De novo Assembly, Annotation, and Analysis of Transcriptome Data of the Ladakh Ground Skink Provide Genetic Information on High-Altitude Adaptation

The Himalayan Arc is recognized as a global biodiversity hotspot. Among its numerous cryptic and undiscovered organisms, this composite high-mountain ecosystem harbors many taxa with adaptations to life in high elevations. However, evolutionary patterns and genomic features have been relatively rarely studied in Himalayan vertebrates. Here, we provide the first well-annotated transcriptome of a Greater Himalayan reptile species, the Ladakh Ground skink Asymblepharus ladacensis (Squamata: Scincidae). Based on tissues from the brain, an embryonic disc, and pooled organ material, using pair-end Illumina NextSeq 500 RNAseq, we assembled ~77,000 transcripts, which were annotated using seven functional databases. We tested ~1600 genes, known to be under positive selection in anurans and reptiles adapted to high elevations, and potentially detected positive selection for 114 of these genes in Asymblepharus. Even though the strength of these results is limited due to the single-animal approach, our transcriptome resource may be valuable data for further studies on squamate reptile evolution in the Himalayas as a hotspot of biodiversity.

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Multi-Tissue Transcriptomes Yield Information on High-Altitude Adaptation and Sex-Determination in Scutiger cf. sikimmensis

Genes ◽

10.3390/genes10110873 ◽

2019 ◽

Vol 10 (11) ◽

pp. 873

Author(s):

Sylvia Hofmann ◽

Heiner Kuhl ◽

Chitra Bahadur Baniya ◽

Matthias Stöck

Keyword(s):

Sex Determination ◽

High Mountain ◽

Mountain Ecosystem ◽

Yield Information ◽

Evolutionary Genomic ◽

Genomic Studies ◽

Altitude Adaptation ◽

Selection For ◽

High Elevations ◽

Himalayan Species

The Himalayas are one of earth’s hotspots of biodiversity. Among its many cryptic and undiscovered organisms, including vertebrates, this complex high-mountain ecosystem is expected to harbour many species with adaptations to life in high altitudes. However, modern evolutionary genomic studies in Himalayan vertebrates are still at the beginning. Moreover, in organisms, like most amphibians with relatively high DNA content, whole genome sequencing remains bioinformatically challenging and no complete nuclear genomes are available for Himalayan amphibians. Here, we present the first well-annotated multi-tissue transcriptome of a Greater Himalayan species, the lazy toad Scutiger cf. sikimmensis (Anura: Megophryidae). Applying Illumina NextSeq 500 RNAseq to six tissues, we obtained 41.32 Gb of sequences, assembled to ~111,000 unigenes, translating into 54362 known genes as annotated in seven functional databases. We tested 19 genes, known to play roles in anuran and reptile adaptation to high elevations, and potentially detected diversifying selection for two (TGS1, SENP5) in Scutiger. Of a list of 37 genes, we also identify 27 candidate genes for sex determination or sexual development, all of which providing the first such data for this non-model megophryid species. These transcriptomes will serve as a valuable resource for further studies on amphibian evolution in the Greater Himalaya as a biodiversity hotspot.

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The L1-dependant and Pol III transcribed Alu retrotransposon, from its discovery to innate immunity

Molecular Biology Reports ◽

10.1007/s11033-021-06258-4 ◽

2021 ◽

Vol 48 (3) ◽

pp. 2775-2789

Author(s):

Ludwig Stenz

Keyword(s):

Human Genome ◽

Viral Infections ◽

De Novo ◽

Current Knowledge ◽

Innate Immune ◽

De Novo Mutation ◽

Neuronal Diversity ◽

Alu Sequences ◽

Pol Iii ◽

The Brain

AbstractThe 300 bp dimeric repeats digestible by AluI were discovered in 1979. Since then, Alu were involved in the most fundamental epigenetic mechanisms, namely reprogramming, pluripotency, imprinting and mosaicism. These Alu encode a family of retrotransposons transcribed by the RNA Pol III machinery, notably when the cytosines that constitute their sequences are de-methylated. Then, Alu hijack the functions of ORF2 encoded by another transposons named L1 during reverse transcription and integration into new sites. That mechanism functions as a complex genetic parasite able to copy-paste Alu sequences. Doing that, Alu have modified even the size of the human genome, as well as of other primate genomes, during 65 million years of co-evolution. Actually, one germline retro-transposition still occurs each 20 births. Thus, Alu continue to modify our human genome nowadays and were implicated in de novo mutation causing diseases including deletions, duplications and rearrangements. Most recently, retrotransposons were found to trigger neuronal diversity by inducing mosaicism in the brain. Finally, boosted during viral infections, Alu clearly interact with the innate immune system. The purpose of that review is to give a condensed overview of all these major findings that concern the fascinating physiology of Alu from their discovery up to the current knowledge.

