scholarly journals Unearthing LTR retrotransposon gag genes co-opted in the deep evolution of eukaryotes

2021 ◽  
Author(s):  
Jianhua Wang ◽  
Guan-Zhu Han
Keyword(s):  
Gene Expression ◽  
Selective Pressure ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Cellular Functions ◽  
The Family ◽  
Family Level ◽  
Gene Expression Analyses ◽  
Comprehensive Picture ◽  
Gypsy Retrotransposons

Abstract LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes, and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.

scholarly journals Intake of a Mixture of Sake Cake and Rice Malt Increases Mucin Levels and Changes in Intestinal Microbiota in Mice

Nutrients ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 449 ◽  
Author(s):  
Shinpei Kawakami ◽  
Ryouichi Ito ◽  
Hiroko Maruki-Uchida ◽  
Asuka Kamei ◽  
Akihito Yasuoka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Intestinal Microbiota ◽  
Barrier Function ◽  
Gene Expression Analysis ◽  
Control Diet ◽  
Intestinal Barrier ◽  
Intestinal Barrier Function ◽  
The Family ◽  
Family Level ◽  
Muc2 Expression

Amazake is a traditional Japanese beverage. Its main ingredients are sake cake and rice malt. In this study, we examined the effect of sake cake and rice malt on the intestinal barrier function and gut microbiota. BALB/c mice were fed a control diet or a diet containing a mixture of sake cake and rice malt powder (SRP) for four weeks. Fecal IgA values did not change between groups, but the fecal mucin level was significantly greater in the SRP-fed group. Gene expression analysis in the ileum by real-time PCR demonstrated Muc2 expression did not change, while the Muc3 expression was upregulated in the SRP-fed group. Furthermore, microbiota analysis demonstrated a change by SRP intake at the family level, and the proportion of Lactobacillaceae significantly increased in the SRP-fed group. At the genus level, the proportion of Lactobacillus also significantly increased in the SRP-fed group. These results suggest that the intake of a mixture of sake cake and rice malt improves intestinal barrier function by increasing mucin levels and inducing changes in intestinal microbiota.

scholarly journals Positive Selection and Gene Expression Analyses from Salivary Glands Reveal Discrete Adaptations within the Ecologically Diverse Bat Family Phyllostomidae

2020 ◽  
Vol 12 (8) ◽  
pp. 1419-1428
Author(s):  
Michael W Vandewege ◽  
Cibele G Sotero-Caio ◽  
Caleb D Phillips
Keyword(s):  
Gene Expression ◽  
Positive Selection ◽  
Salivary Glands ◽  
Acid Synthesis ◽  
Functional Diversification ◽  
Amino Acid Synthesis ◽  
The Family ◽  
Gene Expression Analyses ◽  
Dietary Strategies ◽  
Vampire Bat

Abstract The leaf-nosed bats (Phyllostomidae) are outliers among chiropterans with respect to the unusually high diversity of dietary strategies within the family. Salivary glands, owing to their functions and high ultrastructural variability among lineages, are proposed to have played an important role during the phyllostomid radiation. To identify genes underlying salivary gland functional diversification, we sequenced submandibular gland transcriptomes from phyllostomid species representative of divergent dietary strategies. From the assembled transcriptomes, we performed an array of selection tests and gene expression analyses to identify signatures of adaptation. Overall, we identified an enrichment of immunity-related gene ontology terms among 53 genes evolving under positive selection. Lineage-specific selection tests revealed several endomembrane system genes under selection in the vampire bat. Many genes that respond to insulin were under selection and differentially expressed genes pointed to modifications of amino acid synthesis pathways in plant-visitors. Results indicate salivary glands have diversified in various ways across a functional diverse clade of mammals in response to niche specializations.

scholarly journals Novel germline variant in the histone demethylase and transcription regulator KDM4C induces a multi-cancer phenotype

2021 ◽  
pp. jmedgenet-2021-107747
Author(s):  
Riku Katainen ◽  
Iikki Donner ◽  
Maritta Räisänen ◽  
Davide Berta ◽  
Anna Kuosmanen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rare Variants ◽  
Cancer Susceptibility ◽  
Histone Demethylase ◽  
Interaction Partner ◽  
Transcription Regulator ◽  
H3k9 Trimethylation ◽  
Mutation Carriers ◽  
The Family ◽  
Project Data

