title: 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.
authors.affiliation: Department of Biological Sciences, University of North Texas, Denton, Texas, USA.
authors.forename: Ravi S
authors.initials: RS
authors.lastname: Pandey
authors.affiliation: Department of Biological Sciences, University of North Texas, Denton, Texas, USA.
authors.forename: Garima
authors.initials: G
authors.lastname: Saxena
authors.affiliation: Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA.
authors.forename: Debashish
authors.initials: D
authors.lastname: Bhattacharya
authors.affiliation: Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA.
authors.forename: Huan
authors.initials: H
authors.lastname: Qiu
authors.affiliation: Department of Biological Sciences, University of North Texas, Denton, Texas, USA.|Department of Mathematics, University of North Texas, Denton, Texas, USA.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Azad
mesh_terms: D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D019143:Evolution, Molecular; D000071825:Extremophiles / Q000145:classification / Q000235:genetics*; D022761:Gene Transfer, Horizontal; D058086:Microalgae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D000461:Rhodophyta / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA