Species Complex Research Articles

The Micacocidin Production-Related RSc1806 Deletion Alters the Quorum Sensing-Dependent Gene Regulation of Ralstonia pseudosolanacearum Strain OE1-1.

The soil-borne phytopathogenic gram-negative bacterium Ralstonia solanacearum species complex (RSSC) produces staphyloferrin B and micacocidin as siderophores that scavenge for trivalent iron (Fe3+) in the environment, depending on the intracellular divalent iron (Fe2+) concentration. The staphyloferrin B-deficient mutant reportedly retains its virulence, but the relationship between micacocidin and virulence remains unconfirmed. To elucidate the effect of micacocidin on RSSC virulence, we generated the micacocidin productivity-deficient mutant (ΔRSc1806) that lacks RSc1806, which encodes a putative polyketide synthase/non-ribosomal peptide synthetase, using the RSSC phylotype I Ralstonia pseudosolanacearum strain OE1-1. When incubated in the condition without Fe2+, ΔRSc1806 showed significantly lower Fe3+-scavenging activity, compared with OE1-1. Until 8 days after inoculation on tomato plants, ΔRSc1806 was not virulent, similar to the mutant (ΔphcA) missing phcA, which encodes the LysR-type transcriptional regulator PhcA that regulates the expression of the genes responsible for quorum sensing (QS)-dependent phenotypes including virulence. The transcriptome analysis revealed that RSc1806 deletion significantly altered the expression of more than 80% of the PhcA-regulated genes in the mutant grown in medium with or without Fe2+. Among the PhcA-regulated genes, the transcript levels of the genes whose expression was affected by the deletion of RSc1806 were strongly and positively correlated between the ΔRSc1806 and the phcA-deletion mutant. Furthermore, the deletion of RSc1806 significantly modified QS-dependent phenotypes, similar to the effects of the deletion of phcA. Collectively, our findings suggest that the deletion of micacocidin production-related RSc1806 alters the regulation of PhcA-regulated genes responsible for QS-dependent phenotypes including virulence as well as Fe3+-scavenging activity. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The ManhattAnt: identification, distribution, and colony structure of a new pest in New York City, Lasius emarginatus

AbstractAn unidentified ant species was discovered in the heart of New York City in 2011, which garnered national headlines and created the memorable nickname “ManhattAnt.” New York City is one of the oldest and largest cities in North America and has been the site of introduction for some of North America’s most damaging invasive pests. Nevertheless, there has been little follow up research on the ManhattAnt since its discovery, and it has yet to be formally identified. Here we use genetic and morphological approaches to confirm the identity of the ManhattAnt and characterize its introduced range and colony structure. Results from genetic analyses placed the ManhattAnt within the Lasius emarginatus species complex, and morphological comparisons ruled out closely related species to identify the ManhattAnt as the European ant L. emarginatus with 93–99% certainty depending on the nest sample. Since its initial discovery in the region, the ManhattAnt has become one of the most common ants in New York City and has spread at a rate of 2 km/yr into New Jersey and onto Long Island. Based on the climate it inhabits within its native range, L. emarginatus could expand to cover much of the eastern United states from Massachusetts to Georgia. Although many successful invasive ants display supercoloniality with little aggression between neighboring nests, we found no evidence that L. emarginatus colonies in New York City are supercolonial. Continued monitoring of L. emarginatus is warranted, as it has been increasingly reported as an indoor pest and is known to form mutualisms with honeydew producing pests of street trees.

Diversity and Abundance of Butterfly Species Complex in Two Diverse Habitats of Jawaharlal Nehru Krishi Vishwavidyalaya, India

Butterflies are important bio-indicators that should be protected to conserve the biodiversity and environment. They play an important role in the food chain and are valuable pollinators in the local environment. The present study investigated and compared the butterfly abundance and diversity within two different habitats (i) Undisturbed and (ii) Disturbed, in Jawaharlal Nehru Krishi Vishwavidyalaya Campus, Jabalpur Madhya Pradesh. A total of 24 butterfly species were recorded during the study from June 2022 to July 2023 using transects with the aid of sweep nets. An overall total of 2537 butterflies were recorded, which spread across 05 families 17 genera and 23 species. The most abundant family of butterflies caught in undisturbed ecosystems was Pieridae 38% followed by Nymphalidae 27%, Lycaenidae 14%, Papilionidae and Hesperiidae 7%. In disturbed ecosystems butterflies were distributed as Pieridae being dominated with 52% followed by Lycaenidae at 22%, Nymphalidae at 16%, Hesperiidae at 7% and Papilionidae at 3%. The undisturbed habitat was more diversified (H’-1.59) in butterfly diversity than the disturbed habitat (H’- 1.20).

