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Estimation of Species Abundance Based on the Number of Segregating Sites Using Environmental DNA (eDNA).
IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-02-06 DOI: 10.1111/1755-0998.14076
Qiaoyun Ai, Hao Yuan, Ying Wang, Chenhong Li

The advance of environmental DNA (eDNA) has enabled rapid and non-invasive species detection in aquatic environments. While most studies focus on species detection, recent works explored using eDNA concentration to quantify species abundance. However, the differential individual DNA contribution to eDNA samples could easily obscure the eDNA concentration-species abundance relationship. We propose using the number of segregating sites as a proxy for estimating species abundance. Segregating sites reflect the genetic diversity of the population, which is less sensitive to differential individual DNA contribution than eDNA concentration. We examined the relationship between the number of segregating sites and species abundance in silico, in vitro, and in situ experiments, using two brackish goby species, Acanthogobius hasta and Tridentiger bifasciatus. Analyses of the simulated and in vitro data with DNA mixed from a known number of individuals showed a strong correlation between the number of segregating sites and species abundance (R2 > 0.9; p < 0.01). In the in situ experiments, we analysed eDNA samples collected from mesocosm. The results further validated that the correlation (R2 = 0.70, p < 0.01) was not affected by biotic factors, including body size and feeding behaviour (p > 0.05). The cross-validation test results also showed that the number of segregating sites predicted species abundance with less bias and variability than the eDNA concentration. Overall, the number of segregating sites is less affected by differential DNA contribution among individuals compared to eDNA concentration. This advancement can significantly enhance the proficiency of estimating species abundance using eDNA.

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引用次数: 0
A High-Throughput Ancient DNA Extraction Method for Large-Scale Sample Screening.
IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-02-06 DOI: 10.1111/1755-0998.14077
Alexandre Gilardet, Edana Lord, Gonzalo Oteo García, Georgios Xenikoudakis, Katerina Douka, Matthew J Wooller, Timothy Rowe, Michael D Martin, Mathilde Le Moullec, Michail Anisimov, Peter D Heintzman, Love Dalén

Large-scale DNA screening of palaeontological and archaeological collections remains a limiting and costly factor for ancient DNA studies. Several DNA extraction protocols are routinely used in ancient DNA laboratories and have even been automated on robotic platforms. Robots offer a solution for high-throughput screening but the costs, as well as necessity for trained technicians and engineers, can be prohibitive for some laboratories. Here, we present a high-throughput alternative to robot-based ancient DNA extraction using a 96-column plate. When compared to routine single MinElute columns, we retrieved highly similar endogenous DNA contents, an important metric in ancient DNA screening. Mitogenomes with a coverage depth greater than 0.1× could be generated and allowed for taxonomic assignment. However, average fragment lengths, DNA damage and library complexities significantly differed between methods but these differences became nonsignificant after modification of our library purification protocol. Our high-throughput extraction method allows generation of 96 extracts within approximately 4 hours of laboratory work while bringing the cost down by ~39% compared to using single columns. Additionally, we formally demonstrate that the addition of Tween-20 during the elution step results in higher complexity libraries, thereby enabling higher genome coverage for the same sequencing effort.

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引用次数: 0
Bamboozle: A Bioinformatic Tool for Identification and Quantification of Intraspecific Barcodes.
IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-02-04 DOI: 10.1111/1755-0998.14067
Matthew I M Pinder, Björn Andersson, Hannah Blossom, Marie Svensson, Karin Rengefors, Mats Töpel

