Explanipedia

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads Open

Haoyu Cheng, Han Qu, Sean K. McKenzie, Katherine R. Lawrence, Rachael Windsor , et al. · 2025

Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads which are costly and experimentally chal…

Evolution of odorant receptor repertoires across Hymenoptera is not linked to the evolution of eusociality Open

Shubham Gautam, Sean K. McKenzie, Julian Katzke, Francisco Hita Garcia, Shûhei Yamamoto , et al. · 2024

Communication is essential for social organisms. In eusocial insects, olfaction facilitates communication and recognition between nestmates. The study of certain model organisms has led to the hypothesis that odorant receptors are expanded…

Phased nanopore assembly with Shasta and modular graph phasing with GFAse Open

Ryan Lorig-Roach, Melissa Meredith, Jean Monlong, Miten Jain, Hugh E. Olsen , et al. · 2024

Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive regions of the genome, long-read sequenc…

Genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc 2 155 at room temperature Open

Kirk R. Anders, Antonio Abeyta, Christy C. Andrade, Carla Y. Bonilla, Amanda B. Braley , et al. · 2023

We report the genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc 2 155 at room temperature. The genomes add to the diversity of Clusters A, B, C, G, and K. Collectively, the genomes include 70 novel protein-co…

Benchmarking of small and large variants across tandem repeats Open

Adam C. English, Egor Dolzhenko, Helyaneh Ziaei Jam, Sean K. McKenzie, Nathan D. Olson , et al. · 2023

Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of associated molecular traits, and are linked to over 60 disease phenotypes. However, their complexity often excludes them from at-scale studies due to challe…

Social isolation shortens lifespan through oxidative stress in ants Open

Akiko Koto, Makoto Tamura, Pui Shan Wong, Sachiyo Aburatani, Eyal Privman , et al. · 2023

Social network position is a major predictor of ant behavior, microbiota composition, and brain gene expression Open

Tomas Kay, Joanito Liberti, Thomas O. Richardson, Sean K. McKenzie, Chelsea A. Weitekamp , et al. · 2023

The physiology and behavior of social organisms correlate with their social environments. However, because social environments are typically confounded by age and physical environments (i.e., spatial location and associated abiotic factors…

A caste differentiation mutant elucidates the evolution of socially parasitic ants Open

Waring Trible, Vikram Chandra, Kip D. Lacy, Gina Limón, Sean K. McKenzie , et al. · 2023

Most ant species have two distinct female castes-queens and workers-yet the developmental and genetic mechanisms that produce these alternative phenotypes remain poorly understood. Working with a clonal ant, we discovered a variant strain …

Phased nanopore assembly with Shasta and modular graph phasing with GFAse Open

Ryan Lorig-Roach, Melissa Meredith, Jean Monlong, Miten Jain, Hugh E. Olsen , et al. · 2023

As a step towards simplifying and reducing the cost of haplotype resolved de novo assembly, we describe new methods for accurately phasing nanopore data with the Shasta genome assembler and a modular tool for extending phasing to the chrom…

The genomic basis of army ant chemosensory adaptations Open

Sean K. McKenzie, Max Winston, Felix Grewe, Gabriel Vargas Asensio, Natalia Rodríguez‐Hernández , et al. · 2021

The evolution of mass raiding has allowed army ants to become dominant arthropod predators in the tropics. Although a century of research has led to many discoveries about behavioural, morphological and physiological adaptations in army an…

Comparative Development of the Ant Chemosensory System Open

Anna R. Ryba, Sean K. McKenzie, Leonora Olivos-Cisneros, E. Josephine Clowney, Peter Mussells Pires , et al. · 2020

Globally invasive populations of the clonal raider ant are derived from Bangladesh Open

Waring Trible, Sean K. McKenzie, Daniel J. C. Kronauer · 2020

Identifying the native range of invasive species is useful to understand their evolution and natural history, as well as to develop new methods to control potentially harmful introduced organisms. The clonal raider ant, Ooceraea biroi , is…

Table S2 from Globally invasive populations of the clonal raider ant are derived from Bangladesh Open

Waring Trible, Sean K. McKenzie, Daniel J. C. Kronauer · 2020

Microsatellite genotypes at five loci for all samples in the present study.

Table S2 from Globally invasive populations of the clonal raider ant are derived from Bangladesh Open

Waring Trible, Sean K. McKenzie, Daniel J. C. Kronauer · 2020

Microsatellite genotypes at five loci for all samples in the present study.

The genomic architecture and molecular evolution of ant odorant receptors Open

Sean K. McKenzie, Daniel J. C. Kronauer · 2018

The massive expansions of odorant receptor (OR) genes in ant genomes are notable examples of rapid genome evolution and adaptive gene duplication. However, the molecular mechanisms leading to gene family expansion remain poorly understood,…

First genome‐wide analysis of the endangered, endemic lichen Cetradonia linearis reveals isolation by distance and strong population structure Open

Jessica L. Allen, Sean K. McKenzie, Robin S. Sleith, S. Elizabeth Alter · 2018

Premise of the Study Lichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes that drive their diversification and genetic differentiation. Distributions are often assumed to be wholly…

DNA barcoding Brooklyn (New York): A first assessment of biodiversity in Marine Park by citizen scientists Open

Christine Marizzi, Antonia M. Florio, Melissa Lee, Mohammed Khalfan, Cornel Ghiban , et al. · 2018

DNA barcoding is both an important research and science education tool. The technique allows for quick and accurate species identification using only minimal amounts of tissue samples taken from any organism at any developmental phase. DNA…

First genome-wide analysis of an endangered lichen reveals isolation by distance and strong population structure Open

Jessica L. Allen, Sean K. McKenzie, Robin S. Sleith, S. Elizabeth Alter · 2017

Lichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes driving diversification and genetic differentiation in these lineages. Though few studies have examined population genetic patt…

orco Mutagenesis Causes Loss of Antennal Lobe Glomeruli and Impaired Social Behavior in Ants Open

Waring Trible, Leonora Olivos-Cisneros, Sean K. McKenzie, Jonathan Saragosti, Ni‐Chen Chang , et al. · 2017

orcomutagenesis causes loss of antennal lobe glomeruli and impaired social behavior in ants Open

Waring Trible, Ni‐Chen Chang, Benjamin J. Matthews, Sean K. McKenzie, Leonora Olivos-Cisneros , et al. · 2017

Life inside ant colonies is orchestrated with a diverse set of pheromones, but it is not clear how ants perceive these social cues. It has been proposed that pheromone perception in ants evolved via expansions in the numbers of odorant rec…

Transcriptomics and neuroanatomy of the clonal raider ant implicate an expanded clade of odorant receptors in chemical communication Open

Sean K. McKenzie, Ingrid Fetter-Pruneda, Vanessa Ruta, Daniel J. C. Kronauer · 2016

Significance Despite the importance of sociality in the evolutionary history of life, its molecular basis is still poorly understood. The role of novel genes vs. conserved genes is particularly hotly debated. Here we present evidence that …

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