Amphioxus functional genomics and the origins of vertebrate gene regulation

F Marlétaz, PN Firbas, I Maeso, JJ Tena, O Bogdanovic… - Nature, 2018 - nature.com
Vertebrates have greatly elaborated the basic chordate body plan and evolved highly
distinctive genomes that have been sculpted by two whole-genome duplications. Here we …

Three amphioxus reference genomes reveal gene and chromosome evolution of chordates

Z Huang, L Xu, C Cai, Y Zhou, J Liu… - Proceedings of the …, 2023 - National Acad Sciences
The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our
understanding of the vertebrate origin and innovations. Here we resolve the nearly complete …

The hagfish genome and the evolution of vertebrates

F Marlétaz, N Timoshevskaya, VA Timoshevskiy… - Nature, 2024 - nature.com
As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a crucial
window into early vertebrate evolution,–. Here we investigate the complex history, timing …

Constrained vertebrate evolution by pleiotropic genes

H Hu, M Uesaka, S Guo, K Shimai, TM Lu, F Li… - Nature ecology & …, 2017 - nature.com
Despite morphological diversification of chordates over 550 million years of evolution, their
shared basic anatomical pattern (or 'bodyplan') remains conserved by unknown …

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

LZ Holland, R Albalat, K Azumi… - Genome …, 2008 - genome.cshlp.org
Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over
520 million years ago. To improve our understanding of chordate evolution and the origin of …

Deep conservation of the enhancer regulatory code in animals

ES Wong, D Zheng, SZ Tan, NI Bower, V Garside… - Science, 2020 - science.org
INTRODUCTION In animals, gene regulatory networks specify cell identity in space and
time. Transcription of genes in these networks is modulated by a class of cis-regulatory …

Genome and transcriptome mechanisms driving cephalopod evolution

CB Albertin, S Medina-Ruiz, T Mitros… - Nature …, 2022 - nature.com
Cephalopods are known for their large nervous systems, complex behaviors and
morphological innovations. To investigate the genomic underpinnings of these features, we …

The African coelacanth genome provides insights into tetrapod evolution

CT Amemiya, J Alföldi, AP Lee, S Fan, H Philippe… - Nature, 2013 - nature.com
The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of
lobe-finned fish was thought to have become extinct 70 million years ago. The modern …

The amphioxus genome and the evolution of the chordate karyotype

NH Putnam, T Butts, DEK Ferrier, RF Furlong… - Nature, 2008 - nature.com
Abstract Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage,
with a fossil record dating back to the Cambrian period. Here we describe the structure and …

A map of cis-regulatory elements and 3D genome structures in zebrafish

H Yang, Y Luan, T Liu, HJ Lee, L Fang, Y Wang… - Nature, 2020 - nature.com
The zebrafish (Danio rerio) has been widely used in the study of human disease and
development, and about 70% of the protein-coding genes are conserved between the two …