Evolutionary changes in populations of microbes, such as microalgae, cannot be traced using conventional metabarcoding loci as they lack intraspecific resolution. Consequently, selection and competition processes among strains of the same species cannot be resolved without elaborate isolation, culturing, and genotyping efforts. Bamboozle, a new bioinformatic tool introduced here, scans the entire genome of a species and identifies allele-rich barcodes that enable direct identification of different genetic strains from a population using amplicon sequencing of a single DNA sample. We demonstrate its usefulness by identifying hypervariable barcoding loci (< 500 bp) from genomic data in two microalgal species, the diploid diatom Skeletonema marinoi and the haploid chlorophyte Chlamydomonas reinhardtii. Across the two genomes, four and twenty-two loci, respectively, were identified that could in silico resolve all analysed genotypes. All of the identified loci are within protein-coding genes with various metabolic functions. Single nucleotide polymorphisms (SNPs) provided the most reliable genetic markers, and among 54 strains of S. marinoi, three 500 bp loci contained, on average, 46 SNPs, 103 strain-specific alleles, and displayed 100% heterozygosity. This high level of heterozygosity was identified as a novel opportunity to improve strain quantification and detect false positive artefacts during denoising of amplicon sequences. Finally, we illustrate how metabarcoding of a single genetic locus can be used to track abundances of S. marinoi strains in an artificial selection experiment. As future genomic datasets become available and DNA sequencing technologies develop, Bamboozle has flexible user settings enabling optimal barcodes to be designed for other species and applications.

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引用次数: 0
Comparative Genomics Points to Ecological Drivers of Genomic Divergence Among Intertidal Limpets.
IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-31 DOI: 10.1111/1755-0998.14075
Emily C Giles, Vanessa L González, Paulina Carimán, Carlos Leiva, Ana Victoria Suescún, Sarah Lemer, Marie Laure Guillemin, Daniel Ortiz-Barrientos, Pablo Saenz-Agudelo

Comparative genomic studies of closely related taxa are important for our understanding of the causes of divergence on a changing Earth. This being said, the genomic resources available for marine intertidal molluscs are limited and currently, there are few publicly available high-quality annotated genomes for intertidal species and for molluscs in general. Here we report transcriptome assemblies for six species of Patellogastropoda and genome assemblies and annotations for three of these species (Scurria scurra, Scurria viridula and Scurria zebrina). Comparative analysis using these genomic resources suggest that and recently diverging lineages (10-20 Mya) have experienced similar amounts of contractions and expansions but across different gene families. Furthermore, differences among recently diverged species are reflected in variation in the amount of coding and noncoding material in genomes, such as amount of repetitive elements and lengths of transcripts and introns and exons. Additionally, functional ontologies of species-specific and duplicated genes together with demographic inference support the finding that recent divergence among members of the genus Scurria aligns with their unique ecological characteristics. Overall, the resources presented here will be valuable for future studies of adaptation in molluscs and in intertidal habitats as a whole.

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引用次数: 0
Next-Generation Snow Leopard Population Assessment Tool: Multiplex-PCR SNP Panel for Individual Identification From Faeces.
IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-31 DOI: 10.1111/1755-0998.14074
Katherine A Solari, Shakeel Ahmad, Ellie E Armstrong, Michael G Campana, Hussain Ali, Shoaib Hameed, Jami Ullah, Barkat Ullah Khan, Muhammad A Nawaz, Dmitri A Petrov

In recent years, numerous single nucleotide polymorphism (SNP) panel methods to genotype non-invasive faecal samples have been developed. However, none of these existing methods fit all of the criteria necessary to make a SNP panel broadly usable for conservation projects in any country-cost effective, streamlined lab protocol and user-friendly open-source bioinformatics protocols for panel design and analysis. Here, we present such a method and display its utility by developing a multiplex PCR SNP panel for conducting individual ID of snow leopards, Panthera uncia, from faecal samples. The SNP panel we present consists of 144 SNPs and utilises next-generation sequencing technology. We validate our SNP panel with paired tissue and faecal samples from zoo individuals, showing a minimum of 96.7% accuracy in allele calls per run. We then generate SNP data from 235 field-collected faecal samples from across Pakistan to show that the panel can reliably identify individuals from low-quality faecal samples of unknown age and is robust to contamination. We also show that our SNP panel has the capability to identify first-order relatives among sampled zoo individuals and provides insights into the geographic origin of samples. This SNP panel will empower the snow leopard research community in their efforts to assess local and global snow leopard population sizes. More broadly, we present a SNP panel development method that can be used for any species of interest for which adequate genomic reference data is available.

