Genome assembly, structural variants, and genetic differentiation between Lake Whitefish young species pairs (Coregonus sp.) with long and short reads

The parallel evolution of nascent pairs of ecologically differentiated species offers an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) like insertions, deletions, and other structural rearrangements, allowing further insights into the genetic architecture of speciation and how different variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the Lake Whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both Dwarf and Normal Lake Whitefish, annotated the transposable elements, and analysed the genome in the light of related coregonid species. Next, we used a combination of long-read and short-read sequencing to characterize SVs and genotype them at population-scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species was driven by transposable elements (TEs), suggesting that TE accumulation during a period of allopatry predating secondary contact may have been a key process in the speciation of the Dwarf and Normal Whitefish. Altogether, our results suggest that SVs play an important role in speciation and that by combining second and third generation sequencing we now have the ability to integrate SVs into speciation genomics.

Borrelia Infections in Ageing Ticks: Relationship with Morphometric Age Ratio in Field-Collected Ixodes ricinus Nymphs

In Europe, Ixodes ricinus plays a major role as a vector of Borrelia burgdorferi sensu lato (s.l.) spirochaetes, the causative agents of Lyme borreliosis, among other pathogens. In unfed ticks, Borrelia spirochaetes experience prolonged nutrient restriction. However, only few studies exist with regard to Borrelia infections in unfed ticks of different physiological ages. Changing body dimensions of unfed ticks, due to the consumption of energy reserves, allow physiological age estimation. The present study investigated the relationship of morphometric age with Borrelia prevalence and spirochaete load in 1882 questing I. ricinus nymphs, collected at two different locations in northern Germany in 2020. In addition, Borrelia species composition was investigated by employing a reverse line blot (RLB) probe panel suitable for the detection of ten different B. burgdorferi s.l. species, as well as the relapsing-fever spirochaete B. miyamotoi. Overall, Borrelia prevalence was 25.8% (485/1882). Whilst there was no statistically significant difference in Borrelia prevalence between the different morphometric age groups, Borrelia infection intensity as determined by probe-based quantitative real-time PCR significantly declined with increasing morphometric age. Borrelia species differentiation by RLB was successful in 29.5% of positive ticks, and revealed B. afzelii as the dominating species (65.0% of the differentiated infections). Additionally, B. garinii, B. valaisiana, B. burgdorferi sensu stricto, B. spielmanii, and B. miyamotoi were detected.

Rapid Differentiation of Vector Species: Development of Microsatellite Markers for Population Genetics of Biting Midges and a Potential Tool for Species Identification of Culicoides Sonorensis

Background: Proper vector surveillance relies on the ability to identify species of interest accurately and efficiently, though this can be difficult in groups containing cryptic species. Culicoides is a genus of small biting flies responsible for the transmission of numerous pathogens to a multitude of vertebrates. Regarding pathogen transmission, the C. variipennis species complex is of particular interest in North America. Of the six species within this group, only C. sonorensis is a proven vector of bluetongue virus and epizootic hemorrhagic disease virus. Unfortunately, subtle morphological differences, cryptic species, and mitonuclear discordance make species identification in the C. variipennis complex challenging. Recently, a SNP analysis enabled discrimination between the species of this group; however, this demanding approach is not practical for vector surveillance. Methods: The aim of the current study was to develop a reliable and affordable way of differentiating the species within the C. variipennis complex, especially C. sonorensis. Twenty-five putative microsatellite markers were identified using the C. sonorensis genome and tested for amplification within five species of the C. variipennis complex. Machine learning was then used to determine which markers best explain the genetic differentiation between species. This led to the development of a subset of four and seven markers which were also tested for species differentiation.Results: A total of 21 microsatellite markers were successfully amplified in the species tested. Clustering analyses of all of these markers recover the same species-level identification as the previous SNP data. Additionally, the subset of seven markers was equally capable of accurately differentiating the members of the C. variipennis complex as the 21 microsatellite markers. Finally, one microsatellite marker (C508) was found to be species-specific, only amplifying in the vector species C. sonorensis among the samples tested. Conclusions: These microsatellites provide an affordable way in which to differentiate the species of the C. variipennis complex and could lead to a better understanding of the species dynamics within this group. Additionally, after further testing, marker C508 may allow for the identification of C. sonorensis with a single-tube assay, potentially providing a powerful new tool for vector surveillance in North America.

