PT  - JOURNAL ARTICLE
AU  - Marina Brasó-Vives
AU  - Ferdinand Marlétaz
AU  - Amina Echchiki
AU  - Federica Mantica
AU  - Rafael D. Acemel
AU  - José L. Gómez-Skarmeta
AU  - Lorlane L. Targa
AU  - Pierre Pontarotti
AU  - Juan J. Tena
AU  - Ignacio Maeso
AU  - Hector Escriva
AU  - Manuel Irimia
AU  - Marc Robinson-Rechavi
TI  - Parallel evolution of amphioxus and vertebrate small-scale gene duplications
AID  - 10.1101/2022.01.18.476203
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.01.18.476203
4099  - http://biorxiv.org/content/early/2022/01/18/2022.01.18.476203.short
4100  - http://biorxiv.org/content/early/2022/01/18/2022.01.18.476203.full
AB  - Background Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic chordate body-plan and genome organization with vertebrates but lack their “2R” whole-genome duplications and their developmental complexity. For these reasons, amphioxus are frequently used as an outgroup to study vertebrate genome evolution and Evo-Devo. Aside from whole-genome duplications, genes continuously duplicate on a smaller scale. Small-scale duplicated genes can be found in both amphioxus and vertebrate genomes, while only the vertebrate genome has duplicated genes product of their 2R whole-genome duplications. Here, we explore the history of small-scale gene duplications in the amphioxus lineage and compare it to small- and large-scale gene duplication history in vertebrates.Results We present a study of the European amphioxus (Branchiostoma lanceolatum) gene duplications thanks to a new, high-quality genome reference. We find that, despite its overall slow molecular evolution, the amphioxus lineage has had a history of small-scale duplications similar to the one observed in vertebrates. We find parallel gene duplication profiles between amphioxus and vertebrates, and conserved functional constraints in gene duplication. Moreover, amphioxus gene duplicates show levels of expression and patterns of functional specialization similar to the ones observed in vertebrate duplicated genes. We also find strong conservation of gene synteny between two distant amphioxus species, B. lanceolatum and B. floridae, with two major chromosomal rearrangements.Conclusions In contrast to their slower molecular and morphological evolution, amphioxus small-scale gene duplication history resembles that of the vertebrate lineage both in quantitative and in functional terms.Competing Interest StatementThe authors have declared no competing interest.