De novosequencing, diploid assembly, and annotation of the black carpenter ant,Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing DOI Open Access
Christopher Faulk

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: April 1, 2022

Abstract The black carpenter ant ( Camponotus pennsylvanicus ) is a pest species found widely throughout North America east of the Rocky Mountains. Its frequent infestation in human buildings justifies close genetic examination and its large size small genome make it ideal for individual sequencing. From single I used long-read nanopore sequencing to assemble 306 Mb, with an N50 565 Kb, 60X coverage, quality assessed by 97.0% BUSCO score, improving upon related assemblies. reads provided secondary information form parasitic symbiont genomes, as well epigenetic information. assembled complete Wolbachia bacterial isolate 1.2 Mb 76X commensal bacterium tribe, species-specific Blochmannia , at 791 2400X which matched within 200 bp previously published reference. also produced mitochondrial over 5000X revealing minor rearrangements first assembly this species. DNA methylation hydroxymethylation was measured simultaneously whole genome, base-pair resolution level from same confirmed extremely low levels seen Formicidae family Hymenoptera. A phased diploid built, moderate heterozygosity, 0.16% bases having biallelic SNPs two parental haplotypes. Protein prediction yielded 20,209 putative amino acid sequences annotation identified 86% known proteins. All assemblies were derived Minion flow cell generating 20 Gb sequence cost $1047 including all consumable reagents. Adding fixed costs required equipment batch reagents brings ant-sized less than $5000. Complete analysis performed under 1 week on commodity computer desktop 64 memory.

Language: Английский

Hijacking time: How Ophiocordyceps fungi could be using ant host clocks to manipulate behavior DOI Creative Commons
Charissa de Bekker, Biplabendu Das

Parasite Immunology, Journal Year: 2022, Volume and Issue: 44(3)

Published: Feb. 1, 2022

Ophiocordyceps fungi manipulate ant behaviour as a transmission strategy. Conspicuous changes in the daily timing of disease phenotypes suggest that and other manipulators could be hijacking host clock. We discuss available data support notion clocks consider how altering behavioural rhythms benefit fungal infection cycle. By reviewing time-course transcriptomics for parasite host, we argue has light-entrainable clock might drive expression candidate manipulation genes. Moreover, are seemingly highly plastic involved division labour, which make them susceptible to hijacking. To provisionally test whether plasticity rhythmicity genes affected by manipulation, performed gene co-expression network analysis on linked it data. found reside same modules those during manipulation. These showed significant connectivity with rhythmic modules, suggesting indirectly affecting well.

Language: Английский

Citations

33

Hormonal gatekeeping via the blood-brain barrier governs caste-specific behavior in ants DOI Creative Commons
Linyang Ju, Karl M. Glastad, Lihong Sheng

et al.

Cell, Journal Year: 2023, Volume and Issue: 186(20), P. 4289 - 4309.e23

Published: Sept. 1, 2023

Language: Английский

Citations

17

Molecular circadian rhythms are robust in marine annelids lacking rhythmic behavior DOI Creative Commons
N. Sören Häfker, Laurenz Holcik,

Audrey M. Mat

et al.

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(4), P. e3002572 - e3002572

Published: April 11, 2024

The circadian clock controls behavior and metabolism in various organisms. However, the exact timing strength of rhythmic phenotypes can vary significantly between individuals same species. This is highly relevant for rhythmically complex marine environments where organismal diversity likely permits occupation different microenvironments. When investigating locomotor Platynereis dumerilii , a model system molecular chronobiology, we found strain-specific, high variability individual worms. patterns were maintained several weeks. A diel head transcriptome comparison behaviorally versus arrhythmic wild-type worms showed that 24-h cycling core transcripts identical both behavioral phenotypes. While similar total number compared to their counterparts, annotation categories transcripts, however, differed substantially. Consistent with phenotype, exhibit an enrichment related neuronal/behavioral processes. In contrast, increased metabolism- physiology-related transcripts. prominent role neuropeptide pigment-dispersing factor (PDF) Drosophila prompted us test possible functional involvement pdf . Differing from its loss impacts overall activity levels but shows only indirect effects on rhythmicity. Our results show given process rhythmicity others. Across population, exist as continuum, no distinct “boundaries” arrhythmicity. We suggest such rhythm breadth important biodiversity resource enabling species quickly adapt heterogeneous or changing environments. times massive sequencing, our work also emphasizes importance time series tests.