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De Novo Development of a Cavernous Malformation of the Brain: Significance of Factors with Paracrine and Endocrine Activity: Case Report

Neurosurgery ◽

10.1227/00006123-200203000-00042 ◽

2002 ◽

Vol 50 (3) ◽

pp. 646-650 ◽

Cited By ~ 6

Author(s):

Wolf Lüdemann ◽

Verena Ellerkamp ◽

Alexandru C. Stan ◽

Sami Hussein

Keyword(s):

Case Report ◽

De Novo ◽

Cavernous Malformation ◽

Endocrine Activity ◽

The Brain

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The brain transcriptome of the wolf spider, Schizocosa ocreata

BMC Research Notes ◽

10.1186/s13104-021-05648-y ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Daniel Stribling ◽

Peter L. Chang ◽

Justin E. Dalton ◽

Christopher A. Conow ◽

Malcolm Rosenthal ◽

...

Keyword(s):

Gene Expression ◽

De Novo ◽

Transcriptome Assembly ◽

Model Organisms ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

Wolf Spiders ◽

Schizocosa Ocreata ◽

Genomic Studies ◽

The Brain

Abstract Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

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A novel TSC1 variant associated with tuberous sclerosis and sacrococcygeal teratoma

Human Genome Variation ◽

10.1038/s41439-020-00124-8 ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Saba Ahmad ◽

Luis Manon ◽

Gifty Bhat ◽

Jerry Machado ◽

Alice Zalan ◽

...

Keyword(s):

Tuberous Sclerosis ◽

Tuberous Sclerosis Complex ◽

Cellular Differentiation ◽

Autosomal Dominant ◽

De Novo ◽

Autosomal Dominant Disease ◽

Sacrococcygeal Teratoma ◽

Dominant Disease ◽

The Brain

AbstractTuberous sclerosis complex (TSC) is an autosomal dominant disease associated with tumors and malformed tissues in the brain and other vital organs. We report a novel de novo frameshift variant of the TSC1 gene (c.434dup;p. Ser146Valfs*8) in a child with TSC who initially presented with a sacral teratoma. This previously unreported association between TSC and teratoma has broad implications for the pathophysiology of embryonic tumors and mechanisms underlying cellular differentiation.

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Negative Emotions in Migraineurs Dreams: The Increased Prevalence of Oneiric Fear and Anguish, Unrelated to Mood Disorders

Behavioural Neurology ◽

10.1155/2014/919627 ◽

2014 ◽

Vol 2014 ◽

pp. 1-4 ◽

Cited By ~ 4

Author(s):

F. De Angeli ◽

C. Lovati ◽

L. Giani ◽

C. Mariotti D'Alessandro ◽

E. Raimondi ◽

...

Keyword(s):

Motor Skills ◽

De Novo ◽

Tension Type Headache ◽

Anxiety And Depression ◽

Generalized Anxiety ◽

Migraine Pain ◽

Patient Health ◽

Type Headache ◽

The Brain ◽

Negative Connotation

Background. Migraineurs brain has shown some functional peculiarities that reflect not only in phonophobia, and photophobia, but also in mood and sleep. Dreaming is a universal mental state characterized by hallucinatory features in which imagery, emotion, motor skills, and memory are created de novo. We evaluated dream contents and associated emotions in migraineurs.Materials and Methods. 412 subjects: 219 controls; and 148 migraineurs (66 with aura, MA; 82 without aura, MO), and 45 tension type headache patients (TTH). A semistructured retrospective self-reported questionnaire was used to evaluate dreams. The Generalized Anxiety Disorder Questionnaire (GAD-7), and the Patient Health Questionnaire (PHQ-9) were administered to evaluate anxiety and depression.Results. Migraineurs showed increased levels of anxiety (P=0.0002for MA versus controls,P=0.004for MO versus controls). Fear and anguish during dreaming were more frequently reported by migraine patients compared to controls, independently by anxiety and depression scores.Discussion. The brain of migraineurs seems to dream with some peculiar features, all with a negative connotation, as fear and anguish. It may be due to the recorded negative sensations induced by recurrent migraine pain, but it may just reflect a peculiar attitude of the mesolimbic structures of migraineurs brain, activated in both dreaming and migraine attacks.