Identification and pathogenicity of Clonostachys spp. and its co‐inoculation with Fusarium species on soybean root

AbstractSoybean is an important protein and oil crop around the world, widely cultivated in Heilongjiang province, China. In the summer of 2021, soybean root rot samples were collected from farms in multiple regions of Heilongjiang province to isolate pathogens. Twenty‐seven fungal isolates with similar morphology were found, causing soybean root discolouration and blackness leading to root rot, but which had relatively mild pathogenicity, with an average disease index of 13.69–32.25. Morphological features and multilocus phylogenetic analyses divided these isolates into four species: Clonostachys rosea (48.2%), C. rosea f. sp. rosea (14.8%), C. chloroleuca (29.6%) and Clonostachys sp. (7.4%). Co‐inoculation of these four species with two important pathogenic Fusarium species that can cause soybean root rot, F. annulatum and Fusarium sp. 1 in the Fusarium oxysporum species complex (FOSC), showed that C. rosea and Clonostachys sp. significantly reduced the pathogenicity of F. annulatum to soybean root, while C. rosea f. sp. rosea and C. chloroleuca slightly increased the pathogenicity of F. annulatum. C. rosea, Clonostachys sp., C. chloroleuca and C. rosea f. sp. rosea slightly reduced the pathogenicity of Fusarium sp. 1 in the FOSC. Our research is the first to report Clonostachys sp., C. chloroleuca and C. rosea f. sp. rosea causing soybean root rot in Heilongjiang province, China, and that these four Clonostachys species can affect the pathogenicity of Fusarium species, alleviating or aggravating soybean root rot. The findings of this study provide new insights into exploring the interactions between pathogens and thus effectively controlling them.

Substitution mapping of yield‐related traits utilizing three Cybonnet rice × wild introgression libraries

AbstractImproving rice (Oryza sativa L.) yields is a major objective of breeding programs worldwide. The Oryza rufipogon species complex (ORSC), which includes the rice ancestral species O. rufipogon Griff. and O. nivara S. D. Sharma & Shastry, is an underutilized resource. Using three phenotypically and genotypically diverse ORSC accessions identified as OrA, OrB, and OrC, three Cybonnet × ORSC chromosome segment substitution line (CSSL) libraries were developed to make this genepool more accessible to breeders. The objective was to characterize these libraries for 20 yield‐related traits to discover genes not currently deployed for rice improvement. Cybonnet and 212 CSSLs from these libraries were evaluated for 2 years in field studies for six agronomic, six panicle architecture, and eight seed traits. Across the three libraries, 62 CSSLs were found to be significantly different from Cybonnet for one or more traits. Of these, 27 CSSLs were significantly different for seed size traits. To ascertain the chromosome region and underlying candidate gene(s) causing these differences, substitution mapping was performed with previously reported genotypes. Mapping with the CSSLs, which had delayed heading under long days, revealed five known genes associated with rice flowering time pathways. The OsMADS50, RFT1, HD3A, SE1, and GHD7 genes were mapped in the OrB and OrC derived CSSLs but only OsMADS50 mapped in the OrA derived CSSLs. Employing this approach for the other 19 traits revealed 28 total candidate genes. A total of 12 of these genes are currently not deployed for yield enhancement. The introgressed ORSC regions associated with these genes are potential sources of novel variation for rice improvement.

Core genome multilocus sequence typing (cgMLST) applicable to the monophyletic Klebsiella oxytoca species complex.