Language: Английский

Citations

7

Mechanisms behind the Madness: How Do Zombie-Making Fungal Entomopathogens Affect Host Behavior To Increase Transmission? DOI
Charissa de Bekker, William C. Beckerson, Carolyn Elya

et al.

mBio, Journal Year: 2021, Volume and Issue: 12(5)

Published: Oct. 5, 2021

Transmission is a crucial step in all pathogen life cycles. As such, certain species have evolved complex traits that increase their chances to find and invade new hosts.

Language: Английский

Citations

34

De novosequencing, diploid assembly, and annotation of the black carpenter ant,Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing DOI Creative Commons
Christopher Faulk

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 51(1), P. 17 - 28

Published: June 21, 2022

The black carpenter ant (Camponotus pennsylvanicus) is a pest species found widely throughout North America. From single individual I used long-read nanopore sequencing to assemble phased diploid genome of 306 Mb and 60X coverage, with quality assessed by 97.0% BUSCO score, improving upon other assemblies. mitochondrial reveals minor rearrangements from ants. reads also allowed assembly parasitic symbiont genomes. include complete Wolbachia bacterial size 1.2 Mb, as well commensal Blochmannia pennsylvanicus, at 791 kb. DNA methylation hydroxymethylation were measured base-pair resolution level the same confirmed extremely low levels seen in Formicidae family. There was moderate heterozygosity, 0.16% bases being biallelic parental haplotypes. Protein prediction yielded 14 415 amino acid sequences 95.8% score 86% matching previously known proteins. All assemblies derived MinION flow cell generating 20 Gb sequence for cost $1047 including consumable reagents. Adding fixed costs equipment brings total an ant-sized less than $5000. analyses performed 1 week on desktop computer.Creating reference animal genomes typically large, expensive process. Here sequenced only $1000 sole researcher just one week. Along nuclear genome, assembled two bacteria living within ant. Nanopore technology enabled epigenetic measurements replicated studies showing very methylation. compared favorably continuity protein accuracy. This method will allow low-resource labs create high cost.

Language: Английский

Citations

24

Beyond circadian rhythms: emerging roles of ultradian rhythms in control of liver functions DOI Open Access
Gad Asher, Bokai Zhu

Hepatology, Journal Year: 2022, Volume and Issue: 77(3), P. 1022 - 1035

Published: May 20, 2022

The mammalian liver must cope with various metabolic and physiological changes that normally recur every day primarily stem from daily cycles of rest‐activity fasting‐feeding. Although a large body evidence supports the reciprocal regulation circadian rhythms function, research on hepatic ultradian have largely been lagging behind. However, advent more cost‐effective high‐throughput omics technologies, high‐resolution time‐lapse imaging, robust powerful mathematical tools, several recent studies shed new light presence functions rhythms. In this review, we will first very briefly discuss basic principles rhythms, then cover in greater details literature related to Specifically, highlight prevalence mechanisms 12‐h 8‐h which cycle at second third harmonics frequency. Finally, also refer other frequencies examine limitations current approaches as well challenges identifying rhythm addressing their molecular underpinnings.

Language: Английский

Citations

19

Task-specific odorant receptor expression in worker antennae indicates that sensory filters regulate division of labor in ants DOI Creative Commons
Marcel A. Caminer, Romain Libbrecht, Megha Majoe

et al.

