marine diatoms will serve as excellent proxies of environmental change in marine environments. Thus far, only about a century old marine diatom resting spores could be revived. This severely limited the use of diatom resting spores to investigate the effects of environmental perturbations over longer time scales. Here, we, for the first time report revival of thousands of years old resting spores from the deposits of ancient diatoms (Chaetoceros) in sub-seafloor sediments using a revival protocol that involved recreating the ancient environmental conditions (salinity, temperature and light). Our revived diatom resting spores samples range from recent (0-80 years) to [~]7200 years old. Importantly, we also extracted the DNA from the ancient resting spores of Chaetoceros species from the Baltic Sea. Our findings will enable us to compare DNA sequence data obtained from these natural archives of resurrected organisms and provide predictive models to forecast evolutionary responses of natural populations to environmental changes resulting from natural and anthropogenic stressors, including climate change\n\nSignificance StatementOur results address the important topic of adaptive evolution in marine species due to climate and environmental change induced due to anthropogenic perturbations. We present a new model system Chaetoceros muelleri which will help us address important evolutionary and long-term adaptation questions across evolutionary timescales. Our study reports (1) the revival of recent (0-80 years) to ancient (7200 years old) resting spores of Chaetoceros (2) the extraction of DNA and amplification of chloroplast and ribosomal genes from recent and ancient ([~]1300 years old) resting spores of Chaetoceros (3) Radiocarbon dating to determine age of sediments (4) Identification of species by reviving the resting spores (5) Baltic sea an excellent ecosystem to study long-term effects of environment on species adaptation

evolutionary biology↗