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Cerebellar Atrophy in Epileptic Patients

Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques ◽

10.1017/s0317167100027785 ◽

1988 ◽

Vol 15 (3) ◽

pp. 299-303 ◽

Cited By ~ 39

Author(s):

M.I. Botez ◽

Ezzedine Attig ◽

Jean Lorrain Vézina

Keyword(s):

Statistical Analysis ◽

High Resolution ◽

Posterior Fossa ◽

De Novo ◽

Cerebellar Atrophy ◽

Ct Scans ◽

Control Subjects ◽

Generalized Seizures ◽

Epileptic Patients ◽

The Brain

ABSTRACT:High-resolution CT scans of the brain and posterior fossa were performed on 106 phenytoin (PHT)- treated epileptics, 28 de novo epileptics and 43 control subjects. A higher incidence of cerebellar and brainstem (CBS) atrophy was observed in chronic PHT- or PHT+ phenobarbital-treated epileptics compared to the two other groups. Some control subjects and de novo epileptics presented mild CBS atrophy, whereas moderate to severe atrophy was noted exclusively in chronically-treated patients. In attempting to delineate the etiology of CBS atrophy, epileptic patients were divided in three groups: 55 subjects with normal CT scans, 30 with both cerebral and CBS atrophy, and 49 with pure CBS atrophy. Their ages, length of illness, number of generalized seizures, number of other seizures, and amount of PHT received during their lifetime were assessed. Statistical analysis revealed that posterior fossa atrophy in epileptics was significantly correlated with both the length of the illness and the amount of PHT ingested during the patient's lifetime. The number of seizures appears to not be related to CBS atrophy.

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Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

10.1101/2021.08.16.456461 ◽

2021 ◽

Author(s):

Ching-Ho Chang ◽

Lauren E. Gregory ◽

Kathleen E. Gordon ◽

Colin D. Meiklejohn ◽

Amanda M. Larracuente

Keyword(s):

Positive Selection ◽

Y Chromosome ◽

Related Species ◽

De Novo ◽

Gene Families ◽

Chromosome Organization ◽

End Joining ◽

Sexual Antagonism ◽

Closely Related Species ◽

Y Chromosomes

AbstractY chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposable elements, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism generally contributes to the convergent evolution of Y chromosome organization.

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Comparative Genetic Analysis of Yersinia pestis Strains Isolated on the Ukok Plateau and other Territories of the Altai Mountains

Problems of Particularly Dangerous Infections ◽

10.21055/0370-1069-2020-4-59-69 ◽

2021 ◽

pp. 59-69

Author(s):

G. A. Eroshenko ◽

A. N. Balykova ◽

Ya. M. Krasnov ◽

E. A. Naryshkina ◽

E. N. Rozhdestvensky ◽

...

Keyword(s):

Yersinia Pestis ◽

De Novo ◽

Molecular Genetic ◽

Genetic Identification ◽

Likelihood Method ◽

High Mountain ◽

Altai Mountains ◽

Natural Foci ◽

Ukok Plateau ◽

Average Size

The aim of the study was molecular-genetic identification and analysis of the phylogenetic relationship of Yersinia pestis strains isolated on the Ukok Plateau in 2020, in order to establish the current boundaries of the natural mega focus of plague in the Altai Mountains in Russia and Mongolia.Materials and methods. 37 strains of Y. pestis of the main subspecies isolated in the Tuva mountain and Gorno-Altai high-mountain plague foci and adjacent territories of Mongolia in 1971–2020 were studied. The whole genome sequencing of the strains was performed using the Ion S5 XL System (Thermo Fischer Scientific). Ion Torrent Suite software package 5.12 and Newbler gsAssembler 2.6 were used to process the data and assemble de novo the sequences of raw reads. The average size of the collected genome was 4.55 million base pairs. Core SNPs were detected by aligning the contigs of Y. pestis strains on the CO92 genome using the Snippy 4.6 program, then 28 SNP homoplasies were removed. The resulting set of SNPs contained only the core region of the genome (955 SNPs). The dendrogram was constructed using the Maximum Likelihood method applying the PhyML 3.1 program.Results and discussion. The current population structure of Y. pestis of the main subspecies, antique biovar, phylogenetic line 4.ANT, endemic to the foci of the Altai Mountains in Russia and Mongolia has been determined. The presence of 4.ANT-21 clone, which became widespread in the territory of these natural foci of plague at the begining of the XXI century, was revealed. It is shown that three strains isolated on the Ukok Plateau in 2020 belong to clone 4.ANT-21. According to phylogenetic analysis, evidence of 4.ANT circulation on the Ukok Plateau before 2018 was obtained. The lesson that has been learned is that it is necessary to study the territories of Mongolia, Kazakhstan and China bordering the Ukok Plateau in order to establish the current boundaries of the 4.ANT mega focus.

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