Filtering by Subject: Genomics

The Genomics for Australian Plants (GAP) framework initiative – developing genomic resources for understanding the evolution and conservation of the Australian flora.

Lalita Simpson, David Cantrill, Margaret Byrne, et al.

Published: 2024-07-08
Subjects: Biodiversity, Botany, Genomics

The generation and analysis of genome-scale data—genomics—is driving a rapid increase in plant biodiversity knowledge. However, the speed and complexity of technological advance in genomics presents challenges for its widescale use in evolutionary and conservation biology. Here, we introduce and describe a national-scale collaboration conceived to build genomic resources and capability for [...]

Evolution and maintenance of mtDNA gene content across eukaryotes

Shibani Veeraragavan, Maria Johansen, Iain Johnston

Published: 2024-04-22
Subjects: Evolution, Genetics, Genomics

Across eukaryotes, most genes required for mitochondrial function have been transferred to, or otherwise acquired by, the nucleus. Encoding genes in the nucleus has many advantages. So why do mitochondria retain any genes at all? Why does the set of mtDNA genes vary so much across different species? And how do species maintain functionality in the mtDNA genes they do retain? In this review we [...]

The nitroplast and its relatives support a universal model of features predicting gene retention in endosymbiont and organelle genomes

Iain Johnston

Published: 2024-04-22
Subjects: Evolution, Genomics

Endosymbiotic relationships have shaped eukaryotic life. As endosymbionts coevolve with their host, towards full integration as organelles, their genomes tend to shrink, with genes being completely lost or transferred to the host nucleus. Modern endosymbionts and organelles show diverse patterns of gene retention, and why some genes and not others are retained in these genomes is not fully [...]

Datathons: fostering equitability in data reuse in ecology

Stephanie Jurburg, Maria J. Alvarez Blanco, Antonis Chatzinotas, et al.

Published: 2024-04-04
Subjects: Biodiversity, Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Genetics, Genetics and Genomics, Genomics, Life Sciences, Microbiology

Approaches to rapidly collect global biodiversity data are increasingly important, but biodiversity blindspots persist. We organized a three-day Datathon event to improve the openness of local biodiversity data, and facilitate data reuse by local researchers. The first Datathon, organized among microbial ecologists in Uruguay and Argentina assembled the largest microbiome dataset in the region to [...]

Incomplete lineage sorting and hybridization underlie of tree discordance in Petunia and related genera (Petunieae, Solanaceae)

Pedro Henrique Pezzi, Lucas C Wheeler, Loreta Brandão Freitas, et al.

Published: 2024-03-29
Subjects: Biodiversity, Bioinformatics, Botany, Genomics

Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies [...]

Cryptic species and hybridisation in corals: challenges and opportunities for conservation and restoration

Cynthia Riginos, Iva Popovic, Zoe Meziere, et al.

Published: 2024-02-14
Subjects: Genomics, Marine Biology, Other Ecology and Evolutionary Biology

Conservation and management of coral reef ecosystems will depend on accurate assessments of reef-building coral species diversity. However, the true diversity of corals may be obfuscated by the presence of cryptic species, which are likely much more pervasive than is currently recognised. Additionally, cryptic species may sometimes hybridize, resulting in gene introgression between species. Here, [...]

A universal DNA barcode for the Tree of Life

Bruno A S de Medeiros, Liming Cai, Peter J Flynn, et al.

Published: 2024-01-18
Subjects: Bioinformatics, Computational Biology, Genomics, Other Ecology and Evolutionary Biology

Species identification using DNA barcodes has revolutionized biodiversity sciences and society at large. However, conventional barcoding methods do not reflect genomic complexity, may lack sufficient variation, and rely on limited genomic loci that are not universal across the Tree of Life. Here, we develop a novel barcoding method that uses exceptionally low-coverage genome skim data to create a [...]

otb: Creating a HiC/HiFi Pipeline to Assemble the Prosapia bicincta Genome

David Molik, Amanda R Stahlke, Sharu P Sharma, et al.

