Evolutionary constraint and innovation across hundreds of placental mammals

MJ Christmas, IM Kaplow, DP Genereux, MX Dong… - Science, 2023 - science.org
Zoonomia is the largest comparative genomics resource for mammals produced to date. By
aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect …

The UCSC genome browser database: 2024 update

BJ Raney, GP Barber, A Benet-Pagès… - Nucleic Acids …, 2024 - academic.oup.com
Abstract The UCSC Genome Browser (https://genome. ucsc. edu) is a web-based genomic
visualization and analysis tool that serves data to over 7,000 distinct users per day …

Leveraging base-pair mammalian constraint to understand genetic variation and human disease

PF Sullivan, JRS Meadows, S Gazal, BDN Phan, X Li… - Science, 2023 - science.org
Thousands of genomic regions have been associated with heritable human diseases, but
attempts to elucidate biological mechanisms are impeded by an inability to discern which …

Genome annotation: From human genetics to biodiversity genomics

R Guigó - Cell Genomics, 2023 - cell.com
Within the next decade, the genomes of 1.8 million eukaryotic species will be sequenced.
Identifying genes in these sequences is essential to understand the biology of the species …

Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo

ME Oomen, ME Torres-Padilla - EMBO reports, 2024 - embopress.org
Remnants of transposable elements (TEs) are widely expressed throughout mammalian
embryo development. Originally infesting our genomes as selfish elements and acting as a …

Evolution of a novel adrenal cell type that promotes parental care

N Niepoth, JR Merritt, M Uminski, E Lei, VS Esquibies… - Nature, 2024 - nature.com
Cell types with specialized functions fundamentally regulate animal behaviour, and yet the
genetic mechanisms that underlie the emergence of novel cell types and their …

GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation

B Contreras-Moreira, S Saraf, G Naamati, AM Casas… - Genome Biology, 2023 - Springer
Crop pangenomes made from individual cultivar assemblies promise easy access to
conserved genes, but genome content variability and inconsistent identifiers hamper their …

The evolution history of an allotetraploid mangrove tree analysed with a new tool Allo4D

Y Wang, Y Li, W Wu, S Shao, Q Fang… - Plant Biotechnology …, 2024 - Wiley Online Library
Mangrove species are broadly classified as true mangroves and mangrove associates. The
latter are amphibious plants that can survive in the intertidal zone and reproduce naturally in …

Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine

SU Umu, VM Paynter, H Trondsen, T Buschmann… - Cell Genomics, 2023 - cell.com
The annotation of microRNAs depends on the availability of transcriptomics data and expert
knowledge. This has led to a gap between the availability of novel genomes and high …

ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages

PG Nachtigall, AM Durham, DR Rokyta… - …, 2024 - academic.oup.com
Background The rapid development of sequencing technologies resulted in a wide
expansion of genomics studies using venomous lineages. This facilitated research focusing …