Publications by authors named "Inge Seim"

The amphipod Hirondellea gigas is a dominant species inhabiting the deepest part of the ocean (∼6,800-11,000 m), but little is known about its genetic adaptation and population dynamics. Here, we present a chromosome-level genome of H. gigas, characterized by a large genome size of 13.

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Cetaceans show remarkable diversity in diving capability, implying a range of adaptive strategies to hazards such as hydrostatic pressure and oxidative stress, but few studies have considered the evolution of extreme diving. Here, we first examined the relationship between morphological and physiological factors and diving capability and then considered the molecular evolution of candidate deep-sea diving traits in a genomic dataset of cetaceans. Our dataset included six super-divers, sperm whales (families Physeteridae and Kogiidae) and beaked whales (Ziphiidae), species that can dive deeper than 1000 m for about an hour or longer.

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Background: Lindaspio polybranchiata, a member of the Spionidae family, has been reported at the Lingshui Cold Seep, where it formed a dense population around this nascent methane vent. We sequenced and assembled the genome of L. polybranchiata and performed comparative genomic analyses to investigate the genetic basis of adaptation to the deep sea.

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It is essential to discover and identify animals in species level in the wild to achieve the collection of baseline data and benefit better understanding and conservation of the rare species. However, this is far from being realized for many beaked whales in the deep sea, including the Deraniyagala's beaked whale (), which is one of the least-known whales with no confirmed live sightings at sea yet all over the world. Here, we provide the first robust field identification of , by integrating DNA sequencing of skin biopsies, acoustic data, and photographs.

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  • Bats have unique traits such as flight, echolocation, and a long lifespan, but their genetic relationships and history are not well understood.
  • Researchers sequenced genomes for 17 bat species and identified new genomic regions that may regulate gene expression, with some genes linked to antivirus and cancer resistance features.
  • Their analysis revealed two patterns of ancient population changes in bats, indicating that these changes do not align with their evolutionary relationships and enhancing our knowledge of bat evolution and adaptation.
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Tardigrades are captivating organisms known for their resilience in extreme environments, including ultra-high-dose radiation, but the underlying mechanisms of this resilience remain largely unknown. Using genome, transcriptome, and proteome analysis of , we explored the molecular basis contributing to radiotolerance in this organism. A putatively horizontally transferred gene, DOPA dioxygenase 1 (), responds to radiation and confers radiotolerance by synthesizing betalains-a type of plant pigment with free radical-scavenging properties.

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  • Scientists found a lot of tiny living things called microbes in the ocean, gathering over 43,000 genomes to study.
  • They discovered new tools that could help fight bacteria, like a special CRISPR system and some substances that kill germs.
  • This research shows how the variety of microbes in the ocean can help us create new technology and medicine that can benefit us in the future.
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  • Understanding the cellular architecture and evolution of immune cells in different species helps reveal how immune systems function and their vulnerability to diseases.
  • A study using single-cell RNA sequencing was conducted on immune cells from two types of fish: cartilaginous (white-spotted bamboo shark) and bony fishes (zebrafish and Chinese tongue sole), showing that similar cell types across species have comparable gene expression profiles.
  • The research identified unique immune cell populations in the bamboo shark, suggesting a less specialized approach to immune function compared to the more functionally distinct lymphocytes found in bony fishes, providing insights into the evolution of immune systems in jawed vertebrates.
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  • Sirenians, part of the superorder Afrotheria, were the first mammals to adapt from land to marine environments and are unique as herbivorous marine mammals.
  • A newly generated chromosome-level genome for the dugong (Dugong dugon) reveals genetic adaptations for aquatic life, including changes in circadian patterns and dietary tolerance linked to specific genes (NIS and PER2).
  • The study also identifies gene losses that could be disadvantageous today and highlights the need for extensive genetic research on dugong populations to aid in their conservation.
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Unlabelled: The electric catfish (), belonging to the family Malapteruridae, order Siluriformes (Actinopterygii: Ostariophysi), is one of the six branches that has independently evolved electrical organs. We assembled a 796.75 Mb genome and anchored 88.

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Populations and species are threatened by human pressure, but their fate is variable. Some depleted populations, such as that of the northern elephant seal (Mirounga angustirostris), recover rapidly even when the surviving population was small. The northern elephant seal was hunted extensively and taken by collectors between the early 1800s and 1892, suffering an extreme population bottleneck as a consequence.

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Background: The within-species diversity of symbiotic bacteria represents an important genetic resource for their environmental adaptation, especially for horizontally transmitted endosymbionts. Although strain-level intraspecies variation has recently been detected in many deep-sea endosymbionts, their ecological role in environmental adaptation, their genome evolution pattern under heterogeneous geochemical environments, and the underlying molecular forces remain unclear.