BackgroundGenes involved in epigenetic regulation are central for chromatin structure and gene expression. Specific mutations in these might promote carcinogenesis in several tissue types.MethodsWe used exome, whole-genome and Sanger sequencing to detect rare variants shared by seven affected individuals in a striking early-onset multi-cancer family. The only variant that segregated with malignancy resided in a histone demethylase KDM4C. Consequently, we went on to study the epigenetic landscape of the mutation carriers with ATAC, ChIP (chromatin immunoprecipitation) and RNA-sequencing from lymphoblastoid cell lines to identify possible pathogenic effects.ResultsA novel variant in KDM4C, encoding a H3K9me3 histone demethylase and transcription regulator, was found to segregate with malignancy in the family. Based on Roadmap Epigenomics Project data, differentially accessible chromatin regions between the variant carriers and controls enrich to normally H3K9me3-marked chromatin. We could not detect a difference in global H3K9 trimethylation levels. However, carriers of the variant seemed to have more trimethylated H3K9 at transcription start sites. Pathway analyses of ChIP-seq and differential gene expression data suggested that genes regulated through KDM4C interaction partner EZH2 and its interaction partner PLZF are aberrantly expressed in mutation carriers.ConclusionsThe apparent dysregulation of H3K9 trimethylation and KDM4C-associated genes in lymphoblastoid cells supports the hypothesis that the KDM4C variant is causative of the multi-cancer susceptibility in the family. As the variant is ultrarare, located in the conserved catalytic JmjC domain and predicted pathogenic by the majority of available in silico tools, further studies on the role of KDM4C in cancer predisposition are warranted.

scholarly journals Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 890
Author(s):  
Zifeng Ouyang ◽  
Yimeng Wang ◽  
Tiantian Ma ◽  
Gisele Kanzana ◽  
Fan Wu ◽  
...  
Keyword(s):  
Group Method ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Important Data ◽  
Breeding Programs ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Medicinal Value ◽  
Genome Wide ◽  
Melilotus Albus

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.

scholarly journals The Role of Botanical Families in Medicinal Ethnobotany: A Phylogenetic Perspective

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 163
Author(s):  
Airy Gras ◽  
Oriane Hidalgo ◽  
Ugo D’Ambrosio ◽  
Montse Parada ◽  
Teresa Garnatje ◽  
...  
Keyword(s):  
Diversity Indices ◽  
Specific Level ◽  
Medicinal Uses ◽  
The Family ◽  
Family Level ◽  
Phylogenetic Level ◽  
Molecular Phylogenetic ◽  
Quantitative Analyses ◽  
Medicinal Flora

Studies suggesting that medicinal plants are not chosen at random are becoming more common. The goal of this work is to shed light on the role of botanical families in ethnobotany, depicting in a molecular phylogenetic frame the relationships between families and medicinal uses of vascular plants in several Catalan-speaking territories. The simple quantitative analyses for ailments categories and the construction of families and disorders matrix were carried out in this study. A Bayesian approach was used to estimate the over- and underused families in the medicinal flora. Phylogenetically informed analyses were carried out to identify lineages in which there is an overrepresentation of families in a given category of use, i.e., hot nodes. The ethnobotanicity index, at a specific level, was calculated and also adapted to the family level. Two diversity indices to measure the richness of reported taxa within each family were calculated. A total of 47,630 use reports were analysed. These uses are grouped in 120 botanical families. The ethnobotanicity index for this area is 14.44% and the ethnobotanicity index at the family level is 68.21%. The most-reported families are Lamiaceae and Asteraceae and the most reported troubles are disorders of the digestive and nutritional system. Based on the meta-analytic results, indicating hot nodes of useful plants at the phylogenetic level, specific ethnopharmacological research may be suggested, including a phytochemical approach of particularly interesting taxa.

scholarly journals Inuit plant use in the eastern Subarctic: comparative ethnobotany in Kangiqsualujjuaq, Nunavik, and in Nain, Nunatsiavut

Botany ◽  
2019 ◽  
Vol 97 (5) ◽  
pp. 271-282
Author(s):  
Alain Cuerrier ◽  
Courtenay Clark ◽  
Christian H. Norton
Keyword(s):  
Lifestyle Changes ◽  
Ethnobotanical Knowledge ◽  
Structured Interviews ◽  
Medicinal Species ◽  
Medicinal Uses ◽  
Plant Uses ◽  
The Family ◽  
Plant Names ◽  
Family Level ◽  
Comparative Ethnobotany

Plants are important in traditional Inuit life. They are used for food, tea, medicine, etc. Based on semi-structured interviews with 35 informants, we documented and compared plant names and uses in Kangiqsualujjuaq, Nunavik, and in Nain, Nunatsiavut. Plant names and uses were expected to be similar between communities owing to common boreal–subarctic environments and cultural ties. Both communities reported the same number of taxa, with equivalent proportions of vascular and nonvascular plants, growth forms, use categories, and medicinal uses. Forty-three species were used in each community, for a total of 78 species from 39 families. Despite a high overlap in species distributions, only 35% of nonvascular and 56% of vascular species were used in both communities. Correspondence was higher at the family level (64% of nonvascular and 75% of vascular families shared). The Ericaceae family was the most used, followed by Rosaceae. Thirteen of 30 medicinal species were shared between communities. There was a low correspondence regarding the conditions for which the medicinal species were used. Edible taxa were shared the most (52%). Plant uses unique to either Nain or Kangiqsualujjuaq may reveal separate bodies of traditional knowledge, or may reflect an overall loss of ethnobotanical knowledge in the Subarctic due to recent lifestyle changes.

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