Brain microRNAs among social and solitary bees

Evolutionary transitions to a social lifestyle in insects are associated with lineage-specific changes in gene expression, but the key nodes that drive these regulatory changes are unknown. We examined the relationship between social organization and lineage-specific microRNAs (miRNAs). Genome scans across 12 bee species showed that miRNA copy-number is mostly conserved and not associated with sociality. However, deep sequencing of small RNAs in six bee species revealed a substantial proportion (20–35%) of detected miRNAs had lineage-specific expression in the brain, 24–72% of which did not have homologues in other species. Lineage-specific miRNAs disproportionately target lineage-specific genes, and have lower expression levels than shared miRNAs. The predicted targets of lineage-specific miRNAs are not enriched for genes with caste-biased expression or genes under positive selection in social species. Together, these results suggest that novel miRNAs may coevolve with novel genes, and thus contribute to lineage-specific patterns of evolution in bees, but do not appear to have significant influence on social evolution. Our analyses also support the hypothesis that many new miRNAs are purged by selection due to deleterious effects on mRNA targets, and suggest genome structure is not as influential in regulating bee miRNA evolution as has been shown for mammalian miRNAs.

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Brain microRNAs among social and solitary bees

10.1101/730317 ◽

2019 ◽

Author(s):

Karen M. Kapheim ◽

Beryl M. Jones ◽

Eirik Søvik ◽

Eckart Stolle ◽

Robert M. Waterhouse ◽

...

Keyword(s):

Social Evolution ◽

Genome Structure ◽

Specific Expression ◽

Evolutionary Transitions ◽

Mrna Targets ◽

Regulatory Changes ◽

Social Species ◽

Mirna Evolution ◽

Or Genes ◽

Lineage Specific Genes

ABSTRACTEvolutionary transitions to a social lifestyle in insects are associated with lineage-specific changes in gene expression, but the key nodes that drive these regulatory changes are unknown. We examined the relationship between social organization and lineage-specific microRNAs (miRNAs). Genome scans across 12 bee species showed that miRNA copy-number is mostly conserved and not associated with sociality. However, deep sequencing of small RNAs in six bee species revealed a substantial proportion (20-35%) of detected miRNAs had lineage-specific expression in the brain, 24-72% of which did not have homologs in other species. Lineage-specific miRNAs disproportionately target lineage-specific genes, and have lower expression levels than shared miRNAs. The predicted targets of lineage-specific miRNAs are not enriched for genes with caste-biased expression or genes under positive selection in social species. Together, these results suggest that novel miRNAs may coevolve with novel genes, and thus contribute to lineage-specific patterns of evolution in bees, but do not appear to have significant influence on social evolution. Our analyses also support the hypothesis that many new miRNAs are purged by selection due to deleterious effects on mRNA targets, and suggest genome structure is not as influential in regulating bee miRNA evolution as has been shown for mammalian miRNAs.

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Recombination mapping of the Brazilian stingless bee Frieseomelitta varia confirms high recombination rates in social hymenoptera

BMC Genomics ◽

10.1186/s12864-021-07987-3 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Prashant Waiker ◽

Fabiano Carlos Pinto de Abreu ◽

Danielle Luna-Lucena ◽

Flávia Cristina Paula Freitas ◽

Zilá Luz Paulino Simões ◽

...

Keyword(s):