The environmental bacterium Klebsiella oxytoca displays an alarming increase of antibiotic-resistant strains that frequently cause outbreaks in intensive care units. Due to its prevalence in the environment and opportunistic presence in humans, molecular surveillance (including resistance marker screening) and high-resolution cluster analysis are of high relevance. Furthermore, K. oxytoca previously described in studies is rather a species complex (KoSC) than a single species comprising at least six closely related species that are not easily differentiated by standard typing methods. To reach a discriminatory power high enough to identify and resolve clusters within these species, whole genome sequencing is necessary. The resolution is achievable with core genome multilocus sequence typing (cgMLST) extending typing of a few housekeeping genes to thousands of core genome genes. CgMLST is highly standardized and provides a nomenclature enabling cross laboratory reproducibility and data exchange for routine diagnostics. Here, we established a cgMLST scheme not only capable of resolving the KoSC species but also producing reliable and consistent results for published outbreaks. Our cgMLST scheme consists of 2,536 core genome and 2,693 accessory genome targets, with a percentage of good cgMLST targets of 98.31% in 880 KoSC genomes downloaded from the National Center for Biotechnology Information (NCBI). We also validated resistance markers against known resistance gene patterns and successfully linked genetic results to phenotypically confirmed toxic strains carrying the til gene cluster. In conclusion, our novel cgMLST enables highly reproducible typing of four different clinically relevant species of the KoSC and thus facilitates molecular surveillance and cluster investigations.

Taxonomy of the Cryptopygus complex. IV. Cyclomorphosis in three species of Appendisotoma and description of a new species from Kazakhstan (Collembola, Isotomidae)

Appendisotoma bisetosa Martynova, 1970, A. stebayevae (Grinbergs, 1962) and A. sibirica Stebayeva, 1985 are redescribed based on the material from Palaearctic region. Seasonal cyclomorphosis of the three species is distinguished. The winter form is armed with apical lobe on dens, chitinized furca and larger ocelli. Tenaculum, tenent hairs, and pigmentation can also be affected by cyclomorphosis. Dimorphism of species of Appendisotoma resembles that of several species of Proisotoma s. str. Appendisotoma monomorpha sp. nov. is described from Kazakhstan, taxonomic remarks are given to A. absoloni Rusek, 1966 and A. abiskoensis (Agrell, 1939).

Circadian regulation of macromolecular complex turnover and proteome renewal.

Although costly to maintain, protein homeostasis is indispensable for normal cellular function and long-term health. In mammalian cells and tissues, daily variation in global protein synthesis has been observed, but its utility and consequences for proteome integrity are not fully understood. Using several different pulse-labelling strategies, here we gain direct insight into the relationship between protein synthesis and abundance proteome-wide. We show that protein degradation varies in-phase with protein synthesis, facilitating rhythms in turnover rather than abundance. This results in daily consolidation of proteome renewal whilst minimising changes in composition. Coupled rhythms in synthesis and turnover are especially salient to the assembly of macromolecular protein complexes, particularly the ribosome, the most abundant species of complex in the cell. Daily turnover and proteasomal degradation rhythms render cells and mice more sensitive to proteotoxic stress at specific times of day, potentially contributing to daily rhythms in the efficacy of proteasomal inhibitors against cancer. Our findings suggest that circadian rhythms function to minimise the bioenergetic cost of protein homeostasis through temporal consolidation of protein turnover.

Cryptic or underworked? Taxonomic revision of the Antistrophus rufus species complex (Cynipoidea, Aulacideini)

Cryptic species present challenges across many subdisciplines of biology. Not all “cryptic” species, however, are truly cryptic; many are simply underexplored morphologically. We examined this idea for the Antistrophus rufus species complex, which previously contained three species thought to be morphologically cryptic. To determine whether the A. rufus complex are truly cryptic species, we assessed species boundaries of members of the A. rufus species complex using morphological, ecological, and DNA barcode data, and tested whether a set of 50 morphological characters could adequately diagnose these species. We revealed that this complex includes five species, and that there are useful phenotypic diagnostic characters for all members of this species complex. This enabled redescription of four species and the description of Antistrophus laurenae Nastasi, sp. nov., which induces externally inconspicuous galls in stems of Silphium integrifolium Michx., a host not associated with other members of the complex. We use these new diagnostic characters to construct a key to the five species of the rufus complex. We conclude that the A. rufus complex was not a true case of cryptic species. Our Bayesian analysis of DNA barcode data suggests possible cospeciation of members of the rufus complex and their Silphium host plants, but further study is necessary to better understand the evolution of host use in the lineage.

