Molecular Ecology Resources最新文献

Nematodes are among the most diverse animals, yet only around 28,000 of an estimated one million species have been morphologically described. Their small size, morphological simplicity, and cryptic diversity complicate phylogenetic analyses. Traditional morphological and single-locus molecular approaches often lack resolution for both recent and ancient divergences. To address these limitations, we developed the first ultraconserved elements (UCEs) probe sets for two nematode families: Panagrolaimidae, a group of non-model organisms with limited genomic resources when compared to model taxa, and Rhabditidae, which includes the model species Caenorhabditis elegans. Our probe sets targeted 1612 loci for Panagrolaimidae and 100,397 for Rhabditidae. In vitro testing recovered up to 1457 loci in Panagrolaimidae, supporting robust phylogenetic reconstruction. Results were largely consistent with previous analyses, except for one strain reclassified as Neocephalobus halophilus BSS8. Using machine learning, we determined the minimum number of loci needed for accurate genus-level classification. For Rhabditidae, XGBoost achieved high accuracy with just 46 loci. For Panagrolaimidae, 39 loci were most informative. Our UCE-based approach offers a scalable and cost-effective framework for phylogenomics, enhancing taxonomic resolution and evolutionary inference in nematodes. It is well suited for biodiversity assessments and shallow, field-based sequencing, expanding research possibilities across this ecologically important phylum.

Ancient DNA (aDNA) analysis of archaeological dental calculus has provided a wealth of insights into ancient health, demography and lifestyles. However, the workflow for ancient metagenomics is still evolving, raising concerns about reproducibility. Few systematic investigations have examined how DNA extraction methods and library preparation protocols influence ancient oral microbiome recovery, despite evidence from modern populations suggesting that they do. This leaves a gap in our understanding of how wet-lab protocols impact aDNA recovery from dental calculus. In this study, we apply two DNA extraction and two library preparation methods in the aDNA field on dental calculus samples from Hungary and Niger. Samples from each context have similar chronological ages, but differences in their levels of aDNA preservation are notable, providing additional insights into how the efficacy of wet-lab protocols is impacted by sample preservation. Several metrics were employed to assess intra- and inter-sample variability, such as DNA fragment length recovery, GC content, clonality, endogenous content, DNA deamination and microbial composition. Our findings indicate that both DNA extraction and library preparation protocols can considerably impact ancient DNA recovery from archaeological dental calculus. Furthermore, no single protocol consistently outperformed the others across all assessments, and the effectiveness of specific protocol combinations depended on the preservation of the sample. These findings highlight the challenges of meta-analyses and underscore the need to account for technical variability. Lastly, our study raises the question of whether the field should strive to standardise methods for comparability or optimise protocols based on sample preservation and specific research objectives.

Obligate biotrophic plant pathogens like the powdery mildew fungi commit to a closely dependent relationship with their plant hosts and have lost the ability to grow and reproduce independently. Thus, at present, these organisms are not amenable to in vitro cultivation, which is a prerequisite for effective genetic modification and functional molecular studies. Saprotrophic fungi of the family Arachnopezizaceae are the closest known extant relatives of the powdery mildew fungi and may hold great potential for studying genetic components of their obligate biotrophic lifestyle. Here, we established telomere-to-telomere genome assemblies for two representatives of this family, Arachnopeziza aurata and A. aurelia. Both species harbour haploid genomes that are composed of 16 chromosomes at a genome size of 43.1 and 46.3 million base pairs, respectively, which, in contrast to most powdery mildew genomes that are transposon-enriched, show a repeat content below 5% and signs of repeat-induced point mutation. Both species could be grown in liquid culture and on standard solid media and were sensitive to common fungicides such as hygromycin and fenhexamid. We successfully expressed a red fluorescent protein and hygromycin resistance in A. aurata following polyethylene glycol-mediated protoplast transformation, demonstrating that Arachnopeziza species are amenable to genetic alterations, which may be expanded to include gene replacement, gene modification, and gene complementation in the future. With this work, we established a potential model system that promises to sidestep the need for genetic modification of powdery mildew fungi by using Arachnopeziza species as a proxy to uncover the molecular functions of powdery mildew proteins.

Low-coverage sequencing (LCS) followed by genotype imputation has become a cost-efficient approach for obtaining whole-genome SNPs. Several imputation methods for LCS data have been developed over the last decade. However, comparisons of their accuracy in inferring missing genotypes and their effectiveness for downstream analysis such as population genetics have not been comprehensively studied. In the present study, we assessed the imputation performance of five different tools: GLIMPSE2, GeneImp, QUILT2, STITCH and Beagle5.4, using populations simulated by SLiM4 that represent different levels of genetic relatedness and inbreeding. Imputation accuracy was calculated at the level of variant, haplotype and sample. The effectiveness of using imputed genotypes in recovering genetic structure, relatedness, inbreeding coefficients and demographic history was subsequently evaluated. The imputation accuracy of different methods was further tested in a real population of 283 hihi (stitchbird) samples. Our results suggest a high accuracy of all the tested methods on populations with high levels of genetic relatedness. However, in populations with low relatedness, the imputation accuracy differed across different tools and impacted the results of some downstream analyses. The simulation and imputation pipeline presented here can help determine the most suitable imputation method for different population scenarios.

