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Background: Substantial discoveries during the past century have revealed that transposable elements (TEs) can play a crucial role in genome evolution by affecting gene expression and inducing genetic rearrangements, among other molecular and structural effects. Yet, our knowledge on the role of TEs in adaptation to extreme climates is still at its infancy. The availability of long-read sequencing has opened up the possibility to identify and study potential functional effects of TEs with higher precision. In this work, we used Drosophila montana as a model for cold-adapted organisms to study the association between TEs and adaptation to harsh climates., Results: Using the PacBio long-read sequencing technique, we de novo identified and manually curated TE sequences in five Drosophila montana genomes from eco-geographically distinct populations. We identified 489 new TE consensus sequences which represented 92% of the total TE consensus in D. montana. Overall, 11-13% of the D. montana genome is occupied by TEs, which as expected are non-randomly distributed across the genome. We identified five potentially active TE families, most of them from the retrotransposon class of TEs. Additionally, we found TEs present in the five analyzed genomes that were located nearby previously identified cold tolerant genes. Some of these TEs contain promoter elements and transcription binding sites. Finally, we detected TEs nearby fixed and polymorphic inversion breakpoints., Conclusions: Our research revealed a significant number of newly identified TE consensus sequences in the genome of D. montana, suggesting that non-model species should be studied to get a comprehensive view of the TE repertoire in Drosophila species and beyond. Genome annotations with the new D. montana library allowed us to identify TEs located nearby cold tolerant genes, and present at high population frequencies, that contain regulatory regions and are thus good candidates to play a role in D. montana cold stress response. Finally, our annotations also allow us to identify for the first time TEs present in the breakpoints of three D. montana inversions., (© 2024. The Author(s).)

Background: The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences., Results: Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries., Conclusions: The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms., (© 2024. The Author(s).)

Vitamin has a major role in the functions of the immune system, and the efficacy of this vitamin in reducing inflammation has been identified. Considering the effects of vitamin D, this study research was performed for investigating the relationship between vitamin D and the severity of COVID-19 in children. This cross-sectional study was performed on 101 children infected with the new coronavirus from September 2020 to October 2021. Information on vitamin D levels, demographic factors, and clinical and laboratory findings were documented in information forms and prepared for statistical analyses. The average of children was 2.85 ± 0.85 years. Low oxygen saturation was observed in 35.3% of infected children. The level of involvement was higher in subjects with vitamin D levels higher than 30 and less than 10 ng/ml (p = 0.04). Clinical signs in cases with deficient and sufficient vitamin D levels were more severe in terms of tachypnea and tachycardia (p = 0.01). Children with vitamin D lower than 10 ng/ml showed more frequency (p = 0.02). Cases with moderate vitamin D had fewer gastrointestinal complications (p = 0.03). Also, oxygen levels were lower in children who had low levels of vitamin D (p = 0.02). Vitamin D levels were associated with levels of involvement, tachycardia, tachypnea, clinical signs, gastrointestinal problems, and O2 levels. Moderate vitamin D levels in children are a critical issue that should be considered.

We studied the evolutionary relationship of two widely distributed parapatric butterfly species, Melitaea athalia and Melitaea celadussa , using the ddRAD sequencing approach, as well as genital morphology and mtDNA data. M. athalia was retrieved as paraphyletic with respect to M. celadussa . Several cases of mito-nuclear discordance and morpho-genetic mismatch were found in the contact zone. A strongly diverged and marginally sympatric clade of M. athalia from the Balkans was revealed. An in-depth analysis of genomic structure detected high levels of admixture between M. athalia and M. celadussa at the contact zone, though not reaching the Balkan clade. The demographic modelling of populations supported the intermediate genetic make-up of European M. athalia populations with regards to M. celadussa and the Balkan clade. However, the dissimilarity matrix of genotype data (PCoA) suggested the Balkan lineage having a genetic component that is unrelated to the athalia - celadussa group. Although narrowly sympatric, almost no signs of gene flow were found between the main M. athalia group and the Balkan clade. We propose two possible scenarios on the historical evolution of our model taxa and the role of the last glacial maximum in shaping their current distribution. Finally, we discuss the complexities regarding the taxonomic delimitation of parapatric taxa.