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引用次数: 0
A Long-Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS-MBON 2018-2020.
IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-31 DOI: 10.1111/1755-0998.14073
Nauras Daraghmeh, Katrina Exter, Justine Pagnier, Piotr Balazy, Ibon Cancio, Giorgos Chatzigeorgiou, Eva Chatzinikolaou, Maciej Chelchowski, Nathan Alexis Mitchell Chrismas, Thierry Comtet, Thanos Dailianis, Klaas Deneudt, Oihane Diaz de Cerio, Markos Digenis, Vasilis Gerovasileiou, José González, Laura Kauppi, Jon Bent Kristoffersen, Piotr Kukliński, Rafał Lasota, Liraz Levy, Magdalena Małachowicz, Borut Mavrič, Jonas Mortelmans, Estefania Paredes, Anita Poćwierz-Kotus, Henning Reiss, Ioulia Santi, Georgia Sarafidou, Grigorios Skouradakis, Jostein Solbakken, Peter A U Staehr, Javier Tajadura, Jakob Thyrring, Jesus S Troncoso, Emmanouela Vernadou, Frederique Viard, Haris Zafeiropoulos, Małgorzata Zbawicka, Christina Pavloudi, Matthias Obst

Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document the biodiversity of complex communities over large spatio-temporal scales. We established an international Marine Biodiversity Observation Network (ARMS-MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard-bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018-2019 and retrieved in 2018-2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open-access data set (image, genetic and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to ~5500 amplicon sequence variants and ~1800 operational taxonomic units, and up to ~250 and ~50 species per observatory using the cytochrome c oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non-indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least 3-6 months during the main growth season to use resources as efficiently as possible and that post-sequencing curation is applied to enable statistical comparison of spatio-temporal entities. We suggest that ARMS should be used in biological monitoring programs and long-term ecological research and encourage the adoption of our ARMS-MBON protocols.

{"title":"A Long-Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS-MBON 2018-2020.","authors":"Nauras Daraghmeh, Katrina Exter, Justine Pagnier, Piotr Balazy, Ibon Cancio, Giorgos Chatzigeorgiou, Eva Chatzinikolaou, Maciej Chelchowski, Nathan Alexis Mitchell Chrismas, Thierry Comtet, Thanos Dailianis, Klaas Deneudt, Oihane Diaz de Cerio, Markos Digenis, Vasilis Gerovasileiou, José González, Laura Kauppi, Jon Bent Kristoffersen, Piotr Kukliński, Rafał Lasota, Liraz Levy, Magdalena Małachowicz, Borut Mavrič, Jonas Mortelmans, Estefania Paredes, Anita Poćwierz-Kotus, Henning Reiss, Ioulia Santi, Georgia Sarafidou, Grigorios Skouradakis, Jostein Solbakken, Peter A U Staehr, Javier Tajadura, Jakob Thyrring, Jesus S Troncoso, Emmanouela Vernadou, Frederique Viard, Haris Zafeiropoulos, Małgorzata Zbawicka, Christina Pavloudi, Matthias Obst","doi":"10.1111/1755-0998.14073","DOIUrl":"https://doi.org/10.1111/1755-0998.14073","url":null,"abstract":"<p><p>Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document the biodiversity of complex communities over large spatio-temporal scales. We established an international Marine Biodiversity Observation Network (ARMS-MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard-bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018-2019 and retrieved in 2018-2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open-access data set (image, genetic and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to ~5500 amplicon sequence variants and ~1800 operational taxonomic units, and up to ~250 and ~50 species per observatory using the cytochrome c oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non-indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least 3-6 months during the main growth season to use resources as efficiently as possible and that post-sequencing curation is applied to enable statistical comparison of spatio-temporal entities. We suggest that ARMS should be used in biological monitoring programs and long-term ecological research and encourage the adoption of our ARMS-MBON protocols.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14073"},"PeriodicalIF":5.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Quantifying Bone Collagen Fingerprint Variation Between Species.
IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-29 DOI: 10.1111/1755-0998.14072
Andrew Baker, Michael Buckley