Whole-genome screening for near-diagnostic genetic markers for four western European white oak species identification

Key messageMining genome-wide DNA sequences enabled the discovery of near-diagnostic markers for species assignment in four European white oaks (Quercus petraea (Matt.) Liebl., Quercus pubescens Willd., Quercus pyrenaica Willd., and Quercus robur L.) despite their low interspecific differentiation. Near-diagnostic markers are almost fully fixed in one species and absent in the three others. As a result, only a handful of markers are needed for species identification, making this genetic assay a very promising operational taxonomic assignment procedure in research and forestry.ContextIdentifying species in the European white oak complex has been a long-standing concern in taxonomy, evolution, forest research, and management. Quercus petraea (Matt.) Liebl., Q. robur L., Q. pubescens Willd., and Q. pyrenaica Willd. are part of this species complex in western temperate Europe and hybridize in mixed stands, challenging species identification.AimsOur aim was to identify near-diagnostic single-nucleotide polymorphisms (SNPs) for each of the four species that are suitable for routine use and rapid diagnosis in research and applied forestry.MethodsWe first scanned existing whole-genome and target-capture data sets in a reduced number of samples (training set) to identify candidate diagnostic SNPs, i.e., genomic positions being characterized by a reference allele in one species and by the alternative allele in all other species. Allele frequencies of the candidates SNPs were then explored in a larger, range-wide sample of populations in each species (validation step).ResultsWe found a subset of 38 SNPs (10 for Q. petraea, 7 for Q. pubescens, 9 for Q. pyrenaica, and 12 for Q. robur) that showed near-diagnostic features across their species distribution ranges with Q. pyrenaica and Q. pubescens exhibiting the highest (0.876) and lowest (0.747) diagnosticity, respectively.ConclusionsWe provide a new, efficient, and reliable molecular tool for the identification of the species Q. petraea, Q. robur, Q. pubescens, and Q. pyrenaica, which can be used as a routine tool in forest research and management. This study highlights the resolution offered by whole-genome sequencing data to design near-diagnostic marker sets for taxonomic assignment, even for species complexes with relatively low differentiation.

Interrelationships and Taxonomic Status of some Species of <I>Solanum nigrum</I> Complex

Biosystematic studies have been carried out on some species of the Solanum nigrum complex, viz., diploid S. nigrum, S. nadiflorum, tetraploid S. nigrum, S. luteum and S. villosum. A comparison of fruit colour and chromosome number of the taxa divides them into two groups. Diploid S. nigrum and S. nodiflorum have shiny bluish black fruits and n = 12 chromosomes. In tetraploid S. nigrum the fruits are orange red while in S. luteum and S. villosum the fruits are yellow and the chromosome number in all the three taxa is n = 24. Meiosis was normal in all the species. The close relationship between diploid S. nigrum and S. nodiflorum, and among the species tetraploid S. nigrum, S. luteumand villosum has been confirmed by cytogenetical studies and statistical comparison of mean values of morphological characters.In the light of the foregoing studies a taxonomic revision of the species studied is suggested.

Diversity, Prevalence and Virulence of Colletotrichum Species Causing Anthracnose on Cassava Leaves in the Northern Region of Brazil

Cassava (Manihot esculenta Crantz) is a staple crop widely cultivated by small farmers in tropical countries. However, despite the low level of technology required for its management, it can be affected by several diseases, with anthracnose as the main threat. There is little information about the main species of Colletotrichum that infect cassava in Brazil. Thus, the objective of this work was to study the diversity, prevalence and virulence of Colletotrichum species that cause anthracnose in cassava leaves in northern Brazil. Twenty municipalities of the Pará and Tocantins states were selected, and leaves with symptoms were collected in those locations. Pure cultures were isolated in the laboratory. Species were identified using phylogenetic analyses of multiple loci, and their pathogenicity, aggressivity and virulence levels were assessed. Our results showed the greatest diversity of Colletotrichum associated with anthracnose in cassava plants of the “Formosa” cultivar in the Tocantins and Pará states. We determined the presence of Colletotrichum chrysophilum, C. truncatum, C. siamense, C. fructicola, C. plurivorum, C. musicola and C. karsti, with C. chrysophilum as the most aggressive and virulent. Our findings provide accurate identifications of species of Colletotrichum causing anthracnose in cassava crops, which are of great relevance for cassava breeding programs (e.g., the search for genotypes with polygenic resistance since the pathogen is so diverse) and for developing anthracnose management strategies that can work efficiently against species complexes of Colletotrichum.