Arabica coffee (Coffea arabica) dominates global coffee production, accounting for over 60% of the world's coffee trade. The Mundo Novo cultivar, predominantly grown in Yunnan, China, represents a significant germplasm resource. However, the absence of a high-quality reference genome has hindered comprehensive genetic research and in-depth investigation of secondary metabolic pathways in Arabica. In this study, we present the first near telomere-to-telomere (T2T) genome assembly of Arabica, achieved through the integration of PacBio HiFi, Oxford Nanopore ultra-long, and Hi-C sequencing technologies, representing the highest-quality Arabica genome to date. Phylogenetic analysis of N-methyltransferases (NMTs), the key enzymes responsible for caffeine biosynthesis, revealed their independent evolution across caffeine-producing clades including coffee, cacao, and tea. Furthermore, GO enrichment analysis of expanded gene families at the Arabica ancestral node, combined with fruit-specific transcriptomic profiling, revealed that glycosyltransferases likely play a critical role in the secondary metabolism of Arabica. Notably, functional characterisation demonstrated that a UGT (uridine diphosphate glycosyltransferase, UGT) from the UGT29 subfamily, which exhibited increased gene copy number in the Arabica subgenome C than its ancestor, can directly convert Rebaudioside A (Reb A) into Rebaudioside M (Reb M) through a single-step enzymatic glycosylation. This direct pathway represents a crucial advancement over conventional multi-UGTs biosynthetic routes of Reb M, which is a highly desirable sweetener whereas with limited natural abundance. Taken together, this study not only provides a valuable genomic resource for studying the unique secondary metabolic processes in C. arabica but also accelerates innovative research frontiers for the synthetic biological production of the valuable sweetener Reb M.

Many studies have proposed various comparative genomic methods to probe the molecular basis for adaptive functional convergence between species, conventionally by detecting the convergence of amino acid states between orthologous protein sequences of these species or lineages. However, different amino acids with similar physicochemical properties at a site may contribute to the functional similarity of the protein. Hence, could the convergence of amino acid physicochemical properties, in addition to state convergence, also contribute to adaptive convergence of organismal functions? Here we grouped amino acids into physicochemically similar classes, and developed computational pipelines to detect the Convergence of Amino Acid Properties (CAAP, https://github.com/shanschen33/CAAP) by modifying previous state convergence detection methods. Investigating three organismal convergence cases including echolocating mammals, marine mammals and woody mangroves, we found genes with CAAP that likely contribute to the respective functional adaptation, supported by orthogonal evidence such as functional enrichment and positive selection analyses. Our findings in multiple cases corroborate the hypothesis that CAAP may underlie adaptive convergent evolution of organismal functions, emphasising the importance of considering sequence features more complex than amino acid states when studying adaptive sequence convergence.

DNA technologies have many advantages for biomonitoring and biodiversity analyses, but these depend on the availability of relevant reference DNA barcodes. To be most useful, a DNA barcode should be linked to a taxonomic name, which can in turn be connected to ecological information. This linking can be achieved by DNA barcoding of taxonomically identified specimens. Museums are a promising source of such specimens, but the DNA in museum specimens is often degraded, necessitating carefully optimised DNA extraction methods. In this issue of Molecular Ecology Resources, Holmquist et al. (2025) present a DNA extraction protocol for museum insect specimens, using in-house formulated Solid Phase Reversible Immobilisation (SPRI) beads. The authors carried out several experiments with statistical evaluation to determine optimal DNA extraction parameters, before testing the protocol on a large and diverse pool of museum-held insect specimens. The result is a low-cost and effective DNA extraction protocol for diverse museum insect specimens.

Insects are vitally important components of Earth's biodiversity, but monitoring these communities is challenging due to the huge diversity of species that exist. DNA sequencing technologies enable efficient molecular characterisation of insect diversity, but the resulting molecular taxonomic units are typically disconnected from species or functional information (Meier et al. 2024). This makes ecological insights difficult to achieve for wide swathes of biodiversity. Reference DNA barcodes from taxonomically identified species can bridge this gap (Kress et al. 2015), but the process of taxonomically identifying insect specimens is very difficult due to a scarcity of suitable taxonomic expertise. New workflows that combine machine learning with mass DNA barcoding of trapped insect samples have the potential to resolve this challenge over time (Meier et al. 2024). On the other hand, it is important to consider existing resources such as museum collections as sources of reference DNA barcodes.

Museums often hold rich collections of biological specimens, usually with taxonomic identifications, accumulated over long periods of time (Figure 1). In theory, these collections represent a compelling source of DNA barcodes (Raxworthy and Smith 2021). The DNA in museum specimens is often degraded due to specimen age and suboptimal preservation, however; this makes it difficult to recover DNA barcode sequences from some specimens (Hebert et al. 2013). Assembly of multiple shorter amplicons can be effective in cases where DNA fragmentation makes PCR amplification of standard barcode regions unfeasible (D'Ercole et al. 2021; Prosser et al. 2016), but this is more complex and costly than conventional DNA barcode generation. Therefore, it is important to develop optimal methods of DNA extraction from museum insect collections to