WASTER: Practicalde novophylogenomics from low-coverage short reads

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 24, 2025

The advent of affordable whole-genome sequencing has spurred numerous large-scale projects aimed at inferring the tree life, yet achieving a complete species-level phylogeny remains distant goal due to significant costs and computational demands. Traditional species inference methods, though effective, are hampered by need for high-coverage sequencing, high-quality genomic alignments, extensive resources. To address these challenges, this study introduces WASTER, novel de novo tool trees directly from short-read sequences. WASTER employs k-mer based approach identifying variable sites, circumventing genome assembly alignment. Using simulations, we demonstrate that achieves accuracy comparable traditional alignment-based even low depth, substantially higher than other alignment-free methods. We validate WASTER's efficacy on real data, where it accurately reconstructs phylogenies eukaryotic with as depth 1.5X. provides fast efficient solution estimation in cases and/or alignment may bias analyses or is challenging, example depth. It also method generating guide tree-based algorithms. ability estimate low-coverage data without relying will lead reduced phylogenomic projects.

Language: Английский

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Fine texture Lambertian electromagnetic metasurface generates background blending stealth effect in radar vision

Journal of Applied Physics, Journal Year: 2025, Volume and Issue: 137(4)

Published: Jan. 27, 2025

The emergence of diffuse scattering metasurfaces offers the electromagnetic stealth mechanism. However, background blending effect in radar vision induced by metasurface has not been specially investigated. Here, a Lambertian diffusive reflective for imaging is designed dispersion engineering. Compared to conventional metasurface, achieves more uniform beam over broad frequency range without significant main lobe formation at any point, which provides ways fusion stealth. For conceptual validation, metallic flat plate, coded and are fabricated their images obtained two-dimensional scanning measurement. As anticipated, notably alters edge characteristics images, effectively concealing contours covered area. This work wideband design method new idea designing material structures from perspective immensely helpful practical application jamming recognition coding metasurfaces.

Language: Английский

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The Genomics Revolution Drives a New Era in Entomology

Annual Review of Entomology, Journal Year: 2025, Volume and Issue: 70(1), P. 379 - 400

Published: Jan. 28, 2025

Thanks to the fast development of sequencing techniques and bioinformatics tools, genome an insect species for specific research purposes has become increasingly popular practice. Insect genomes not only provide sets gene sequences but also represent a change in focus from reductionism systemic biology field entomology. Using genomes, researchers are able identify study functions all members family, pathway, or network associated with trait interest. Comparative genomics studies new insights into evolution, addressing long-lasting controversies taxonomy. It is now feasible uncover genetic basis important traits by identifying variants using resequencing data individual insects, followed genome-wide association analysis. Here, we review current progress projects application uncovering phylogenetic relationships between insects unraveling mechanisms life-history traits. We summarize challenges sharing possible solutions. Finally, guidance fully deeply mining data.

Language: Английский

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CASTER: Direct species tree inference from whole-genome alignments

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 6, 2023

Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference tree life. While genome-wide data are routinely used for discordance-aware phylogenomic analyses, due to modeling and scalability limitations, current practice leaves out large chunks genomes. As more high-quality genomes become available, we urgently need methods infer directly from a multiple genome alignment. Here, introduce CASTER, site-based method that eliminates predefine recombination-free loci. CASTER is statistically consistent under incomplete lineage sorting scalable hundreds mammalian whole We show both in simulations on real its per-site scores can reveal interesting patterns evolution across genome.

Language: Английский

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Genomics, Population Divergence, and Historical Demography of the World's Largest and Endangered Butterfly, The Queen Alexandra's Birdwing

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(4)

Published: March 9, 2023

Abstract The world's largest butterfly is the microendemic Papua New Guinean Ornithoptera alexandrae. Despite years of conservation efforts to protect its habitat and breed this up-to-28-cm butterfly, species still figures as endangered in IUCN Red List only known from two allopatric populations occupying a total ∼140 km². Here we aim at assembling reference genomes for investigate genomic diversity, historical demography determine whether population structured, which could provide guidance programs attempting (inter)breed populations. Using combination long short DNA reads RNA sequencing, assembled six tribe Troidini, with four annotated O. alexandrae related priamus Troides oblongomaculatus. We estimated diversity three species, proposed scenarios using polymorphism-based methods taking into account characteristics low-polymorphic invertebrates. Indeed, chromosome-scale assemblies reveal very low levels nuclear heterozygosity across appears be exceptionally (lower than 0.01%). Demographic analyses demonstrate steadily declining Ne throughout history, divergence distinct about 10,000 ago. These results suggest that distribution has been time. It should also make local aware populations, not ignored if any attempt made cross