Linkage Map ◽

Social Evolution ◽

Stingless Bee ◽

Recombination Rates ◽

Social Hymenoptera ◽

Social Species ◽

A Genome ◽

Study Results ◽

Worker Caste ◽

Genomic Recombination

Abstract Background Meiotic recombination is a fundamental genetic process that shuffles allele combinations and promotes accurate segregation of chromosomes. Analyses of the ubiquitous variation of recombination rates within and across species suggest that recombination is evolving adaptively. All studied insects with advanced eusociality have shown exceptionally high recombination rates, which may represent a prominent case of adaptive evolution of recombination. However, our understanding of the relationship between social evolution and recombination rates is incomplete, partly due to lacking empirical data. Here, we present a linkage map of the monandrous, advanced eusocial Brazilian stingless bee, Frieseomelitta varia, providing the first recombination analysis in the diverse Meliponini (Hymenoptera, Apidae). Results Our linkage map includes 1417 markers in 19 linkage groups. This map spans approximately 2580 centimorgans, and comparisons to the physical genome assembly indicate that it covers more than 75 % of the 275 Megabasepairs (Mbp) F. varia genome. Thus, our study results in a genome-wide recombination rate estimate of 9.3–12.5 centimorgan per Mbp. This value is higher than estimates from nonsocial insects and comparable to other highly social species, although it does not support our prediction that monandry and strong queen-worker caste divergence of F. varia lead to even higher recombination rates than other advanced eusocial species. Conclusions Our study expands the association between elevated recombination and sociality in the order Hymenoptera and strengthens the support for the hypothesis that advanced social evolution in hymenopteran insects invariably selects for high genomic recombination rates.

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The weird eusociality of polyembryonic parasites

Biology Letters ◽

10.1098/rsbl.2021.0026 ◽

2021 ◽

Vol 17 (4) ◽

Author(s):

Brian A. Whyte

Keyword(s):

Larval Stage ◽

Social Evolution ◽

Parasitoid Wasps ◽

Biological Organization ◽

Evolutionary Transitions ◽

Evolutionary Theories ◽

Transitions Theory ◽

Animal Societies ◽

Social Behaviours

Some parasitoid wasps possess soldier castes during their parasitic larval stage, but are often neglected from our evolutionary theories explaining caste systems in animal societies. This is primarily due to the polyembryonic origin of their societies. However, recent discoveries of polyembryonic trematodes (i.e. flatworms) possessing soldier castes require us to reconsider this reasoning. I argue we can benefit from including these polyembryonic parasites in eusocial discussions, for polyembryony and parasitism are taxonomically vast and influence the evolution of social behaviours and caste systems in various circumstances. Despite their polyembryony, their social evolution can be explained by theories of eusociality designed for parent–offspring groups, which are the subjects of most social evolution research. Including polyembryonic parasites in these theories follows the trend of major evolutionary transitions theory expanding social evolution research into all levels of biological organization. In addition, these continued discoveries of caste systems in parasites suggest social evolution may be more relevant to parasitology than currently acknowledged.

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Genome-Wide Identification, Characterization and Function Analysis of Lineage-Specific Genes in the Tea Plant Camellia sinensis

Frontiers in Genetics ◽

10.3389/fgene.2021.770570 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhizhu Zhao ◽

Dongna Ma

Keyword(s):

Camellia Sinensis ◽

Function Analysis ◽

Gc Content ◽

Tea Plant ◽

Pentose Phosphate ◽

Specific Expression ◽

Phenotypic Alteration ◽

Genome Wide ◽

The Rich ◽

Lineage Specific Genes

Genes that have no homologous sequences with other species are called lineage-specific genes (LSGs), are common in living organisms, and have an important role in the generation of new functions, adaptive evolution and phenotypic alteration of species. Camellia sinensis var. sinensis (CSS) is one of the most widely distributed cultivars for quality green tea production. The rich catechins in tea have antioxidant, free radical elimination, fat loss and cancer prevention potential. To further understand the evolution and utilize the function of LSGs in tea, we performed a comparative genomics approach to identify Camellia-specific genes (CSGs). Our result reveals that 1701 CSGs were identified specific to CSS, accounting for 3.37% of all protein-coding genes. The majority of CSGs (57.08%) were generated by gene duplication, and the time of duplication occurrence coincide with the time of two genome-wide replication (WGD) events that happened in CSS genome. Gene structure analysis revealed that CSGs have shorter gene lengths, fewer exons, higher GC content and higher isoelectric point. Gene expression analysis showed that CSG had more tissue-specific expression compared to evolutionary conserved genes (ECs). Weighted gene co-expression network analysis (WGCNA) showed that 18 CSGs are mainly associated with catechin synthesis-related pathways, including phenylalanine biosynthesis, biosynthesis of amino acids, pentose phosphate pathway, photosynthesis and carbon metabolism. Besides, we found that the expression of three CSGs (CSS0030246, CSS0002298, and CSS0030939) was significantly down-regulated in response to both types of stresses (salt and drought). Our study first systematically identified LSGs in CSS, and comprehensively analyzed the features and potential functions of CSGs. We also identified key candidate genes, which will provide valuable assistance for further studies on catechin synthesis and provide a molecular basis for the excavation of excellent germplasm resources.

