Transcriptomic analysis confirms differences among nuclear genomes of cryptic earthworm lineages living in sympatry

Earthworm (Oligochaeta, Lumbricidae) intraspecific genetic variation and polyploidy

Earthworms are known for their intricate systematics and a diverse range of reproduction modes, including outcrossing, self-fertilization, parthenogenesis, and some other modes, which can occasionally coexist in a single species. Moreover, they exhibit considerable intraspecific karyotype diversity, with ploidy levels varying from di- to decaploid, as well as high genetic variation. In some cases, a single species may exhibit significant morphological variation, contain several races of different ploidy, and harbor multiple genetic lineages that display significant divergence in both nuclear and mitochondrial DNA. However, the relationship between ploidy races and genetic lineages in earthworms remains largely unexplored. To address this question, we conducted a comprehensive review of available data on earthworm genetic diversity and karyotypes. Our analysis revealed that in many cases, a single genetic lineage appears to encompass populations with different ploidy levels, indicating recent polyploidization. On the other hand, some other cases like Octolasion tyrtaeum and Dendrobaena schmidti/D. tellermanica demonstrate pronounced genetic boundaries between ploidy races, implying that they diverged long ago. Certain cases like the Eisenia nordenskioldi complex represent a complex picture with ancient divergence between lineages and both ancient and recent polyploidization. The comparison of phylogenetic and cytological data suggests that some ploidy races have arisen independently multiple times, which supports the early findings by T.S. Vsevolodova-Perel and T.V. Malinina. The key to such a complex picture is probably the plasticity of reproductive modes in earthworms, which encompass diverse modes of sexual and asexual reproduction; also, it has been demonstrated that even high-ploidy forms can retain amphimixis.

Coelomocytes of the Oligochaeta earthworm Lumbricus terrestris (Linnaeus, 1758) as evolutionary key of defense: a morphological study

Metazoans have several mechanisms of internal defense for their survival. The internal defense system evolved alongside the organisms. Annelidae have circulating coelomocytes that perform functions comparable to the phagocytic immune cells of vertebrates. Several studies have shown that these cells are involved in phagocytosis, opsonization, and pathogen recognition processes. Like vertebrate macrophages, these circulating cells that permeate organs from the coelomic cavity capture or encapsulate pathogens, reactive oxygen species (ROS), and nitric oxide (NO). Furthermore, they produce a range of bioactive proteins involved in immune response and perform detoxification functions through their lysosomal system. Coelomocytes can also participate in lithic reactions against target cells and the release of antimicrobial peptides. Our study immunohistochemically identify coelomocytes of Lumbricus terrestris scattered in the epidermal and the connective layer below, both in the longitudinal and in the smooth muscle layer, immunoreactive for TLR2, CD14 and α-Tubulin for the first time. TLR2 and CD14 are not fully colocalized with each other, suggesting that these coelomocytes may belong to two distinct families. The expression of these immune molecules on Annelidae coelomocytes confirms their crucial role in the internal defense system of these Oligochaeta protostomes, suggesting a phylogenetic conservation of these receptors. These data could provide further insights into the understanding of the internal defense system of the Annelida and of the complex mechanisms of the immune system in vertebrates.

Systematic evaluation of chiral fungicide penflufen for the bioactivity improvement and input reduction using alphafold2 models and transcriptome sequencing

Traditional risk assessment of pesticide concludes at the racemic level, which is often incomprehensive. In this study, systematic studies on environmental stability, bioactivity, and ecotoxicological effects of fungicide penflufen were carried out at the enantiomeric level. The single-enantiomer of penflufen was successfully separated and prepared, and their stability was verified in different environmental matrices. Meanwhile, bioactivity test indicated that S-(+)-penflufen had increased bioactivity with its bioactivities against Rhizoctonia solani, Fusarium oxysporum, and Fusarium moniliforme being factors of 7.8, 1.8, and 4.7, respectively greater than those of R-(-)-penflufen. Molecular docking results showed the strong hydrogen bond interactions with Leu300, enantiomer-specific hydrophobic interactions with Cys299, Arg91, and His93, and the greater binding energy between S-(+)-penflufen and succinate dehydrogenase of Rhizoctonia solani caused the selective bioactivity. Additionally, two enantiomers showed low acute toxicity whereas selective sub-chronic toxicity to earthworms. In sub-chronic toxicity test, the accumulated enantiomers caused abnormalities in intestinal tract structure, enzyme activities, and gene expression of earthworms, especially in the S-(+)-penflufen treatment. The selective interactions between penflufen enantiomers and key proteins were elucidated using molecular docking, which may be the main reason of stereoselective subchronic toxicity. S-(+)-penflufen has high bioactivity and low acute risk, it has great potential for development.