Results: Here, we conducted a fine-scale metagenomic analysis of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont collected from distinct habitats: hydrothermal vent and methane seep.

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The six species of lungfish possess both lungs and gills and are the closest extant relatives of tetrapods. Here, we report a single-cell transcriptome atlas of the West African lungfish (Protopterus annectens). This species manifests the most extreme form of terrestrialization, a life history strategy to survive dry periods that can last for years, characterized by dormancy and reversible adaptive changes of the gills and lungs.

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Chaetodontidae, known as butterflyfishes, are typical fish in coral ecosystems, exhibiting remarkable interspecific differences including body colour patterns and feeding ecology. In this study, we report genomes of three butterflyfish species (Chelmon rostratus, Chaetodon trifasciatus and Chaetodon auriga) and a closely related species from the Pomacanthidae family, Centropyge bicolour, with an average genome size of 65,611 Mb. Chelmon rostratus, comprising 24 chromosomes assembled to the chromosome level, could be served as a reference genome for butterflyfish.

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Lifespan varies significantly among mammals, with more than 100-fold difference between the shortest and longest living species. This natural difference may uncover the evolutionary forces and molecular features that define longevity. To understand the relationship between gene expression variation and longevity, we conducted a comparative transcriptomics analysis of liver, kidney, and brain tissues of 103 mammalian species.

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  • Prostate cancer varies greatly in severity, ranging from slow-growing forms to aggressive types, but existing research cell lines mostly come from advanced cases, highlighting the need for new lines from early-stage localized disease.
  • Researchers established four new cell lines from patients with localized prostate cancer, two from benign tissue and two from tumor tissue, using techniques like HPV16 immortalization and RNA sequencing to analyze their characteristics.
  • The new cell lines retained an epithelial structure and showed a slower growth rate, differing significantly in gene expression from common metastatic prostate cancer cell lines, which may be important for further understanding of the disease's early stages.
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Background: Bivalves have independently evolved a variety of symbiotic relationships with chemosynthetic bacteria. These relationships range from endo- to extracellular interactions, making them ideal for studies on symbiosis-related evolution. It is still unclear whether there are universal patterns to symbiosis across bivalves.

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  • Antarctic krill (Euphausia superba) is the most abundant wild animal on Earth, and its large biomass is essential for the Southern Ocean ecosystem.
  • Researchers have sequenced a 48.01-Gb genome, highlighting significant inter-genic transposable element expansions and revealing key gene families related to molting and energy metabolism that help the krill adapt to extreme Antarctic conditions.
  • Population studies show no clear structure, but indicate natural selection influenced by environmental changes, with a significant population size reduction 10 million years ago followed by a rebound around 100,000 years ago linked to climate events.
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Cetaceans (dolphins, whales, and porpoises) have large and anatomically sophisticated brains. To expand our understanding of the cellular makeup of cetacean brains and the similarities and divergence between the brains of cetaceans and terrestrial mammals, we report a short-finned pilot whale (Globicephala macrorhynchus) single-nucleus transcriptome atlas. To achieve this goal, we assembled a chromosome-scale reference genome spanning 2.

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Background: Coleoid cephalopods have distinctive neural and morphological characteristics compared to other invertebrates. Early studies reported massive genomic rearrangements occurred before the split of octopus and squid lineages (Proc Natl Acad Sci U S A 116:3030-5, 2019), which might be related to the neural innovations of their brain, yet the details remain elusive. Here we combine genomic and single-nucleus transcriptome analyses to investigate the octopod chromosome evolution and cerebral characteristics.

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  • Cultivated peanuts (Arachis hypogaea) are essential for global nutrition, yet there's limited understanding of their genetic diversity and traits related to seeds.
  • The study aimed to analyze peanut population structure, selection signatures from breeding, and identify genes tied to seed characteristics.
  • Results showed distinct genetic groups among peanut accessions, a notable population size increase in the last few centuries, and identified two key genes that influence seed weight and length, enhancing future peanut breeding efforts.
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Many mammals risk damage from oxidative stress stemming from frequent dives (i.e., cycles of ischemia/reperfusion and hypoxia/reoxygenation), high altitude and subterranean environments, or powered flight.

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Marine mammals are exposed to the oxidative stress induced by hypoxia/reoxygenation cycles yet resist cellular damage. The availability of high-quality genomes promises to provide insights on how this is achieved. In this study, we considered the ubiquitinconjugating enzymes (E2) gene family, genes, which encodes enzymes with critical roles in cellular physiology, including the oxidative stress response.

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