Ecological correlates of population genetics in Linum suffruticosum, an heterostylous polyploid and taxonomic complex endemic to the western Mediterranean Basin

Abstract Linum suffruticosum s.l. is a taxonomic complex widespread in the western Mediterranean basin. The complex is characterized by a high phenotypic and cytogenetic diversity, and by a unique three-dimensional heterostyly system that makes it an obligate outcrosser. We studied the patterns of genetic diversity and structure of populations throughout the entire distribution of L. suffruticosum s.l. with microsatellite markers. We analyzed their relationships with various biological and ecological variables, including the morph ratio and sex organ reciprocity of populations measured with a novel multi-dimensional method. Populations consistently showed an approximate 1:1 morph ratio with high sex organ reciprocity and high genetic diversity. We found high genetic differentiation of populations, showing a pattern of isolation by distance. The Rif mountains in NW Africa were the most important genetic barrier. The taxonomic treatment within the group was not related to the genetic differentiation of populations, but to their environmental differentiation. Genetic diversity was unrelated to latitude, elevation, population size, niche suitability or breeding system. However, there was a clear influence of ploidy level on the genetic diversity of populations, and a seeming center-periphery pattern in its distribution. Our results suggest that polyploidization events, high outcrossing rates, isolation by distance and important geographical barriers to gene flow have played major roles in the microevolutionary history of this species complex.

Apple Bitter Rot and Glomerella Leaf Spot: A Comprehensive Review of Causal Species and Their Biology, Fungicide Sensitivities, and Management Strategies.

Bitter rot and Glomerella leaf spot (GLS) are two distinct diseases of apple fruit and foliage caused by members of the ascomycete fungal genus Colletotrichum. While GLS is restricted to subtropical and in some areas to temperate climates, bitter rot is responsible for significant yield loss worldwide, particularly during the post-harvest period. Initially thought to be caused by just two species of Colletotrichum, C. acutatum and C. gloeosporioides, advances in molecular biology and sequencing techniques enabled the identification of 25 different species capable of causing bitter rot and/or GLS of apple belongs to the C. gloeosporioides species complex (CGSC), C. acutatum species complex (CASC) and C. boninense species complex (CBSC). Three species (C. gloeosporioides, C. fructicola, and C. chrysophilum) of CGSC cause both bitter rot and GLS, 18 species (6 of CGSC and 12 of CASC) only cause bitter rot, and four species (C. aenigma and C. asianum of CGSC, C. limetticola of CASC and C. karstii of CBSC) only cause GLS. These species were found to differ in their geographical distribution, environmental and host tissue preference, pathogenicity, and fungicide sensitivities. In this review, we summarize the distribution, life cycle, and pathogenicity mechanisms of all currently known Colletotrichum species responsible for bitter rot and GLS of apple. Furthermore, we describe known apple defense mechanisms and management strategies for the control of these economically significant pathogens and identify gaps in our present understanding for future research.

Death simulation behavior of the lizard Lygodactylus klugei of the Gekkonidae (Reptilia: Squamata) family in northeastern Brazil

Natural selection favors primary defense strategies that reduce the chance of prey being spotted and discovered by a potential predator, such as camouflage, aposematism, and secondary defense strategies that include tail loss and escape, immobility, and thanatosis. The behavior of thanatosis (playing dead) or tonic immobility (body paralysis) is a strategy adopted by the prey, in which the animal simulates immobility to avoid being ingested. This simulation is effective against visually oriented predators or predators that do not feed on dead prey. Belonging to a complex of cryptic species, Lygodactylus klugei is a gecko that has a wide distribution in Northeast Brazil, occupying areas of the Caatinga and Cerrado, and that has a diurnal habit. On August 25th and September 2nd, 2021, three individuals of L. klugei were observed exhibiting thanatosis behavior during plant suppression work in the Curaçá municipality, Bahia state, Brazil. This behavior is reported for the first time in for L. klugei, and the species may use it if it is unable to escape from visually oriented predators. However, we suggest that future observations may generate new hypotheses about the benefits of this behavior in the species. Our observation adds important data to the behavioral repertoire of lizards from the Gekkonidae family, providing important natural history data to try to understand the defense mechanisms adopted by lizards in general.

Patterns of genomic variation reveal a single evolutionary origin of the wild allotetraploid Mimulus sookensis.