Collagen is the most ubiquitous protein in the animal kingdom and one of the most abundant proteins on Earth. Despite having a relatively repetitive amino acid sequence motif that enables its triple helical structure, in type 1 collagen, that dominates skin and bone, there is enough variation for its increasing use for the biomolecular species identification of animal tissues processed or degraded beyond the amenability of DNA-based analyses. In recent years, this has been most commonly achieved through the technique of collagen peptide mass fingerprinting (PMF) known as ZooMS (Zooarchaeology by Mass Spectrometry), applied to the analysis of tens of thousands of samples across over one hundred studies in the past decade alone. However, a robust means to quantify variation between these fingerprints remains elusive, despite being increasingly required due to the shift towards a wider range of wild fauna and those that are more distantly related from currently known sequences. This is particularly problematic in fish due to their greater sequence variation. Here we evaluate the quantification of the relative closeness of collagen fingerprints between families using ANOSIM and a modified SIMPER analysis, incorporating relative peak intensity. Our results show a clear correlation between sequence differentiation and statistical distance of PMFs, indicating that the additional complexity of type 1 collagen in fish could directly affect the efficacy of biomolecular techniques such as ZooMS. Furthermore, this multivariate statistical analysis demonstrates that PMFs in fish are substantively more distinct than those of mammalian or amphibian taxa.

{"title":"Quantifying Bone Collagen Fingerprint Variation Between Species.","authors":"Andrew Baker, Michael Buckley","doi":"10.1111/1755-0998.14072","DOIUrl":"https://doi.org/10.1111/1755-0998.14072","url":null,"abstract":"<p><p>Collagen is the most ubiquitous protein in the animal kingdom and one of the most abundant proteins on Earth. Despite having a relatively repetitive amino acid sequence motif that enables its triple helical structure, in type 1 collagen, that dominates skin and bone, there is enough variation for its increasing use for the biomolecular species identification of animal tissues processed or degraded beyond the amenability of DNA-based analyses. In recent years, this has been most commonly achieved through the technique of collagen peptide mass fingerprinting (PMF) known as ZooMS (Zooarchaeology by Mass Spectrometry), applied to the analysis of tens of thousands of samples across over one hundred studies in the past decade alone. However, a robust means to quantify variation between these fingerprints remains elusive, despite being increasingly required due to the shift towards a wider range of wild fauna and those that are more distantly related from currently known sequences. This is particularly problematic in fish due to their greater sequence variation. Here we evaluate the quantification of the relative closeness of collagen fingerprints between families using ANOSIM and a modified SIMPER analysis, incorporating relative peak intensity. Our results show a clear correlation between sequence differentiation and statistical distance of PMFs, indicating that the additional complexity of type 1 collagen in fish could directly affect the efficacy of biomolecular techniques such as ZooMS. Furthermore, this multivariate statistical analysis demonstrates that PMFs in fish are substantively more distinct than those of mammalian or amphibian taxa.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14072"},"PeriodicalIF":5.5,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Pangenomics Links Boll Weevil Divergence With Ancient Mesoamerican Cotton Cultivation 泛基因组学:棉铃象鼻虫分化与古代中美洲棉花种植
IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-22 DOI: 10.1111/1755-0998.14054
Zachary P. Cohen, Lindsey C. Perkin, Tyler J. Raszick, Sheina B. Sim, Scott M. Geib, Anna K. Childers, Gregory A. Sword, Charles P.-C. Suh

The boll weevil, Anthonomus grandis grandis Boheman, and thurberia weevil, Anthonomus grandis thurberiae Pierce, together comprise a species complex that ranges throughout Mexico, the southwestern regions of the United States and parts of South America. The boll weevil is a historically damaging and contemporaneously threatening pest to commercial upland cotton, Gossypium hirsutum L. (Malvales: Malvaceae), whereas the thurberia weevil is regarded as an innocuous non-pest subspecies that is mostly found on non-cultivated Thurber's or Arizona cotton, Gossypium thurberi L., throughout its native range in western Mexico and the southwestern United States. Recent independent analyses, using mitochondrial and whole-genome markers, have suggested the independent evolution of these lineages is more attributable to geographic isolation than biotic factors. We suggest a combination of drivers after employing comparative genomic, population genetic and pangenome methodologies to identify large and small polymorphisms. By leveraging genetic differences, we determined 39,310 diagnostic loci between the subspecies, find genes under selection, and model the subspecies' shared and unique evolutionary history. Interestingly, structural variations capture a large proportion of genes at the population level and demographic reconstruction suggests a split between approximately 3,320–16,300 before present (YBP), which coincides with cotton cultivation in Mesoamerica, approximately 3,000-5,000 YBP. Observed polymorphisms are enriched for reproductive, regulatory, and metabolic genes, which may be attributed to the subspecies split and coevolution with cultivated cotton. Our results demonstrate the utility of a holistic, comparative framework utilising small and large polymorphisms to reconstruct demography and identify genetic novelty via pangenomics.

