Incongruence in the phylogenomics era

JL Steenwyk, Y Li, X Zhou, XX Shen… - Nature Reviews Genetics, 2023 - nature.com
Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

The NIH Comparative Genomics Resource: addressing the promises and challenges of comparative genomics on human health

K Bornstein, G Gryan, ES Chang, A Marchler-Bauer… - BMC genomics, 2023 - Springer
Comparative genomics is the comparison of genetic information within and across
organisms to understand the evolution, structure, and function of genes, proteins, and non …

Comparative genomics of the major parasitic worms

Nature genetics, 2019 - nature.com
Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating
chronic infections of humans and animals, decimate crop production and are a major …

Harmonizing model organism data in the Alliance of Genome Resources

Genetics, 2022 - academic.oup.com
Abstract The Alliance of Genome Resources (the Alliance) is a combined effort of 7
knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse …

PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity

A Rozanski, HK Moon, H Brandl… - Nucleic acids …, 2019 - academic.oup.com
Flatworms (Platyhelminthes) are a basally branching phylum that harbours a wealth of
fascinating biology, including planarians with their astonishing regenerative abilities and the …

A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence

M Ivanković, JN Brand, L Pandolfini, T Brown… - Nature …, 2024 - nature.com
The planarian Schmidtea mediterranea is being studied as a model species for
regeneration, but the assembly of planarian genomes remains challenging. Here, we report …

Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms

G Moggioli, B Panossian, Y Sun, D Thiel… - Nature …, 2023 - nature.com
Bacterial symbioses allow annelids to colonise extreme ecological niches, such as
hydrothermal vents and whale falls. Yet, the genetic principles sustaining these symbioses …

The promise and pitfalls of synteny in phylogenomics

JL Steenwyk, N King - Plos Biology, 2024 - journals.plos.org
Reconstructing the tree of life remains a central goal in biology. Early methods, which relied
on small numbers of morphological or genetic characters, often yielded conflicting …

Nemertean, brachiopod, and phoronid neuropeptidomics reveals ancestral spiralian signaling systems

D Thiel, LA Yanez-Guerra… - Molecular Biology …, 2021 - academic.oup.com
Neuropeptides are diverse signaling molecules in animals commonly acting through G-
protein coupled receptors (GPCRs). Neuropeptides and their receptors underwent extensive …

Spiralian genomics and the evolution of animal genome architecture

IJY Liao, TM Lu, ME Chen, YJ Luo - Briefings in Functional …, 2023 - academic.oup.com
Recent developments in sequencing technologies have greatly improved our knowledge of
phylogenetic relationships and genomic architectures throughout the tree of life. Spiralia, a …