Polyploidy occurs across the tree of life and is especially common in plants. Because newly formed cytotypes are often incompatible with their progenitors, polyploidy is also said to trigger "instantaneous" speciation. If a polyploid can self-fertilize or reproduce asexually, it is even possible for one individual to produce an entirely new lineage, but how often this scenario occurs is unclear. Here, we investigate the evolutionary history of the wild allotetraploid Mimulus sookensis, which was formed through hybridization between self-compatible, diploid species in the Mimulus guttatus complex. We generate a chromosome-scale reference assembly for M. sookensis and define its distinct subgenomes. Despite previous reports suggesting multiple origins of this highly selfing polyploid, we discover patterns of population genomic variation that provide unambiguous support for a single origin. One M. sookensis subgenome is clearly derived from the selfer M. nasutus, which organellar variation suggests is the maternal progenitor. The ancestor of the other subgenome is less certain, but it shares variation with both M. decorus and M. guttatus, two outcrossing diploids with geographic ranges that overlap broadly with M. sookensis. This study establishes M. sookensis as an example of instantaneous speciation, likely facilitated by the polyploid's predisposition to self-fertilize.

Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi

Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. In this manuscript, we present a genome for a laboratory-tractable Entomophthora muscae isolate that infects fruit flies. Our E. muscae assembly is 1.03 Gb, consists of 7810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with recent datasets from entomophthoralean fungi, we show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity. In addition, we find that E. muscae and its closest allies possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae’s species-specific, biotrophic lifestyle. Finally, we offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex that support the need for taxonomic revision within this group. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.

Continuous Monoculture Alters the Fungal Community and Accumulates Potential Pathogenic Strains in the Rhizosphere of Codonopsis pilosula

Codonopsis pilosula (known as dangshen) is experiencing a serious replant disease caused by continuous monoculture in its main and endemic cultivation region in Dingxi, China. In this study, changes in physicochemical properties, fungal microbiomes, and isolated strains were investigated in the rhizosphere soil of 1-, 2-, 3-, and 5-year continuous monoculture natural fields. It was observed that wilted seedlings and a variety of root rot diseases occurred after the third year of continuous monoculture in the field. The soil-available potassium content and the pH value decreased significantly in the 3- and 5-year fields. Using Illumina sequencing, it was demonstrated that the 3- and 5-year fields had a higher diversity of fungal communities compared with the 1- and 2-year fields. At the genus level, abundance of some potentially pathogenic fungal taxa also increased. A total of 33 isolated strains belonging to the Fusarium species complexes Plectosphaerella cucumerina, Paraphoma ledniceana, Alternaria alstroemeriae, Mucor hiemalis, and Clonostachys rosea were obtained from the roots in 3- and 5-year fields. The correlation analysis revealed that the abundance of the fungal community at the genus level was positively correlated with the available phosphorus, total nitrogen, and soil organic matter. The results revealed that continuous monoculture has a negative impact on the fungal community and enriches potential pathogenic fungi in the rhizosphere of C. pilosula.

Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi.

Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. In this manuscript, we present a genome for a laboratory-tractable Entomophthora muscae isolate that infects fruit flies. Our E. muscae assembly is 1.03 Gb, consists of 7810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with recent datasets from entomophthoralean fungi, we show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity. In addition, we find that E. muscae and its closest allies possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Finally, we offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex that support the need for taxonomic revision within this group. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.

Large‐scale integrative taxonomy of Swedish grass flies (Diptera, Chloropidae) reveals hitherto unknown complexity of a dark taxon

AbstractThe study of biodiversity is fundamental to preserving life on Earth but a challenging endeavour due to the taxonomic neglect associated with hyperdiverse lineages. To overcome this problem, we have implemented for the first time a Large‐scale integrative taxonomic (LIT) approach on the hyperdiverse insect family Chloropidae. This lineage of flies is a great fit for implementing emerging protocols such as LIT due to their ecological relevance, abundance and global distribution, poorly known genetic diversity and challenging taxonomy. In this study, we test cost‐effective barcoding workflows on nonoptimally preserved chloropid flies from Sweden and then apply targeted morphological validation to accelerate the species recognition process. Our dataset yielded DNA barcodes of 63 species that represent almost one‐third of the species diversity from Sweden and 15% of the European diversity. Applying LIT allowed us to uncover two new species and address for the first time three troublesome species complexes through a comprehensive framework. We also provide previously unknown DNA barcodes for 35% of the described species found and address distribution patterns with a focus on grassland environments. We have thus contributed significantly to overcoming the taxonomic neglect of this hyperdiverse lineage by tackling the diversity of chloropids using complementary sources of data, scalable techniques and quickly translating multiple sources of evidence into named species.