Communications Biology, Journal Year: 2023, Volume and Issue: 6(1)

Published: Oct. 2, 2023

Division of labor (DOL) is a characteristic trait insect societies, where tasks are generally performed by specialized individuals. Inside workers focus on brood or nest care, while others take risks foraging outside. Theory proposes that have different thresholds to perform certain when confronted with task-related stimuli, leading specialization and consequently DOL. Workers presumed vary in their response cues rather than how they perceive such information. Here, we test the hypothesis DOL instead stems from varying efficiency detect stimuli specific tasks. We use transcriptomics measure mRNA expression levels antennae brain nurses foragers ant Temnothorax longispinosus. find seven times as many genes be differentially expressed between behavioral phenotypes compared brain. Moreover, half all odorant receptors expressed, an overrepresentation 9-exon gene family upregulated nurses. Nurses thus apparently differ perception olfactory environment signals. Our study supports antennal sensory filters predispose specialize

Language: Английский

Citations

10

Social insect transcriptomics and the molecular basis of caste diversity DOI
Sarah E. Orr, Michael A. D. Goodisman

Current Opinion in Insect Science, Journal Year: 2023, Volume and Issue: 57, P. 101040 - 101040

Published: April 25, 2023

Language: Английский

Citations

9

Effects of pairing on color change and central gene expression in lined seahorses DOI

Sabrina L. Mederos,

Rafael C. Duarte, Mira Mastoras

et al.

Genes Brain & Behavior, Journal Year: 2022, Volume and Issue: 21(5)

Published: June 1, 2022

Abstract Social monogamy is a reproductive strategy characterized by pair living and defense of common territory. Pair bonding, sometimes displayed monogamous species, an affective construct that includes preference for specific partner, distress upon separation, the ability partner to buffer against stress. Many seahorse species show social structure in wild, but their bond has not been well studied. We examined gene expression lined seahorses ( Hippocampus erectus ) during after process pairing laboratory as color change (luminance), potential form communication behavioral synchrony between mates. When either sex was interacting with its mate, changes luminance (“brightness”) were correlated larger than when opposite‐sex stranger. At conclusion testing, subjects euthanized, RNA extracted from whole brains analyzed via sequencing. Changes paired males versus those unpaired included processes governing metabolic activity, hormones cilia. Perhaps most interesting overlap induced both male prairie voles, including components hormone systems regulating reproduction. Because our limited sample size, we consider results interpretations be preliminary, prompts further exploration. Future studies will expand these findings investigate neuroendocrine genetic basis behaviors.

Language: Английский

Citations

10

28 minutes later: investigating the role of aflatrem-like compounds in Ophiocordyceps parasite manipulation of zombie ants DOI Creative Commons
William C. Beckerson, Courtney Krider,

Umar A. Mohammad

et al.

Animal Behaviour, Journal Year: 2023, Volume and Issue: 203, P. 225 - 240

Published: July 14, 2023

Coevolutionary relationships between parasites and their hosts can lead to the emergence of diverse phenotypes over time, as seen in Ophiocordyceps fungi that manipulate insect arachnid behaviour aid fungal spore transmission. The most conspicuous examples are found ants Camponotini tribe, colloquially known 'zombie ants'. While behaviours induced during infection well described, molecular underpinnings remain unknown. Recent genomics transcriptomics analyses camponoti-floridani have identified several highly upregulated biomolecules produced by fungus Camponotus floridanus. Among them is an ergot alkaloid related mycotoxin aflatrem, cause 'staggers syndrome' cows. Staggering, defined unsteady movements side side, also observed C. floridanus late-stage infection. To test whether aflatrem-like compounds could be responsible, we injected healthy with aflatrem recorded for 30 min. Using both automated object-tracking software MARGO manual behavioural quantification, reduced ant activity speed increased staggering behaviours. examine underlying transcriptomic changes, performed RNA-seq on heads aflatrem-injected ants, keeping step previous work Ophiocordyceps-manipulated ants. We 261 genes were significantly dysregulated compared sham-injected controls. When data from groups shared 113 differentially regulated genes. These included sensory neuron membrane protein genes, odorant-binding musculoskeletal such titin obscurin. Together, these results indicate affect neuromuscular function conservation staggers phenotype Bos taurus suggests behaviour-manipulating strategies exhibited across Tree Life may more similar approach, if not widely different application, than realize.

Language: Английский

Citations

5