High‐quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (Collembola)

The collembolan Folsomia candida Willem, 1902, is an important representative soil arthropod that is widely distributed throughout the world and has been frequently used as a test organism in soil ecology and ecotoxicology studies. However, it is questioned as an ideal “standard” because of differences in reproductive modes and cryptic genetic diversity between strains from various geographical origins. In this study, we present two high-quality chromosome-level genomes of F. candida, for the parthenogenetic Danish strain (FCDK, 219.08 Mb, N50 of 38.47 Mb, 25,139 protein-coding genes) and the sexual Shanghai strain (FCSH, 153.09 Mb, N50 of 25.75 Mb, 21,609 protein-coding genes). The seven chromosomes of FCDK are each 25–54% larger than the corresponding chromosomes of FCSH, showing obvious repetitive element expansions and large-scale inversions and translocations but no whole-genome duplication. The strain-specific genes, expanded gene families and genes in nonsyntenic chromosomal regions identified in FCDK are highly related to its broader environmental adaptation. In addition, the overall sequence identity of the two mitogenomes is only 78.2%, and FCDK has fewer strain-specific microRNAs than FCSH. In conclusion, FCDK and FCSH have accumulated independent genetic changes and evolved into distinct species since diverging 10 Mya. Our work shows that F. candida represents a good model of rapidly cryptic speciation. Moreover, it provides important genomic resources for studying the mechanisms of species differentiation, soil arthropod adaptation to soil ecosystems, and Wolbachia-induced parthenogenesis as well as the evolution of Collembola, a pivotal phylogenetic clade between Crustacea and Insecta.

Unique spicules may confound species differentiation: taxonomy and biogeography of Melonanchora Carter, 1874 and two new related genera (Myxillidae: Poecilosclerida) from the Okhotsk Sea

Sponges are amongst the most difficult benthic taxa to properly identify, which has led to a prevalence of cryptic species in several sponge genera, especially in those with simple skeletons. This is particularly true for sponges living in remote or hardly accessible environments, such as the deep-sea, as the inaccessibility of their habitat and the lack of accurate descriptions usually leads to misclassifications. However, species can also remain hidden even when they belong to genera that have particularly characteristic features. In these cases, researchers inevitably pay attention to these peculiar features, sometimes disregarding small differences in the other “typical” spicules. The genus Melonanchora Carter, 1874, is among those well suited for a revision, as their representatives possess a unique type of spicule (spherancorae). After a thorough review of the material available for this genus from several institutions, four new species of Melonanchora, M. tumultuosa sp. nov., M. insulsa sp. nov., M. intermedia sp. nov. and M. maeli sp. nov. are formally described from different localities across the Atlanto-Mediterranean region. Additionally, all Melonanchora from the Okhotsk Sea and nearby areas are reassigned to other genera; Melonanchora kobjakovae is transferred to Myxilla (Burtonanchora) while two new genera, Hanstoreia gen. nov. and Arhythmata gen. nov. are created to accommodate Melonanchora globogilva and Melonanchora tetradedritifera, respectively. Hanstoreia gen. nov. is closest to Melonanchora, whereas Arhythmata gen. nov., is closer to Stelodoryx, which is most likely polyphyletic and in need of revision.