Improving the quality of barley transcriptome de novo assembling by using a hybrid approach for lines with varying spike and stem coloration

De novo transcriptome assembly is an important stage of RNA-seq data computational analysis. It allows the researchers to obtain the sequences of transcripts presented in the biological sample of interest. The availability of accurate and complete transcriptome sequence of the organism of interest is, in turn, an indispensable condition for further analysis of RNA-seq data. Through years of transcriptomic research, the bioinformatics community has developed a number of assembler programs for transcriptome reconstruction from short reads of RNA-seq libraries. Different assemblers makes it possible to conduct a de novo transcriptome reconstruction and a genome-guided reconstruction. The majority of the assemblers working with RNA-seq data are based on the De Bruijn graph method of sequence reconstruction. However, specif ics of their procedures can vary drastically, as do their results. A number of authors recommend a hybrid approach to transcriptome reconstruction based on combining the results of several assemblers in order to achieve a better transcriptome assembly. The advantage of this approach has been demonstrated in a number of studies, with RNA-seq experiments conducted on the Illumina platform. In this paper, we propose a hybrid approach for creating a transcriptome assembly of the barley Hordeum vulgare isogenic line Bowman and two nearly isogenic lines contrasting in spike pigmentation, based on the results of sequencing on the IonTorrent platform. This approach implements several de novo assemblers: Trinity, Trans-ABySS and rnaSPAdes. Several assembly metrics were examined: the percentage of reference transcripts observed in the assemblies, the percentage of RNA-seq reads involved, and BUSCO scores. It was shown that, based on the summation of these metrics, transcriptome meta-assembly surpasses individual transcriptome assemblies it consists of.

DNA Barcoding: Molecular Identification and Phylogenetic Analysis of Pheretimoid Earthworm (Metaphire sp. and Amynthas sp.) Based on Mitochondrial Partial COI Gene from Sialkot, Pakistan

The extremely difficult and challenging process is identifying pheretimoid species, genus Metaphire and Amynthas involving increased homoplasy in various morphological characteristics. The molecular identification, phylogenetic relationships, and evolutionary divergence time of earthworms belonging to the pheretimoid complex were investigated in this study using partial mitochondrial COI (cytochrome C oxidase subunit I) gene sequences ranging from 550-680 bp. Results revealed that 86 pheretimoid earthworms were morphologically different from a total of 342 mature worms. Moreover, 11 pheretimoid species were molecularly identified, including Metaphire posthuma (02), M. anomala (01), M. houlleti (02), M. californica (01), M. birmanica (02), Amynthas minimus (01), A. morrisi (01), and M. bununa (01). A phylogenetic tree was constructed with bootstrap values of 95%, which supported a monophyletic lineage of two well-supported clades formed by 12 partial COI sequences and 48 GenBank sequences using Hirudo medicinalis as an outgroup. The monophyly of these obtained genera indicated overall similarity at species level. Today, species like Amynthas, Metaphire and Pheretima have worm diversity in the form of pheretimoid earthworms, which dates to the Late Miocene (11.2-5.3 Mya) and the Pliocene (5.3-2.4 Mya). Compared to all relevant pheretimoid species, genetic p-distance values ranged from 0.0% to 0.57% (less than 1%). These low range values demonstrated that both genera Metaphire and Amynthas, supported the theory, which states that there are shared similarities among the species, despite different morphology. The current study is the first attempt in Pakistan to identify earthworms through DNA barcoding thus providing a genomic stamp. The work explored the significance of COI gene sequences to construct molecular tools that will be useful to overcome the different obstacles in morphologically similar earthworm identification and their phylogenetic study.

Variation in nuclear genome size within the Eisenia nordenskioldi complex (Lumbricidae, Annelida)

The size of the nuclear genome in eukaryotes is mostly determined by mobile elements and noncoding sequences and may vary within wide limits. It can differ signif icantly both among higher-order taxa and closely related species within a genus; genome size is known to be uncorrelated with organism complexity (the so-called C-paradox). Less is known about intraspecif ic variation of this parameter. Typically, genome size is stable within a species, and the known exceptions turn out be cryptic taxa. The Eisenia nordenskioldi complex encompasses several closely related earthworm species. They are widely distributed in the Urals, Siberia, and the Russian Far East, as well as adjacent regions. This complex is characterized by signif icant morphological, chromosomal, ecological, and genetic variation. The aim of our study was to estimate the nuclear genome size in several genetic lineages of the E. nordenskioldi complex using f low cytometry. The genome size in different genetic lineages differed strongly, which supports the hypothesis that they are separate species. We found two groups of lineages, with small (250–500 Mbp) and large (2300–3500 Mbp) genomes. Moreover, different populations within one lineage also demonstrated variation in genome size (15–25 %). We compared the obtained data to phylogenetic trees based on transcriptome data. Genome size in ancestral population was more likely to be big. It increased or decreased independently in different lineages, and these processes could be associated with changes in genome size and/or transition to endogeic lifestyle.

Morphological differences between genetic lineages of the peregrine earthworm : Aporrectodea caliginosa (Savigny, 1826)

Aporrectodea caliginosa is a universally distributed and highly abundant peregrine earthworm that is the object of many ecological and ecotoxicological studies. Molecular phylogenetic analysis suggested that A. caliginosa consists of three highly diverged genetic lineages. In this study, we investigated morphological diversity within a sample of these three lineages from Belarus. We detected a variety of forms with different degrees of pigmentation and a shift in the clitellum position. The three genetic lineages of A. caliginosa demonstrated different propensity to particular morphological variants, including size, colour, and the clitellum position, yet no character could be used to distinguish among the lineages with sufficient accuracy. Thus, our results suggest that identification of the genetic lineage should be recommended for ecological studies involving A. caliginosa to account for possible differences between them.