棉铃象鼻虫(Anthonomus grandis grandis Boheman)和thurberiae象鼻虫(Anthonomus grandis thurberiae Pierce)共同构成了一个物种复合体,分布在整个墨西哥、美国西南部地区和南美洲部分地区。棉铃象鼻虫是一种历史上具有破坏性的害虫,同时也威胁着商业陆地棉花棉花(棉花科:棉花科),而thurberia象鼻虫则被认为是一种无害的非害虫亚种,主要存在于非栽培的Thurber's棉花或亚利桑那州棉花(Gossypium thurberi L.)上,其原产范围遍布墨西哥西部和美国西南部。最近使用线粒体和全基因组标记的独立分析表明,这些谱系的独立进化更多地归因于地理隔离,而不是生物因素。我们建议采用比较基因组学、群体遗传学和泛基因组学方法来确定大小多态性后的驱动因素组合。通过利用遗传差异,我们确定了亚种之间的39,310个诊断位点,找到了选择下的基因,并建立了亚种共享和独特的进化史模型。有趣的是,结构变异在种群水平上捕获了很大一部分基因,人口结构重建表明,大约在3320 - 16300年前(YBP)之间分裂,这与中美洲棉花种植的大约3000 - 5000 YBP相吻合。观察到的生殖、调控和代谢基因多态性丰富,这可能归因于亚种分裂和与栽培棉花的共同进化。我们的研究结果证明了利用小型和大型多态性来重建人口统计学和通过泛基因组学识别遗传新颖性的整体比较框架的效用。
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引用次数: 0
Exploring Environmental Microfungal Diversity Through Serial Single Cell Screening 通过连续单细胞筛选探索环境微真菌多样性。
IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-20 DOI: 10.1111/1755-0998.14055
Joana Mariz, Ali Nawaz, Yvonne Bösch, Christian Wurzbacher

Known for its remarkable diversity and ecological importance, the fungal kingdom remains largely unexplored. In fact, the number of unknown and undescribed fungi is predicted to exceed the number of known fungal species by far. Despite efforts to uncover these dark fungal taxa, we still face inherent sampling biases and methodological limitations. Here, we present a framework that combines taxonomic knowledge, molecular biology and data processing to explore the fungal biodiversity of enigmatic aquatic fungal lineages. Our work is based on serial screening of environmental fungal cells to approach unknown fungal taxa. Microscopic documentation is followed by DNA analysis of laser micro-dissected cells, coupled with a ribosomal operon barcoding step realised by long-read sequencing, followed by an optional whole genome sequencing step. We tested this approach on a range of aquatic fungal cells mostly belonging to the ecological group of aquatic hyphomycetes derived from environmental samples. From this initial screening, we were able to identify 60 potentially new fungal taxa in the target dataset. By extending this methodology to other fungal lineages associated with different habitats, we expect to increasingly characterise the molecular barcodes of dark fungal taxa in diverse environmental samples. This work offers a promising solution to the challenges posed by unknown and unculturable fungi and holds the potential to be applied to the diverse lineages of undescribed microeukaryotes.