The new species Leptopus gakalae is described from caves in Iran and compared to congeners occurring in the western Palearctic region. Figures are provided of the dorsal habitus and diagnostic morphological characters. Also provided are additional records for other species of Leptopus Latrielle, 1809, occurring from India westward through Europe and North Africa, as well as the first North American record of Leptopus marmoratus (Goeze, 1778) based on an agricultural quarantine intercept. A key is provided to all species of Leptopus occurring in the Western Palearctic region. Notes are also provided on other species of Heteroptera occurring in Iranian caves, with special reference to the small water strider Velia affinis Kolenati, 1857.

A survey of wingless insects belonging to the orders Microcoryphia (=Archaeognatha) and Zygentoma (=Thysanura s. str.) has been performed in subterranean habitats of central Iran. As a result, several new species have been discovered. In this work, three new species are described: a new species of bristletail of the family Machilidae, Haslundiellairanica sp. n. , a new silverfish of the family Lepismatidae, Ctenolepismasubterraneum sp. n. , and a new Nicoletiidae, Lepidospora (Brinckina) momtaziana sp. n. These new taxa are compared with related species in their respective genera and keys for their identification are provided: one for all known species of Haslundiella and one for all basal insects of subterranean environments of Iran which includes those previously reported. Moreover, the previously published keys of Iranian Ctenolepisma and the subgenus Brinckina are modified to include the new species. Three additional species of Lepismatidae are reported in this work: Neoasterolepìsma palmonii and Ctenolepismatargionii are newly recorded from Iran and both species, together with Acrotelsacollaris , are cited for the first time in the subterranean habitats. This survey progresses the knowledge on the biodiversity of these insects in Iran.

The first records of the family Nicoletiidae in Iran are given, based on material from subterranean habitats in Fars Province. Two new species are described, one belonging to a new genus of Atelurinae, Persiatelurina farsiana gen. n. sp. n., the other to the genus Lepidospora but representing a new subgenus, Brinckiletinia subgen. n., this new subgenus is close to the subgenus Brinckina, but lacks scales on the thorax. Both new taxa are compared with related species. Nipponatelurina caucasica Kaplin, 2016 is transferred to Persiatelurina caucasica n. comb. The new atelurine was collected in Momtaz and Khan Caves and Lepidospora (Brinckiletinia) malousjanica sp. n. was found in Malousjan Cave. An additional specimen of Lepidospora was collected in Momtaz Cave, and although its specific identity is not clear, it represents a third taxon belonging to the subgenus Brinckina. Data about the habitats of these subterranean Nicoletiidae are presented.

The species belonging to the Sphodrine genus Laemostenus Bonelli, 1810 from central and southern Zagros Mts. and central zones of Iran were studied. Two new species-groups of the subgenus Antisphodrus Schaufuss, 1865 are proposed, and seven new species belonging to subgenera Antisphodrus Schaufuss, 1865 and Iranosphodrus Lohaj & Casale, 2011 are described. Morphological characters of the habitus and shape of male genitalia were used to delimit the species. New species of subgenus Antisphodrus are: L. (A.) zagrosensis sp. nov. and L. (A.) speleophilus sp. nov. from Chaharmahal and Bakhtiari province, and L. (A.) farsicus sp. nov. from Fars province (zagrosensis species-group); Laemostenus (A) zakariyiensis sp. nov. from Fars province (aequalis species-group), and L. (A.) shirazensis sp. nov. from Fars province (glasunowi species-group).  Based on the newly collected material, the subgenus Iranosphodrus is redefined and two new species from Yazd province are described: L.(I.) yazdensis sp. nov. and L.(I.) troglophilus sp. nov. An identification key for the Laemostenus species of the studied area is provided, and a check list for Iranian representatives of subgenera Antisphodrus and Iranosphodrus are given.