Molecular Ecology Resources最新文献

{"title":"Towards Large-Scale Museomics Projects: A Cost-Effective and High-Throughput Extraction Method for Obtaining Historical DNA From Museum Insect Specimens.","authors":"Anna Holmquist, Holly Tavris, Grace Kim, Lauren Esposito, Brian Fisher, Athena Lam","doi":"10.1111/1755-0998.14117","DOIUrl":"https://doi.org/10.1111/1755-0998.14117","url":null,"abstract":"<p><p>Natural history collections serve as invaluable repositories of biodiversity data. Large-scale genomic analysis would greatly expand the utility and accessibility of museum collections, but the high cost and time-intensive nature of genomic methods limit such projects, particularly for invertebrate specimens. This paper presents an innovative, cost-effective and high-throughput approach for extracting genomic DNA from diverse insect specimens using single-phase reverse immobilisation (SPRI) beads. We optimised PEG-8000 and NaCl concentrations to balance DNA yield and purity, reducing reagent cost to 4.0-11.6¢ per sample, cost dependent on sample type. Our method was validated against three widely used extraction protocols and showed comparable DNA yield and amplification success to the widely used Qiagen DNeasy kit. We successfully applied the protocol in a high-throughput manner, extracting DNA from 3786 insect specimens across a broad range of ages, taxonomies and tissue types. A detailed protocol and instructional video are provided to facilitate the adoption of the method by other researchers. By improving one of the most crucial steps in any molecular project, this SPRI bead-based DNA extraction approach has significant potential for enabling large-scale museomics projects, thereby increasing the utility of historical collections for biodiversity research and conservation efforts.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14117"},"PeriodicalIF":5.5,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959253","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}

{"title":"Beyond Presence and Absence: Using eDNA and Microsatellite Genotyping to Estimate Densities of Microscopic Life Forms in Wild Populations.","authors":"L M Liggan, K C Rolheiser, O Pontier, B Ramírez-Ibaceta, I Giménez, F Alberto","doi":"10.1111/1755-0998.14116","DOIUrl":"https://doi.org/10.1111/1755-0998.14116","url":null,"abstract":"<p><p>Many challenges arise when monitoring organisms with cryptic life-histories. For example, some cryptic life-stages are hard to identify or sample due to their microscopic nature, which creates unknowns surrounding an organism's population dynamics. Environmental DNA (eDNA) is a non-invasive sampling technique used to monitor cryptic species when traditional survey methods are challenging. Generally, eDNA has been used to quantify the presence/absence of species in various habitats. However, recent advances in high-throughput amplicon sequencing techniques have enabled researchers to detect intraspecific genetic diversity with eDNA. In this study, we present two complementary R packages that can be used to estimate the number of individuals in an eDNA sample. The first package (Amplicomsat) cleans high-throughput amplicon microsatellite sequences and counts the observed alleles identified in eDNA. Our second package (GenotypeQuant) then uses a numerical maximum likelihood estimator (NMLE) to estimate the number of contributors most likely to have produced the sequenced panel of microsatellite alleles amplified from eDNA. We first present simulations to characterise the accuracy and precision of the method. We then estimated densities of Nereocystis luetkeana (bull kelp) microscopic gametophytes from eDNA collected from an experiment with a manipulated number of gametophytes. Finally, we analysed benthic eDNA from kelp forest habitats. We found that gametophyte estimates produced by the NMLE varied within +3/-2 individuals when processing eDNA from rocks with 8 seeded gametophytes. We estimated 500 to 800 gametophytes·m^-2 densities in July, five or more months since spore germination and before the current year's spore release. Gametophyte abundance scaled with the sampling area and numbers were higher than total sporophyte densities.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14116"},"PeriodicalIF":5.5,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959940","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}