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The Draft Genome of the Endangered Sichuan Partridge (Arborophila rufipectus) with Evolutionary Implications

Genes ◽

10.3390/genes10090677 ◽

2019 ◽

Vol 10 (9) ◽

pp. 677 ◽

Cited By ~ 1

Author(s):

Chuang Zhou ◽

Hongmei Tu ◽

Haoran Yu ◽

Shuai Zheng ◽

Bo Dai ◽

...

Keyword(s):

De Novo ◽

Genome Structure ◽

Draft Genome ◽

Enrichment Analysis ◽

Phylogenetic Position ◽

Nucleotide Polymorphisms ◽

Protein Coding ◽

Go Enrichment ◽

And Behavior ◽

Or Genes

The Sichuan partridge (Arborophila rufipectus, Phasianidae, Galliformes) is distributed in south-west China, and classified as endangered grade. To examine the evolution and genomic features of Sichuan partridge, we de novo assembled the Sichuan partridge reference genome. The final draft assembly consisted of approximately 1.09 Gb, and had a scaffold N50 of 4.57 Mb. About 1.94 million heterozygous single-nucleotide polymorphisms (SNPs) were detected, 17,519 protein-coding genes were predicted, and 9.29% of the genome was identified as repetitive elements. A total of 56 olfactory receptor (OR) genes were found in Sichuan partridge, and conserved motifs were detected. Comparisons between the Sichuan partridge genome and chicken genome revealed a conserved genome structure, and phylogenetic analysis demonstrated that Arborophila possessed a basal phylogenetic position within Phasianidae. Gene Ontology (GO) enrichment analysis of positively selected genes (PSGs) in Sichuan partridge showed over-represented GO functions related to environmental adaptation, such as energy metabolism and behavior. Pairwise sequentially Markovian coalescent analysis revealed the recent demographic trajectory for the Sichuan partridge. Our data and findings provide valuable genomic resources not only for studying the evolutionary adaptation, but also for facilitating the long-term conservation and genetic diversity for this endangered species.

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ARCHIPELAGO: A Dedicated Resource for Exploiting Past, Present, and Future Genomic Data on Disease Resistance Regulation in Rice

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-21-7-0869 ◽

2008 ◽

Vol 21 (7) ◽

pp. 869-878 ◽

Cited By ~ 24

Author(s):

E. Vergne ◽

E. Ballini ◽

G. Droc ◽

D. Tharreau ◽

J.-L. Nottéghem ◽

...

Keyword(s):

Expression Patterns ◽

Genome Structure ◽

Defense Genes ◽

Defense Gene Expression ◽

Specific Expression ◽

Defense Gene ◽

Biotic Stresses ◽

Qtl Cloning ◽

Pathogenesis Related ◽

Micro Level

Large amounts of expression data dealing with biotic stresses in rice have been produced in the past 5 years. Here, we extensively review approximately 70 publications and gather together information on more than 2,500 genes of the rice defense arsenal. This information was integrated into the OryGenesDB database. Several genes (e.g., metallothioneins and PBZ1) appear to be hallmarks of rice–pathogen interactions. Cross-referencing this information with the rice kinome highlighted some defense genes and kinases as possible central nodes of regulation. Cross referencing defense gene expression and quantitative trait loci (QTL) information identified some candidate genes for QTL. Overall, pathogenesis-related genes and disease regulators were found to be statistically associated with disease QTL. At the genomic level, we observed that some regions are richer than others and that some chromosomes (e.g., 11 and 12), which contain a lot of resistance gene analogs, have a low content of defense genes. Finally, we show that classical defense genes and defense-related genes such as resistance genes are preferentially organized in clusters. These clusters are not always coregulated and individual paralogs can show specific expression patterns. Thus, the rice defense arsenal has an ARCHIPELAGO-like genome structure at the macro and micro level. This resource opens new possibilities for marker-assisted selection and QTL cloning.

