Parallel evolution of amphioxus and vertebrate small-scale gene duplications

Abstract

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.

Evolution of tissue-specific expression of ancestral genes across vertebrates and insects

“…For other eight species, we downloaded GTF and genome FASTA files from Ensembl Metazoa [https://metazoa.ensembl.org/]: sea urchin ( Strongylocentrotus purpuratus: Spu: Spur_5.0 v51), fruit fly ( Drosophila melanogaster, Dme : dm6, v26), yellow fever mosquito ( Aedes aegypti, Aae : AaegL5, v46), domestic silk moth ( Bombyx mori, Bmo : ASM15162v1, v45), red flour beetle ( Tribolium castaneum, Tca : Tcas5.2, v45), honey bee ( Apis mellifera, Ame : Amel_4.5, v35), centipede ( Strigamia maritima , Sma: Smar1, v26), California two-spot octopus ( Octopus bimaculoides, Obi : ASM119413v2). For other three species, we used the GTF and genome FASTA files from the relative publications: amphioxus ( Branchiostoma lanceolatum , Bla: 54 ), marmalade hoverfly ( Episyrphus balteatus , Eba: 55 ), mayfly ( Cloeon dipterum , Cdi: 12 ). For the cockroach ( Blattella germanica , Bge) we downloaded the GFF3 (blager_OGSv1.2.1.gff3) and the genome FASTA (GCA_000762945.2_Bger_2.0_genomic.fna.gz) from https://i5k.nal.usda.gov/content/data-downloads.…”

Parallel evolution of amphioxus and vertebrate small-scale gene duplications

“…BraLan3 genome reference and annotation and the B. lanceolatum whole-genome PacBio sequencing data and chromatin conformation capture data (HiC) we used to build it are available in the European Nucleotide Archive (ENA) under the accession number PRJEB49647 [74]. Code used for the analysis is available in GitHub [75] and in Zenodo [76].…”

Gene Novelties in Amphioxus Illuminate the Early Evolution of Deuterostomes

“…Therefore, amphioxus is considered an irreplaceable model organism for evolutionary studies. With the advent of highthroughput sequencing, genome-based investigation has revolutionized the study of amphioxus evolution and greatly expanded our knowledge of the origin and evolution of vertebrates (Holland et al 2008;Putnam et al 2008;Huang et al 2014;Acemel et al 2016;Marlétaz et al 2018;Simakov et al 2020;Brasó-Vives et al 2022;Huang et al 2023). Whole-genome comparison of the three chordate groups provided evidence supporting the 2R hypothesis, which posits that two rounds of whole-genome duplication occurred in the early vertebrate lineage (Holland et al 2008;Putnam et al 2008).…”