Gene Novelties in Amphioxus Illuminate the Early Evolution of Deuterostomes

Abstract

Horizontal gene transfer (HGT) enables novel gene establishment but has rarely been reported in the genomes of deuterostomes. Using the genomes of four amphioxi, massive HGT events were identified that introduced novel genes in different functional groups. Innate immunity of amphioxi that have no adaptative immune system was enriched by HGT genes. Anaerobic adaptation of amphioxi may have been enabled by the HGT of genes for alcohol dehydrogenase and ferredoxin. A proximally arrayed cluster of EF-hand calcium-binding protein genes, of which the copy number was linearly correlated to the sea salinity of the collection region, may foster their survival at different calcium concentrations. Combining phylogenetic analysis and conservation among deuterostomes, this comprehensive analysis of HGT in amphioxi revealed insights into the early evolution of deuterostomes.

Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences

“…Genome sequencing and de novo genome assembly of B. belcheri beihai has been reported [37]. In brief, the genomic DNA was sequenced by Illumina HiSeq 2000 in 500-bp and 3000-bp libraries to generate paired-end NGS short reads and PacBio RS system for third-generation long reads.…”

“…In this study, the adult Beihai amphioxus was suggested as a B. belcheri subspecies and was tentatively named B. belcheri beihai. A high-quality B. belcheri beihai genome was assembled and annotated by our team [37]. A total of 347 HFs in the B. belcheri beihai genome were identified, and the genomic features of the HFs were analyzed.…”