真菌王国以其显著的多样性和生态重要性而闻名,但在很大程度上仍未被探索。事实上,未知和未描述的真菌的数量预计将远远超过已知真菌物种的数量。尽管努力揭示这些黑暗的真菌分类群,我们仍然面临固有的抽样偏差和方法的局限性。在这里,我们提出了一个框架,结合分类学知识,分子生物学和数据处理来探索神秘的水生真菌谱系的真菌多样性。我们的工作是基于环境真菌细胞的系列筛选,以接近未知的真菌分类群。显微记录之后是激光微解剖细胞的DNA分析,再加上通过长读测序实现的核糖体操纵子条形码步骤,然后是可选的全基因组测序步骤。我们在一系列水生真菌细胞上测试了这种方法,这些细胞大多属于来自环境样本的水生菌丝菌的生态组。从最初的筛选中,我们能够在目标数据集中确定60个潜在的新真菌分类群。通过将这种方法扩展到与不同栖息地相关的其他真菌谱系,我们期望在不同环境样品中越来越多地表征深色真菌分类群的分子条形码。这项工作为未知和不可培养真菌带来的挑战提供了一个有希望的解决方案,并有可能应用于未描述的微真核生物的不同谱系。
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引用次数: 0
Genomic and Methylomic Signatures Associated With the Maintenance of Genome Stability and Adaptive Evolution in Two Closely Allied Wolf Spiders. 两种亲缘关系密切的狼蛛基因组稳定性维持和适应性进化相关的基因组和甲基组特征。
IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-20 DOI: 10.1111/1755-0998.14071
Qing Zuo, Run-Biao Wu, Li-Na Sun, Tian-Yu Ren, Zheng Fan, Lu-Yu Wang, Bing Tan, Bin Luo, Muhammad Irfan, Qian Huang, Yan-Jun Shen, Zhi-Sheng Zhang

Pardosa spiders, belonging to the wolf spider family Lycosidae, play a vital role in maintaining the health of forest and agricultural ecosystems due to their function in pest control. This study presents chromosome-level genome assemblies for two allied Pardosa species, P. laura and P. agraria. Both species' genomes show a notable expansion of helitron transposable elements, which contributes to their large genome sizes. Methylome analysis indicates that P. laura has higher overall DNA methylation levels compared to P. agraria. DNA methylation may not only aids in transposable element-driven genome expansion but also positively affects the three-dimensional organisation of P. laura after transposon amplification, thereby potentially enhancing genome stability. Genes associated with hyper-differentially methylated regions in P. laura (compared to P. agraria) are enriched in functions related to mRNA processing and energy production. Furthermore, combined transcriptome and methylome profiling has uncovered a complex regulatory interplay between DNA methylation and gene expression, emphasising the important role of gene body methylation in the regulation of gene expression. Comparative genomic analysis shows a significant expansion of cuticle protein and detoxification-related gene families in P. laura, which may improve its adaptability to various habitats. This study provides essential genomic and methylomic insights, offering a deeper understanding of the relationship between transposable elements and genome stability, and illuminating the adaptive evolution and species differentiation among allied spiders.

狼蛛是狼蛛科的一种蜘蛛,具有防治害虫的功能,对维持森林和农业生态系统的健康起着至关重要的作用。本研究介绍了两种亲缘种紫穗槐(P. laura)和黑穗槐(P. agraria)的染色体水平基因组组装。这两个物种的基因组都显示出螺旋转座因子的显著扩展,这有助于它们的大基因组大小。甲基组分析表明,与黑麦相比,劳拉草具有更高的DNA甲基化水平。DNA甲基化不仅有助于转座子驱动的基因组扩增,而且还对转座子扩增后的劳拉p.l aora的三维组织产生积极影响,从而潜在地增强了基因组的稳定性。与小麦相比,劳拉草中与超差异甲基化区域相关的基因在mRNA加工和能量产生相关的功能中丰富。此外,结合转录组和甲基组分析揭示了DNA甲基化与基因表达之间复杂的调控相互作用,强调了基因体甲基化在基因表达调控中的重要作用。比较基因组分析显示,劳拉草中角质层蛋白和解毒相关基因家族显著扩增,这可能提高了其对各种生境的适应性。该研究提供了重要的基因组和甲基组学见解,为转座因子与基因组稳定性之间的关系提供了更深入的理解,并阐明了亲缘蜘蛛的适应进化和物种分化。
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引用次数: 0
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