{"title":"EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes.","authors":"Guillaume Lentendu, David Singer, Sabine Agatha, Mohammad Bahram, S Emilia Hannula, Johannes Helder, Leho Tedersoo, Walter Traunspurger, Stefan Geisen, Enrique Lara","doi":"10.1111/1755-0998.14118","DOIUrl":"https://doi.org/10.1111/1755-0998.14118","url":null,"abstract":"<p><p>The soil eukaryome constitutes a significant portion of Earth's biodiversity that drives major ecosystem functions, such as controlling carbon fluxes and plant performance. Currently, however, we miss a standardised approach to functionally classify the soil eukaryome in a holistic way. Here we compiled EukFunc, the first functional reference database that characterises the most abundant and functionally important soil eukaryotic groups: fungi, nematodes and protists. We classified the 14,060 species in the database based on their mode of nutrient acquisition into the main functional classes of symbiotroph (40%), saprotroph (26%), phototroph (17%), predator (16%) and unknown (2%). EukFunc provides further detailed information about nutrition mode, including a secondary functional class (i.e., for organisms with multiple nutrition modes), and preyed or associated organisms for predatory or symbiotic taxa, respectively. EukFunc is available in multiple formats for user-friendly functional analyses of specific taxa or annotations of metabarcoding datasets, both embedded in the R package EukFunc. Using a soil dataset from alpine and subalpine meadows, we highlighted the extended ecological insights obtained from combining functional information across the entire soil eukaryome as compared to focusing on fungi, protists or nematodes individually. EukFunc streamlines the annotation process, enhances efficiency and accuracy, and facilitates the investigation of the functional roles of soil eukaryotes-a prerequisite to better understanding soil systems.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14118"},"PeriodicalIF":5.5,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958506","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}

{"title":"Performance of DNA Metabarcoding vs. Morphological Methods for Assessing Intertidal Turf and Foliose Algae Diversity.","authors":"Gabriela Borer, Cátia Monteiro, Fernando P Lima, Filipa M S Martins","doi":"10.1111/1755-0998.14115","DOIUrl":"https://doi.org/10.1111/1755-0998.14115","url":null,"abstract":"<p><p>Large biogeographical shifts in marine communities are taking place in response to climate change and biological invasions yet we still lack a full understanding of their diversity and distribution. An important example of this is turf and foliose algae that are key coastal primary producers in several regions and are expanding into new environments. Traditionally, monitoring turf and foliose algae communities involves species identification based on morphological traits, which is challenging due to their reduced dimensions and highly variable morphology. Molecular methods promise to revolutionise this field, but their effectiveness in detecting turf and foliose algae has yet to be tested. Here, we evaluate the performance of DNA metabarcoding (COI and rbcL markers) and morphological identification (in situ and photoquadrat) to describe intertidal turf and foliose algae communities along the Portuguese coast. Both molecular markers detected more taxa than the morphological methods and showed greater discrimination of turf and foliose algae communities between regions, matching our knowledge of the geographical and climatic patterns for the region. In sum, our multi-marker metabarcoding approach was more efficient than morphology-based methods in characterising turf and foliose algae communities along the Portuguese coast, differentiating morphologically similar species, and detecting unicellular organisms. However, certain taxa that were identified by in situ and photoquadrat approaches were not detected through metabarcoding, partly due to lack of reference barcodes or taxonomic resolution. Metabarcoding emerges as a valuable tool for monitoring these communities, particularly in long-term programmes requiring accuracy, speed, and reproducibility.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14115"},"PeriodicalIF":5.5,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143960983","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}

{"title":"A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies.","authors":"Philipp E Bayer, Adam Bennett, Georgia Nester, Shannon Corrigan, Eric J Raes, Madalyn Cooper, Marcelle E Ayad, Philip McVey, Anya Kardailsky, Jessica Pearce, Matthew W Fraser, Priscila Goncalves, Stephen Burnell, Sebastian Rauschert","doi":"10.1111/1755-0998.14107","DOIUrl":"https://doi.org/10.1111/1755-0998.14107","url":null,"abstract":"<p><p>Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic approaches are used for eDNA-based community composition analysis. Simulation studies and careful evaluation of taxonomic classifiers are essential to establish reliable benchmarks to improve the accuracy and reproducibility of eDNA-based findings. Here we present a comprehensive evaluation of nine taxonomic classifiers exploring three widely used mitochondrial markers (12S rDNA, 16S rDNA and COI) in Australian marine vertebrates. Curated reference databases and exclusion database tests were used to simulate diverse species compositions, including three positive control and two negative control datasets. Using these simulated datasets ranging from 36 to 302 marker genes, we were able to identify between 19% and 89% of marine vertebrate species using mitochondrial markers. We show that MMSeqs2 and Metabuli generally outperform BLAST with 10% and 11% higher F1 scores for 12S and 16S rDNA markers, respectively, and that Naive Bayes Classifiers such as Mothur outperform sequence-based classifiers except MMSeqs2 for COI markers by 11%. Database exclusion tests reveal that MMSeqs2 and BLAST are less susceptible to false positives compared to Kraken2 with default parameters. Based on these findings, we recommend that MMSeqs2 is used for taxonomic classification of marine vertebrates given its ability to improve species-level assignments while reducing the number of false positives. Our work contributes to the establishment of best practices in eDNA-based biodiversity analysis to ultimately increase the reliability of this monitoring tool in the context of marine vertebrate conservation.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14107"},"PeriodicalIF":5.5,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143953435","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}