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The Use of Urine Marking in the Scavenging Behavior of the Red Fox (Vulpes v uLpes)

Behaviour ◽

10.1163/156853977x00496 ◽

1977 ◽

Vol 61 (1-2) ◽

pp. 82-105 ◽

Cited By ~ 89

Author(s):

J. David Henry

Keyword(s):

Social Life ◽

Social Evolution ◽

Red Fox ◽

Future Research ◽

Red Foxes ◽

Social Species ◽

Urine Marking ◽

The Social ◽

Free Ranging ◽

Solitary Species

AbstractThe eleven different functions for which mammals use urine marking are reviewed in this paper, and the urine marking behavior of the red fox (Vulpes vulpes) is described in detail. A new hypothesis is advanced that urine marking may serve as a "book keeping system" in the red fox's scavenging behavior. Foxes consistently investigate and urine mark inedible food remnants (e.g., bones, bird wings, and dried out pieces of hide). When a fox re-investigates a marked remnant, the urine mark signals "no food present," and the fox investigates this object for only a brief period of time. This use of urine marking may increase the efficiency of its scavenging behavior, i.e. more food-items found per hour of scavenging. This efficiency may be particularly important during periods of food shortage. The hypothesis is tested in three different experiments, using free-ranging red foxes as subjects. Experiment I establishes that fox do urine mark food remnants. Experiment II shows that foxes investigate for a significantly shorter period of time (P<0.001) food remnants exhibiting both the odor of food and the odor of urine as compared to remnants exhibiting just the odor of food. Experiment III suggests that there a hierarchy of stimuli which determines different responses in the fox's scavenging behavior. The experiments also suggest that there is a degree of social behavior in the scavenging activities of red foxes. Foxes appear to use each other's urine marks to increase the efficiency of their scavenging behavior. Thus this study definitely support LEYHAUSEN'S (1965) statement that the social life of solitary animals is frequently more complex than we realize. Solitary species probably show many ingeniously adapted mechanisms for occupying niches where highly social species could not be maintained. The social evolution and ecological advantages of solitary species deserve to be the focus of future research.

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Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1702072114 ◽

2017 ◽

Vol 114 (22) ◽

pp. E4435-E4441 ◽

Cited By ~ 36

Author(s):

Tianying Lan ◽

Tanya Renner ◽

Enrique Ibarra-Laclette ◽

Kimberly M. Farr ◽

Tien-Hao Chang ◽

...

Keyword(s):

Genome Structure ◽

Nuclear Genome ◽

Carnivorous Plant ◽

Plant Genome ◽

Peptide Transport ◽

Special Importance ◽

Specific Expression ◽

Gene Copies ◽

Duplication Events ◽

Syntenic Gene

Utricularia gibba, the humped bladderwort, is a carnivorous plant that retains a tiny nuclear genome despite at least two rounds of whole genome duplication (WGD) since common ancestry with grapevine and other species. We used a third-generation genome assembly with several complete chromosomes to reconstruct the two most recent lineage-specific ancestral genomes that led to the modern U. gibba genome structure. Patterns of subgenome dominance in the most recent WGD, both architectural and transcriptional, are suggestive of allopolyploidization, which may have generated genomic novelty and led to instantaneous speciation. Syntenic duplicates retained in polyploid blocks are enriched for transcription factor functions, whereas gene copies derived from ongoing tandem duplication events are enriched in metabolic functions potentially important for a carnivorous plant. Among these are tandem arrays of cysteine protease genes with trap-specific expression that evolved within a protein family known to be useful in the digestion of animal prey. Further enriched functions among tandem duplicates (also with trap-enhanced expression) include peptide transport (intercellular movement of broken-down prey proteins), ATPase activities (bladder-trap acidification and transmembrane nutrient transport), hydrolase and chitinase activities (breakdown of prey polysaccharides), and cell-wall dynamic components possibly associated with active bladder movements. Whereas independently polyploid Arabidopsis syntenic gene duplicates are similarly enriched for transcriptional regulatory activities, Arabidopsis tandems are distinct from those of U. gibba, while still metabolic and likely reflecting unique adaptations of that species. Taken together, these findings highlight the special importance of tandem duplications in the adaptive landscapes of a carnivorous plant genome.