Cryptic Clitellata: Molecular Species Delimitation of Clitellate Worms (Annelida): An Overview

Methods for species delimitation using molecular data have developed greatly and have become a staple in systematic studies of clitellate worms. Here we give a historical overview of the data and methods used to delimit clitellates from the mid-1970s to today. We also discuss the taxonomical treatment of the cryptic species, including the recommendation that cryptic species, as far as possible, should be described and named. Finally, we discuss the prospects and further development of the field.

Species Delimitation of the Eisenia nordenskioldi Complex (Oligochaeta, Lumbricidae) Using Transcriptomic Data

Eisenia nordenskioldi (Eisen, 1879) is the only autochthonous Siberian earthworm with a large distribution that ranges from tundra to steppe and broadleaved forests. This species has a very high morphological, ecological, karyological, and genetic diversity, so it was proposed that E. nordenskioldi should be split into several species. However, the phylogeny of the complex was unclear due to the low resolution of the methods used and the high diversity that should have been taken into account. We investigated this question by (1) studying the diversity of the COI gene of E. nordenskioldi throughout its range and (2) sequencing transcriptomes of different genetic lineages to infer its phylogeny. We found that E. nordenskioldi is monophyletic and is split into two clades. The first one includes the pigmented genetic lineages widespread in the northern and western parts of the distribution, and the second one originating from the southern and southeastern part of the species' range and representing both pigmented and non-pigmented forms. We propose to split the E. nordenskioldi complex into two species, E. nordenskioldi and Eisenia sp. 1 (aff. E. nordenskioldi), corresponding to these two clades. The currently recognized non-pigmented subspecies E. n. pallida will be abolished as a polyphyletic and thus a non-natural taxon, while Eisenia sp. 1 will be expanded to include several lineages earlier recognized as E. n. nordenskioldi and E. n. pallida.

Morphotypes and genetic diversity of Dendrobaena schmidti (Lumbricidae, Annelida)

Dendrobaena schmidti (Michaelsen, 1907) is a polymorphic earthworm species from the Caucasus and adjacent regions. Adult D. schmidti individuals have highly variable body size (from 1.5 to well over 10 cm) and color (from dark purple to total lack of pigmentation), so a lot of subspecies of D. schmidti have been described; however, the existence of most of them is currently under dispute. We studied the genetic diversity of D. schmidti from seven locations from the Western Caucasus using mitochondrial (a fragment of the cytochrome oxidase I gene) and nuclear (internal ribosomal transcribed spacer 2) DNA. For both genes studied, we found that our sample was split into two groups. The first group included somewhat bigger (3–7.5 cm) individuals that were only slightly pigmented or totally unpigmented (when fixed by ethanol). The second group contained small (1.7–3.5 cm) specimens with dark purple pigmentation. In one of the studied locations these two groups were found in sympatry. However, there were no absolute differences either in general appearance (pigmented/unpigmented, small/big) or among diagnostic characters. Although the two groups differed in size (the majority of individuals from the first group were 5–6 cm long, and of the second one, 2–3 cm), the studied samples overlapped to a certain degree. Pigmentation, despite apparent differences, was also unreliable, since it was heavily affected by fixation of the specimens. Thus, based on the obtained data we can conclude that D. schmidti consists of at least two species that have identical states of diagnostic characters, but differ in general appearance.

Local adaptation fuels cryptic speciation in terrestrial annelids

Uncovering the genetic and evolutionary basis of cryptic speciation is a major focus of evolutionary biology. Next Generation Sequencing (NGS) allows the identification of genome-wide local adaptation signatures, but has rarely been applied to cryptic complexes - particularly in the soil milieu - as it is the case with integrative taxonomy. The earthworm genus Carpetania, comprising six previously suggested putative cryptic lineages, is a promising model to study the evolutionary phenomena shaping cryptic speciation in soil-dwelling lineages. Genotyping-By-Sequencing (GBS) was used to provide genome-wide information about genetic variability between 17 populations, and geometric morphometrics analyses of genital chaetae were performed to investigate unexplored cryptic morphological evolution. Genomic analyses revealed the existence of three cryptic species, with half of the previously-identified potential cryptic lineages clustering within them. Local adaptation was detected in more than 800 genes putatively involved in a plethora of biological functions (most notably reproduction, metabolism, immunological response and morphogenesis). Several genes with selection signatures showed shared mutations for each of the cryptic species, and genes under selection were enriched in functions related to regulation of transcription, including SNPs located in UTR regions. Finally, geometric morphometrics approaches partially confirmed the phylogenetic signal of relevant morphological characters such as genital chaetae. Our study therefore unveils that local adaptation and regulatory divergence are key evolutionary forces orchestrating genome evolution in soil fauna.