Discrimination of forest species using medium spatial resolution images

This research aimed to evaluate the potential of orbital images from the Landsat-8/OLI and Sentinel-2 /MSI sensors in the distinction of species from a forest stand located in Campo Belo do Sul, State of Santa Catarina, Brazil. A total of 53 plots were allocated in the field, in which the central coordinate of the plot was collected using GPS receivers. In SIG environment, two images were used, one from each sensor, closely dated to the field campaign and with no clouds and other atmospheric factors. Then, the images were processed, and 17 vegetation indexes were calculated for each one. The indices were compared statistically by the t-Student test for independent samples. The indices that provided the best species differentiation were: CRI, GNDVI, NDI11, NDI12, NDVI, RDVI, SAVI, and SR. In addition, the species with greater prominence in the Landsat-8/OLI images was Eucalyptus spp. whereas Cunninghamia lanceolata (Lamb.) Hooker was easily distinguished in Sentinel-2 images. It was possible to differentiate the species from remote data derived from the Sentinel-2/MSI and Landsat-8/OLI sensors. However, further studies using other Remote Sensing data sources and other species are suggested.

A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics Analysis

The variety of Earth’s organisms is manifold. However, it is the small-scale marine community that makes the world goes round. Microbial organisms of pro- and eukaryotic origin drive the carbon supply and nutrient cycling, thus are mediating the primary productivity within the world largest ecosystem called ocean. But due to the ocean’s great size and large number of biogeographically habitats, the total of microbial species can hardly be grabbed and therefore their functional roles not fully described. However, recent advances in high-throughput sequencing technologies are revolutionizing our understanding of the marine microbial diversity, ecology and evolution. Nowadays, research questions on species differentiation can be solved with genomic approaches such as metabarcoding, while transcriptomics offers the possibility to assign gene functions even to a single cell, e.g., single-cell transcriptomics. On the other hand, due to the diversified amount of sequencing data, the certainty of a data crisis is currently evolving. Scientists are forced to broaden their view on bioinformatics resources for analysis and data storage in from of, e.g., cloud services, to ensure the data’s exchangeability. Which is why time resources are now shifting toward solving data problems rather than answering the eco-evolutionary questions stated in the first place. This review is intended to provide exchange on *omics approaches and key points for discussions on data handling used to decipher the relevant diversity and functions of microbial organisms in the marine ecosystem.

Molecular epidemiology of Paracoccidiodes spp. recovered from patients with paracoccidioidomycosis in a teaching hospital from Minas Gerais State of Brazil

Introduction Paracoccidioidomycosis (PCM) is caused by several species of the Paracoccidioides genus which can be differentiated by interspecific genetic variations, morphology and geographic distribution. Intraspecific variability correlation with clinical and epidemiological aspects of these species still remains unclear. This study aimed to sequence the loci GP43, exon 2 and ARF of 23 clinical isolates of Paracoccidioides spp. from patients in the Southeast Region of Brazil. Methodology and main findings GenBank was used to compare the present (23) with previous described sequences (151) that included ARF and GP43. It was identified a high polymorphism rate among the 23 isolates in comparison to the other 151. Among the isolates, 22 (95,66%) were S1/P. brasiliensis and 1 (4,34%) was identified as PS2/P. americana. A total of 45 haplotypes were found as follows: 19 from S1/P. brasiliensis (13 from the present study), 15 from P. lutzii, 6 from PS2/P. americana (1 from the present study), 3 from PS3/P. restrepiensis and 2 from PS4/P. venezuelensis. Moreover, exclusive haplotypes according to clinical origin and geographical area were found. S1/P. brasiliensis (HD = 0,655 and K = 4,613) and P. lutzii (HD = 0,649 and K = 2,906) presented the highest rate of polymorphism among all species, from which 12 isolates of the present study were clustered within S1b/P. brasiliensis. The GP43 locus showed a higher variability and was found to be the main reason for the species differentiation. Conclusions The results herein decribed show a high intraspecific genetic variability among S1/P. brasiliensis isolates and confirm the predominance of this species in the Southeast region of Brazil. The finding of exclusive haplotypes according to clinical origin and geographical area would suggest correlation between the molecular profile with the clinical form and geographic origin of patients with PCM.

