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 genomes have 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.

Insights into deuterostome evolution from the biphasic transcriptional programme of hemichordates

“…RNA-Seq reads of Branchiostoma lanceolatum from (Marlétaz et al 2018) were mapped against the set of longest isoforms per gene of the currently available transcriptome (Brasó-Vives et al 2022) using kallisto (Bray et al 2016). Read counts were imported to R using the ‘tximport‘ package.…”

The BioGenome Portal: a web-based platform for biodiversity genomics data management

“…As of December 2023, the CBP instance contains a total of 58 organisms ( Figure 4 ), five of them with already published assemblies (12–16).…”

“…As of December 2023, the CBP instance contains a total of 58 organisms (Figure 4), five of them with already published assemblies (12)(13)(14)(15)(16). One of the unique features tailored for this instance is the integration of region-specific taxonomic information, focusing on the biodiversity found in Catalonia.…”

Genomic Resources and Annotations for a Colonial Ascidian, the Light-Bulb Sea Squirt Clavelina lepadiformis

“…Predicted proteins from the genome annotation were compared with proteins from C. robusta (KY21) ( Satou et al 2022 ), Branchiostoma lanceolatum (BraLan3, NCBI) ( Brasó-Vives et al 2022 ), Corella inflata ( DeBiasse et al 2020 ), S. clava (ASM1312258v2, NCBI) ( Wei et al 2020 ), Homo sapiens (GRCh38.p13, NCBI), and Swiss-Prot dataset (Release 2023_03) ( The UniProt Consortium 2023 ) using blastp (v2.11.0), or with the whole genome assemblies of A. turbinatum (kaAplTurb1.1) ( Bishop et al 2022 ) using tblastn (hits were considered positive for evalue <5 × 10 −5 ). Similarly, coding transcripts from the DRAP transcriptome assembly were assessed against C. robusta and Swiss-Prot datasets using blastx (hits were considered positive for evalue <5 × 10 −5 ).…”