{"title":"Optimization and Evaluation of the bestRAD Sequencing Approach: Towards Ascertainment of the Invasion Routes of the Oriental Fruit Fly, Bactrocera dorsalis.","authors":"Emeline Charbonnel, Laure Benoit, Sabine Nidelet, Enrique Ortega-Abboud, Bernhard Gschloessl, Raphaël Leblois, David Ouvrard, Marie-Pierre Chapuis","doi":"10.1111/1755-0998.14114","DOIUrl":"https://doi.org/10.1111/1755-0998.14114","url":null,"abstract":"<p><p>The bestRAD technique is a reduced genome representation approach with high-capacity sample multiplexing and physical isolation of biotin-labelled target DNA fragments using streptavidin beads, which should reduce total cost and genotyping errors. While we here formalise the relevance of this approach within the HTS landscape, our foremost aim was to improve its replicability, validity, and transparency. We first optimised the molecular laboratory protocol and shared the associated protocols (e.g., final detailed methodologies, quality control, best practices) under the FAIR principles. Using 84 worldwide individual samples of the Oriental fruit fly, Bactrocera dorsalis, a major invasive pest, we revealed a low rate of PCR duplicates, robustness to DNA quality and quantity, high genotype call rate, insignificant genotyping error rate, high nuclear and mitochondrial genome representativeness, and a high level of genetic information. This in-depth data quality assessment, along with total cost and handling time reduced by an estimated one-third relative to the parent RAD-Seq version, demonstrates that bestRAD is an excellent compromise between cost and quality. While we generated high-quality genomic resources for B. dorsalis, we also share details and recommendations for the bestRAD technique that can be readily used in any laboratory and applied to all organisms, even without published genome sequence.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14114"},"PeriodicalIF":5.5,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959099","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}