Published: 2023-12-05
Subjects: Agriculture, Bioinformatics, Computational Biology, Genomics, Other Animal Sciences

The implementation of a new genomic assembly pipeline named only the best [Genome Assembly Tools] (otb) has effectively addressed various challenges associated with data management during the development and storage of genome assemblies. otb, which incorporates a comprehensive pipeline involving a setup layer, quality checks, templating, and the integration of Nextflow and Singularity. The [...]

Withdrawn: Datathons: fostering equitability in data reuse in ecology

Stephanie Jurburg, Maria J. Alvarez Blanco, Antonis Chatzinotas, et al.

Published: 2023-10-06
Subjects: Biodiversity, Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Genetics, Genetics and Genomics, Genomics, Life Sciences, Microbiology

Duplicate of

Building a Portuguese Coalition for Biodiversity Genomics

João Pedro Marques, Paulo Célio Alves, Isabel R. Amorim, et al.

Published: 2023-07-10
Subjects: Genomics

The diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene glacial cycles, leading to a remarkable diversity of species and ecosystems. This rich biodiversity is under threat from anthropogenic drivers, such as climate change, invasive species, [...]

How do monomorphic bacteria evolve? The Mycobacterium tuberculosis complex and the awkward population genetics of extreme clonality

Christoph Stritt, Sebastien Gagneux

Published: 2022-12-15
Subjects: Evolution, Genetics and Genomics, Genomics, Life Sciences, Molecular Genetics, Pathogenic Microbiology, Population Biology

Exchange of genetic material through sexual reproduction or horizontal gene transfer is ubiquitous in nature. Among the few outliers that rarely recombine and mainly evolve by de novo mutation are a group of deadly bacterial pathogens, including the causative agents of leprosy, plague, typhoid, and tuberculosis. The interplay of evolutionary processes is poorly understood in these organisms. [...]

Advances in the reconstruction of the Spider Tree of Life: a roadmap for spider systematics and comparative studies

Siddharth Kulkarni, Hannah Wood, Gustavo Hormiga

Published: 2022-12-14
Subjects: Biodiversity, Ecology and Evolutionary Biology, Entomology, Evolution, Genomics, Life Sciences, Other Ecology and Evolutionary Biology

In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field as studying morphological characters; a few genetic markers have given way to genomic data sets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or [...]

Hybridization boosters diversification in a Neotropical orchid group

Cecilia F. Fiorini, Eric de Camargo Smidt, L. Lacey Knowles, et al.

Published: 2022-12-14
Subjects: Biodiversity, Genomics, Other Ecology and Evolutionary Biology, Plant Biology, Population Biology

Genetic data shows that cryptic hybrids are more common than previously thought and that hybridization and introgression are widespread processes in nature. Regardless of this, studies on hybridization are scarce for the highly speciose Bulbophyllum. The genus presents more than 2,200 species and many examples of recent radiations, in which hybridization is expected to be frequent. Currently, [...]

Alternative reading frames are an underappreciated source of protein sequence novelty

Zachary Ardern

Published: 2022-12-05
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Life Sciences

Alternative reading frames of protein coding genes are a major contributor to the evolution of novel protein products. Recent studies demonstrating this include examples across the three domains of cellular life and in viruses. Alternative frame sequences both increase the number of trials available for the evolutionary invention of new genes and have unusual properties which may facilitate gene [...]

Amphibians' expansion to record elevations influences Batrachochytrium dendrobatidis (Batrachochytriaceae) infection dynamics

Emma Cathleen Steigerwald, Cassandra Gendron, Juan Carlos Chaparro, et al.

Published: 2022-11-23
Subjects: Genomics, Other Ecology and Evolutionary Biology, Other Immunology and Infectious Disease

Climate change impacts emerging infectious disease events through multiple mechanisms, but the influence it exerts through driving host range shifts has been little explored. Not only might we expect range shifts to affect pathogen transmission by altering the connectivity of host populations, but range expanding hosts and pathogens will have different physiological responses to the suites of [...]


You can search by:

  • Title
  • Keywords
  • Author Name
  • Author Affiliation