Language: Английский

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Genome‐wide identification of yellow gene family in Hermetia illucens and functional analysis of yellow‐y by CRISPR/Cas9

Insect Science, Journal Year: 2024, Volume and Issue: unknown

Published: April 29, 2024

Abstract The yellow gene family plays a crucial role in insect pigmentation. It has potential for use as visible marker genetic manipulation and transgenic engineering several model non‐model insects. Sadly, genes have rarely been identified Stratiomyidae species the functions of are relatively unknown. In present study, we first manually annotated curated 10 black soldier fly (BSF), Hermetia illucens (Stratiomyidae). Then, conserved amino acids major royal jelly proteins (MRJPs) domain, structural architecture phylogenetic relationship BSF were analyzed. We found that yellow‐y , yellow‐c yellow‐f expressed at all developmental stages, especially prepupal stage. Using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated protein 9 (Cas9) system, successfully disrupted BSF. Consequently, mutation clearly resulted pale‐yellow body color prepupae, pupae adults, instead typical wild type. However, or did not result any change insects, when compared with Our study indicates pigmentation, providing an optimal

Language: Английский

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What Exactly Can Bionic Strategies Achieve for Flexible Sensors?

ACS Applied Materials & Interfaces, Journal Year: 2024, Volume and Issue: 16(30), P. 38811 - 38831

Published: July 20, 2024

Flexible sensors have attracted great attention in the field of wearable electronic devices due to their deformability, lightness, and versatility. However, property improvement remains a key challenge. Fortunately, natural organisms exhibit many unique response mechanisms various stimuli, corresponding structures compositions provide advanced design ideas for development flexible sensors. Therefore, this Review highlights recent advances sensing performance functional characteristics from perspective bionics first time. First, "twins" are introduced. Second, enhancements electrical mechanical through bionic strategies summarized according prototypes humans, plants, animals. Third, discussed detail, including self-healing, color-changing, tangential force, strain redistribution, interfacial resistance. Finally, we summarize challenges trends bioinspired This aims deepen understanding innovative references manufacture next-generation

Language: Английский

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Extreme genetic signatures of local adaptation in a notorious rice pest, Chilo suppressalis

National Science Review, Journal Year: 2024, Volume and Issue: 12(3)

Published: June 25, 2024

Climatic variation stands as a significant driving force behind genetic differentiation and the evolution of adaptive traits. Chilo (C.) suppressalis, commonly known rice stem borer, is highly destructive pest that crucially harms production. The lack natural population genomics data has hindered more thorough understanding its climate adaptation, particularly basis underlying To overcome this obstacle, our study employed completely resequenced genomes 384 individuals to explore structure, demographic history, gene flow C. suppressalis in China. This observed occurred asymmetrically, moving from central populations peripheral populations. Using genome-wide selection scans genotype-environment association studies, we identified potential loci may be associated with climatic adaptation. most robust signal was found cold tolerance, linked homeobox gene, goosecoid (GSC), whose expression level significantly different low high latitudes. Moreover, downregulating by RNAi enhances tolerance phenotypes. Our findings have uncovered delved into foundation ability adapt environment. essential ensuring continued effectiveness sustainability novel control techniques.

Language: Английский

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A glimpse into the biodiversity of insects in Yunnan: An updated and annotated checklist of butterflies (Lepidoptera, Papilionoidea)

动物学研究, Journal Year: 2022, Volume and Issue: 43(6), P. 1009 - 1010

Published: Jan. 1, 2022

Language: Английский

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Roof of the world: Home and border in the genomic era

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: unknown

Published: June 28, 2023

Himalaya and the Tibetan Plateau, known as ‘land of snow’ ‘roof world’, is home to tens millions indigenous people who live with a staggering amount biological diversity. In past decade scientists have applied genomic tools methods substantially advance understanding phylogeography genetic mechanisms behind high‐elevation adaptation local biota. However, contributions from researchers native institutions are underrepresented in this scientific endeavour. We point higher degree contribution within discipline conservation biology how recognizing prominence traditional ecological knowledge (TEK) could deliver keen molecular insights. Since Himalaya‐Tibet interface spans five countries, comprehensive biogeographical phylogeographical taxon sampling region requires multi‐national collaborations across lands well community participation at both national international levels. For next generation ecologists, researching cataloguing evolutionary history information Himalayan landscape race against melting glacier. At roof world, their judgement stewardship will environmental impacts that percolate far beyond lands.

Language: Английский

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