xRead: a coverage-guided approach for scalable construction of read overlapping graph

GigaScience, Год журнала: 2025, Номер 14

Опубликована: Янв. 1, 2025

The development of long-read sequencing is promising for the high-quality and comprehensive de novo assembly various species around world. However, it still challenging assemblers to handle thousands genomes, tens gigabase-level sizes, terabase-level datasets efficiently, which a bottleneck large-scale studies. A major cause read overlapping graph construction that state-of-the-art tools usually have cost terabyte-level RAM space days large genomes. Such lower performance scalability are not suited numerous samples being sequenced. Herein, we propose xRead, novel iterative approach achieves high performance, scalability, yield simultaneously. Under guidance its coverage-based model, xRead converts read-overlapping heuristic read-mapping incremental tasks with highly controllable faster speed. It enables processing very (such as 1.28 Tb Ambystoma mexicanum dataset) less than 64 GB obviously time costs. Moreover, benchmarks suggest can produce accurate well-connected graphs, also supportive kinds downstream strategies. able break through lays new foundation assembly. This tool number from genomes may play important roles in many

Язык: Английский

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Optimal input DNA thresholds for genome skimming in marine crustacean zooplankton

PeerJ, Год журнала: 2025, Номер 13, С. e19054 - e19054

Опубликована: Фев. 26, 2025

Crustacean zooplanktons are key secondary and tertiary producers in marine ecosystems, yet their genomic resources remain poorly understood. To advance biodiversity research on crustacean zooplankton, this study evaluated the effectiveness of genome skimming, a method that assembles genetic regions, including mitogenome, from shotgun sequencing data. Because small amount DNA available is limitation zooplankton genetics, different input amounts (1 pg–10 ng) were prepared for library construction skimming using two large species: Euphausia pacifica (Euphausiacea) Calanus glacialis (Copepoda). Additionally, de novo assembly was used to obtain long contigs short reads because reference-guided can not be applied all zooplankton. Evaluation raw sequence showed increased proportions high-quality distinct (low duplication levels) inputs. By contrast, low quality high observed ≤ 10 pg samples, owing amplification cycles. Complete mitogenomes, 37 genes, successfully retrieved ≥ ( E. ) 100 C. DNA. Despite estimated sizes these species, only 1 3 M sufficient mitogenome , respectively. Nuclear ribosomal repeats histone identified assembled contigs. As obtaining (≥ pg) feasible even powerful approach robust phylogenetics population genetics

Язык: Английский

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Sedimentary DNA insights into Holocene Adélie penguin (Pygoscelis adeliae) populations and ecology in the Ross Sea, Antarctica

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Март 5, 2025

We report 156 sediment metagenomes from Adélie penguin (Pygoscelis adeliae) colonies dating back 6000 years along the Ross Sea coast, Antarctica, and identify marine terrestrial eukaryotes, including locally occurring bird seal species. The data reveal spatiotemporal patterns of diet, spatial in consumption cnidarians, a historically overlooked component diets. Relative proportions mitochondrial lineages detected at each colony are comparable to those previously reported bones. Elevated levels nucleotide diversity upper stratigraphic samples several active consistent with recent population growth. Moreover, highest recovered surface layers two largest colonies, indicating that sedaDNA could provide estimates for former size abandoned colonies. SedaDNA also reveals prior occupation Cape Hallett site by southern elephant (Mirounga leonina), demonstrating how can detect faunal turnover events Antarctica driven past climate or sea ice conditions. Low rates cytosine deamination indicate exceptional preservation within region, suggesting there is high potential recovering much older records local Pleistocene sediments.

Язык: Английский

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Increasing the Thermostability of Luciferase from Antarctic Krill by Rational Design for Biotechnological Applications

Applied Sciences, Год журнала: 2025, Номер 15(7), С. 3563 - 3563

Опубликована: Март 25, 2025

The first luciferase from Antarctic krill (LAK) was cloned and successfully expressed in Escherichia coli BL21(DE3). LAK exhibits the unique ability to emit bright violet fluorescence at an emission wavelength of 350 nm, which represents lowest reported bioluminescence for luciferases. However, its low thermal stability poses a limitation broader application. In this study, we employed rational design approach introduce three pairs artificial disulfide bonds into LAK. Circular dichroism (CD) analysis revealed that introduction resulted significant increase secondary structural content α-helices β-sheets compared wild-type (WT) enzyme. these modifications did not influence spectrum. Among resultant mutant strains, two exhibited markedly enhanced stability. Notably, Mut2 demonstrated 6.18-fold half-life 50 °C. Molecular docking studies indicated D-fluorescein can form additional hydrogen with surrounding amino acid residues (A323, T347, K534). energies between enzyme substrate WT were −19.5 kcal/mol −23.4 kcal/mol, respectively, thereby establishing strong interactions within catalytic pocket region. These likely contribute 2.92-fold improvement affinity, as evidenced by reduced Michaelis–Menten constant (Km). Our activity analyses linker region N- C-domains plays crucial role overall Furthermore, C-terminus does participate substrate-binding catalysis; local excessive rigidity found restrict release AMP product, negatively impacting activity. findings offer new insights mutagenesis luciferases pave way further optimization various biotechnological applications.

Язык: Английский

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“A circadian clock drives behavioral activity in Antarctic krill (Euphausia superba) and provides a potential mechanism for seasonal timing”

Опубликована: Апрель 3, 2025

Antarctic krill is a species with fundamental importance for the Southern Ocean ecosystem. Their large biomass and synchronized movements, like diel vertical migration (DVM), significantly impact ecosystem structure biological carbon pump. Despite decades of research, mechanistic basis DVM remains unclear. Circadian clocks help organisms anticipate daily environmental changes, optimizing adaptation. In this study, we used recently developed activity monitor to record swimming individual, wild-caught under various light conditions across different seasons. Our data demonstrate how circadian clock, in combination light, drives distinct bimodal pattern activity, which could facilitate ecologically important behavioral patterns, such as DVM. Rapid damping flexible synchronization indicate that clock adapted life at high latitudes seasonal recordings suggest clock-based mechanism timing processes. findings advance our understanding high-latitude adaptation key species.

Язык: Английский

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