The Capability of Sentinel-MSI (2A/2B) and Landsat-OLI (8/9) for Seagrass and Algae Species Differentiation using Spectral Reflectance

This paper assesses the reflectance difference values between the homologous visible and near-infrared (VNIR) spectral bands of Sentinel-MSI-2A/2B and Landsat-OLI-8/9 sensors for seagrass, algae, and mixed species discrimination and monitoring in a shallow marine environment southeastern of Bahrain in the Arabian Gulf. To achieve these, a field survey was conducted to collect samples of seawater, underwater sediments, seagrass (Halodule uninebell.netrvis and Halophila stipulacea) and algae (green and brown). As well, an experimental mode was established in a Goniometric-Laboratory to simulate the marine environment, and spectral measurements were performed using an ASD spectroradiometer over each separate and different case of seagrass and algae mixed species at different coverage rate (0, 10, 30, 75, and 100 %) considering the bottom sediments with clear and dark colors. All measured spectra were analyzed and transformed using continuum-removed reflectance spectral (CRRS) approach to assess spectral separability among separate or mixed species at varying coverage rates. Afterward, the spectra were resampled and convolved in the solar-reflective spectral bands of MSI and OLI sensors and converted into water vegetation indices (WVI) to investigate the potential of red, green, and blue bands for seagrass and algae species discrimination. For comparison and sensor differences quantification, statistical fits (p < 0.05) were conducted between reflectances in homologous bands and also between homologous WVI; as well as the coefficient of determination (R2) and root mean square difference (RMSD) were calculated. The results of spectral and CRRS analyses highlighted the importance of the blue, green, and NIR wavelengths for seagrass and algae detection and probable discrimination based on hyperspectral measurements. However, when resampled and convolved in MSI and OLI bands, spectral information loses the specific and unique absorption features and becomes more generalized and less precise. Therefore, relying on the multispectral bandwidth of MSI and OLI sensors, it is difficult or even impossible to differentiate or to map seagrass and algae individually at the species level. Additionally, instead of the red band, the integration of the blue or the green bands in WVI increases their discriminating power of submerged aquatic vegetation (SAV), particularly Water Adjusted Vegetation Index (WAVI), Water Enhance Vegetation Index (WEVI), and Water Transformed Vegetation Index (WTDVI) indices. These results corroborate the spectral analysis and the CRRS transformations that the blue and green electromagnetic radiation allows better marine vegetation differentiation. However, despite the power of blue wavelength to penetrate deeper into the water, it also leads to a relative overestimation of dense SAV coverage due to the higher scattering in this part of the spectrum. Furthermore, statistical fits between the reflectance in the VNIR homologous bands of SMI and OLI revealed excellent linear relationships (R2 of 0.999) with insignificant RMSD (≤ 0.0015). Important agreements (0.63 ≤ R2 ≤ 0.96) were also obtained between homologous WVI regardless of the integrated spectral bands (i.e., red, green, and blue), yielding insignificant RMSD (≤ 0.01). Accordingly, these results pointed out that MSI and OLI sensors are spectrally similar, and their data can be used jointly to monitor accurately the spatial distribution of SAV and its dynamic in time and space in shallow marine environment, provided that rigorous data pre-processing issues are addressed.

A novel filamentous cyanobacterium Microseira minor sp. nov. (Oscillatoriaceae, Cyanobacteria) from the Ganfu Channel, Jiangxi, China

Two filamentous cyanobacterial strains were isolated from the mats attached to rock surfaces in the Ganfu Channel, Jiangxi Province, China. A polyphasic approach based on the combination of morphological and molecular features was used to characterize the two strains. Both strains showed the Lyngbya-like morphology under the light microscopy, and had the highest similarity range of 16S rRNA gene sequences as 95.00-96.01% to clones of Microseira wollei, exceeding the cutoff for species delimitation in cyanobacteria. Phylogenetic analyses based on both 16S rRNA and nifH genes and smaller sizes of trichomes in the two Lyngbya-like strains supported them to be proposed as a new species in the genus Microseira as Microseira minor, which is the second species of the genus Microseira. The difference of the 16S-23S ITS region between the two Microseira minor strains and its implication for the evaluation on cyanobacterial diversity and species differentiation were also discussed.