{"title":"Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals.","authors":"Kuldeep D More, Ophélie Lebrasseur, Jaime Lira Garrido, Andaine Seguin-Orlando, Emmanuel Discamps, Oscar Estrada, Laure Tonasso-Calvière, Loreleï Chauvey, Gaëtan Tressières, Stéphanie Schiavinato, Morgane Gibert, Horacio Padula, Horacio Chiavazza, Pablo M Fernández, Nicolás M Guardia, Caroline Borges, Stéphane Bertani, Juan Contreras-Mancilla, Diana Allccarima-Crisóstomo, Miguel Fhon, Eric Barrey, Léa Charliquart, Emilie Robbe, Thibault de Noblet, Rinat Zhumatayev, Samat Shakenov, Emmanuelle Vila, Rémi Berthon, Marjan Mashkour, Roya Khazaeli, Ahmad Nikgoftar, Ali A Vahdati, Pavel Kosintsev, Jean-Luc Houle, Jamsranjav Bayarsaikhan, Jaroslaw Wilczynski, Magdalena Moskal-Del Hoyo, Marek Nowak, William Taylor, Adrian Bălășescu, Roxana Dobrescu, Norbert Benecke, Benjamin Arbuckle, Sharon Steadman, Gregory McMahon, Petra Rajić Šikanjić, Marcel Buric, Tajana Trbojević Vukičević, Nadir Alvarez, Jean-Christophe Castel, Myriam Boudadi-Maligne, Bastiaan Star, Julian Robert Post-Melbye, Christian Løchsen Rødsrud, David W G Stanton, Sophy Charlton, Victoria E Mullin, Kevin G Daly, Nohemi Sala Burgos, Adrian Pablos, Love Dalen, Daniel G Bradley, Laurent Frantz, Greger Larson, Ludovic Orlando","doi":"10.1111/1755-0998.14112","DOIUrl":"https://doi.org/10.1111/1755-0998.14112","url":null,"abstract":"<p><p>In the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct the history of animal domestication. However, osteological assemblages of key archaeological contexts are not always available or do not necessarily preserve enough ancient DNA for a cost-effective genetic analysis. Here, we develop an in-solution target-enrichment approach, based on 80-mer species-specific RNA probes (ranging from 306 to 1686 per species) to characterise (in single experiments) the mitochondrial genetic variation from eight domesticated animal species of major economic interest: cattle, chickens, dogs, donkeys, goats, horses, pigs and sheep. We also illustrate how our design can be adapted to enrich DNA library content and map the Y-chromosomal diversity within Equus caballus. By applying our target-enrichment assay to an extensive panel of ancient osteological remains, farm soil, and cave sediments spanning the last 43 kyrs, we demonstrate that minimal sequencing efforts are necessary to exhaust the DNA library complexity and to characterise mitogenomes to an average depth-of-coverage of 19.4 to 2003.7-fold. Our assay further retrieved horse mitogenome and Y-chromosome data from Late Pleistocene coprolites, as well as bona fide mitochondrial sequences from species that were not part of the probe design, such as bison and cave hyena. Our methodology will prove especially useful to minimise costs related to the genetic analyses of maternal and paternal lineages of a wide range of domesticated and wild animal species, and for mapping their diversity changes over space and time, including from environmental samples.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14112"},"PeriodicalIF":5.5,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810160","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}

{"title":"Leveraging Synteny to Generate Reference Genomes for Conservation: Assembling the Genomes of Hector's and Māui Dolphins.","authors":"S Alvarez-Costes, C S Baker, R Constantine, E L Carroll, J Guhlin, L Dutoit, S Ferreira, D Heimeier, N J Gemmell, J Gillum, R M Hamner, W Rayment, W Roe, B Te Aikā, L Urban, A Alexander","doi":"10.1111/1755-0998.14109","DOIUrl":"https://doi.org/10.1111/1755-0998.14109","url":null,"abstract":"<p><p>Escalating concern regarding the impacts of reduced genetic diversity on the conservation of endangered species has spurred efforts to obtain chromosome-level genomes through consortia such as the Vertebrate Genomes Project. However, assembling reference genomes for many threatened species remains challenging due to difficulties obtaining optimal input samples (e.g., fresh tissue, cell lines) that can characterise long-term conservation collections. Here, we present a pipeline that leverages genome synteny to construct high-quality genomes for species of conservation concern despite less-than-optimal samples and/or sequencing data, demonstrating its use on Hector's and Māui dolphins. These endemic New Zealand dolphins are threatened by human activities due to their coastal habitat and small population sizes. Hector's dolphins are classified as endangered by the IUCN, while the Māui dolphin is among the most critically endangered marine mammals. To assemble reference genomes for these dolphins, we created a pipeline combining de novo assembly tools with reference-guided techniques, utilising chromosome-level genomes of closely related species. The pipeline assembled highly contiguous chromosome-level genomes (scaffold N50: 110 MB, scaffold L50: 9, miniBUSCO completeness scores > 96.35%), despite non-optimal input tissue samples. We demonstrate that these genomes can provide insights relevant for conservation, including historical demography revealing long-term small population sizes, with subspecies divergence occurring ~20 kya, potentially linked to the Last Glacial Maximum. Māui dolphin heterozygosity was 40% lower than Hector's and comparable to other cetacean species noted for reduced genetic diversity. Through these exemplar genomes, we demonstrate that our pipeline can provide high-quality genomic resources to facilitate ongoing conservation genomics research.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14109"},"PeriodicalIF":5.5,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778690","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}

