Using complementary approaches to identify trans‐domain nuclear gene transfers in the extremophile Galdieria sulphuraria (Rhodophyta)

Abstract

Identification of horizontal gene transfers (HGTs) has primarily relied on phylogenetic tree based methods, which require a rich sampling of sequenced genomes to ensure a reliable inference. Because the success of phylogenetic approaches depends on the breadth and depth of the database, researchers usually apply stringent filters to detect only the most likely gene transfers in the genomes of interest. One such study focused on a highly conservative estimate of trans-domain gene transfers in the extremophile eukaryote, Galdieria sulphuraria (Galdieri) Merola (Rhodophyta), by applying multiple filters in their phylogenetic pipeline. This led to the identification of 75 inter-domain acquisitions from Bacteria or Archaea. Because of the evolutionary, ecological, and potential biotechnological significance of foreign genes in algae, alternative approaches and pipelines complementing phylogenetics are needed for a more comprehensive assessment of HGT. We present here a novel pipeline that uncovered 17 novel foreign genes of prokaryotic origin in G. sulphuraria, results that are supported by multiple lines of evidence including composition-based, comparative data, and phylogenetics. These genes encode a variety of potentially adaptive functions, from metabolite transport to DNA repair.

Reconstructing horizontal gene flow network to understand prokaryotic evolution

“…For understanding the pattern of horizontal gene flow, phylogenetic methods have often been invoked and therefore, a large body of literature exists on the usage of phylogenetic approaches in this context. Composition-based methods have sparingly been used in deciphering the pattern, although successive studies have highlighted the complementary strengths of these methods [8,24,33]. Although these methods may not be able to detect ancient gene transfers due to the amelioration of composition of the acquired genes to the native genome composition with the passage of time, they could be used for assessing genome-scale impact of recent HGTs.…”