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Relationship Between Inter-individual Variation in Circadian Rhythm and Sociality: A case Study Using Halictid Bees

10.1101/2021.09.03.458748 ◽

2021 ◽

Author(s):

Sofia Melendez Cartagena ◽

Carlos A Ortiz-Alvarado ◽

Patricia Ordonez ◽

Claudia S Cordero-Martinez ◽

Alexandria F Ambrose ◽

...

Keyword(s):

Puerto Rico ◽

Circadian Rhythm ◽

Circadian Rhythms ◽

Individual Variation ◽

Social Evolution ◽

Optimal Model ◽

Social Species ◽

Circadian Behavior ◽

Solitary Species

The bee family Halictidae is considered to be an optimal model for the study of social evolution due to its remarkable range of social behaviors. Past studies in circadian rhythms suggest that social species may express more diversity in circadian behaviors than solitary species. However, these previous studies did not make appropriate taxonomic comparisons. To further explore the link between circadian rhythms and sociality, we examine four halictid species with different degrees of sociality, three social species of Lasioglossum, one from Greece and two from Puerto Rico, and a solitary species of Systropha from Greece. Based on our previous observations, we hypothesized that species with greater degree of sociality will show greater inter-individual variation in circadian rhythms than solitary species. We observed distinct differences in their circadian behavior that parallel differences across sociality, where the most social species expressed the highest inter-individual variation. We predict that circadian rhythm differences will be informative of sociality across organisms.

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Integrative Analysis Extracts a Core ceRNA Network of the Fetal Hippocampus With Down Syndrome

Frontiers in Genetics ◽

10.3389/fgene.2020.565955 ◽

2020 ◽

Vol 11 ◽

Author(s):

Shengran Wang ◽

Xia Tang ◽

Litao Qin ◽

Weili Shi ◽

Shasha Bian ◽

...

Keyword(s):

Down Syndrome ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Expression Patterns ◽

Cell Type ◽

Specific Expression ◽

Cerna Network ◽

Mrna Targets ◽

Cell Type Specific Expression ◽

Cell Type Specific

Accumulating evidence suggests that circular RNAs (circRNAs)—miRNA–mRNA ceRNA regulatory network—may play an important role in neurological disorders, such as Alzheimer’s disease (AD). Interestingly, neuropathological changes that closely resemble AD have been found in nearly all Down syndrome (DS) cases > 35 years. However, few studies have reported circRNA transcriptional profiling in DS cases, which is caused by a chromosomal aberration of trisomy 21. Here, we characterized the expression profiles of circRNAs in the fetal hippocampus of DS patients (n = 8) and controls (n = 6) by using microarray. MiRNA, mRNA expression profiling of DS from our previous study and scRNA-seq data describing normal fetal hippocampus development (GEO) were also integrated into the analysis. The similarity between circRNAs/genes with traits/cell-types was calculated by weighted correlation network analysis (WGCNA). miRanda and miRWalk2 were used to predict ceRNA network interactions. We identified a total of 7,078 significantly differentially expressed (DE) circRNAs, including 2,637 upregulated and 4,441 downregulated genes, respectively. WGCNA obtained 15 hub circRNAs and 6 modules with cell type–specific expression patterns among scRNA-seq data. Finally, a core ceRNA network was constructed by 14 hub circRNAs, 17 DE miRNA targets and 245 DE mRNA targets with a cell type–specific expression pattern annotation. Known functional molecules in DS or neurodegeneration (e.g., miR-138, OLIG1, and TPM2) were also included in this network. Our findings are the first to delineate the landscape of circRNAs in DS and the first to effectively integrate ceRNA regulation with scRNA-seq data. These data may provide a valuable resource for further research on the molecular mechanisms or therapeutic targets underlying DS neuropathy.

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