{"title":"CCS-Consensuser: A Haplotype-Aware Consensus Generator for PacBio Amplicon Sequences.","authors":"Carlos Congrains, Forest Bremer, Julian R Dupuis, Norman B Barr, Ivonne J Garzón-Orduña, Daniel Rubinoff, Camiel Doorenweerd, Michael San Jose, Kimberley Morris, Angela Kauwe, Scott Geib","doi":"10.1111/1755-0998.14113","DOIUrl":"https://doi.org/10.1111/1755-0998.14113","url":null,"abstract":"<p><p>DNA sequencing technology has undergone substantial improvements in recent years, to the extent that Third Generation Sequencing platforms are capable of massively generating long-reads. Amplicon sequencing has been among the most popular techniques due to its wide application in diverse fields of biological sciences. However, there is a lack of software specifically designed to analyse intra-individual genetic variation using amplicon long-read data. Here, we present CCS-consensuser, an end-to-end pipeline that generates consensus sequences from amplicon sequencing using high-fidelity reads produced by PacBio circular consensus sequencing (CCS). We evaluated the concordance of the results produced using CCS + CCS-consensuser and other sequencing platforms (Illumina and Sanger), as well as accuracy using a simulated dataset. This assessment showed that CCS amplicon data coupled with CCS-consensuser can produce high-quality sequences (PHRED > 30). The pipeline resulted in high proportions of identical sequence bins for real data, achieving up to 94.94% concordance with COI Sanger sequences and 92.61% with nuclear loci Illumina sequences (considering heterozygous loci), and 95.55% with a fully phased nuclear simulated dataset. Furthermore, our pipeline can be used to detect heteroplasmy in mtDNA, cross-contamination, resolve the phase of nuclear genes in diploid organisms, and conceivably for multi-copy gene systems such as rDNA. These results not only support its potential for application in studies using haploid data such as DNA barcoding, but also demonstrate its unique capacity to explore within individual haplotype variation. Therefore, our strategy shows promise for a broad range of applications in biology and medicine that have been challenging to assess using traditional techniques.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14113"},"PeriodicalIF":5.5,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778677","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}

{"title":"Chromosome-Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution.","authors":"Tzi-Yuan Wang, Yu-Wei Wu, Hao-Jun Lu, Te-Yu Liao, Jui-Hung Tai, Shih-Pin Huang, Feng-Yu Wang, Tsung-Han Yu, Chau-Ti Ting, Shu-Miaw Chaw, Hurng-Yi Wang","doi":"10.1111/1755-0998.14110","DOIUrl":"https://doi.org/10.1111/1755-0998.14110","url":null,"abstract":"<p><p>The percomorph fish clade Gobioidei is a suborder that comprises over 2200 species distributed in nearly all aquatic habitats. To understand the genetics underlying their species diversification, we sequenced and annotated the genome of the loach goby, Rhyacichthys aspro, an early-diverging group, and compared it with nine additional Gobioidei species. Within Gobioidei, the loach goby possesses the smallest genome at 594 Mb, and a rise in species diversity from early-diverging to more recently diverged lineages is mirrored by enlarged genomes and a higher presence of transposable elements (TEs), particularly DNA transposons. These DNA transposons are enriched in genic and regulatory regions and their copy number increase is strongly correlated with substitution rate, suggesting that DNA repair after transposon excision/insertion leads to nearby mutations. Consequently, the proliferation of DNA transposons might be the crucial driver of Gobioidei diversification and adaptability. The loach goby genome also points to mechanisms of ecological adaptation. It contains relatively few genes for lateral line development but an overrepresentation of synaptic function genes, with genes putatively under selection linked to synapse organisation and calcium signalling, implicating a sensory system distinct from other Gobioidei species. We also see an overabundance of genes involved in neurocranium development and renal function, adaptations likely connected to its flat morphology suited for strong currents and an amphidromous life cycle. Comparative analyses with hill-stream loaches and the European eel reveal convergent adaptations in body shape and saltwater balance. These findings shed new light on the loach goby's survival mechanisms and the broader evolutionary trends within Gobioidei.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14110"},"PeriodicalIF":5.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762458","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}