Systematic and functional analysis of horizontal gene transfer events in diatoms

Abstract

1.AbstractDiatoms are a diverse group of mainly photosynthetic algae, responsible for 20% of worldwide oxygen production, which can rapidly respond to favourable conditions and often outcompete other phytoplankton. We investigated the contribution of horizontal gene transfer (HGT) to its ecological success. A systematic phylogeny-based bacterial HGT detection procedure across nine sequenced diatoms showed that 3-5% of their proteome has a horizontal origin and a large influx occurred at the ancestor of diatoms. More than 90% of HGT genes are expressed, and species-specific HGT genes in Phaeodactylum tricornutum undergo strong purifying selection. They are implicated in several processes including environmental sensing, and expand the metabolic toolbox. Cobalamin (vitamin B12) is an essential cofactor for roughly half of the diatoms and is only produced by bacteria. Genes involved in its final synthesis were detected as HGT, including five consecutive enzymes in Fragilariopsis cylindrus. This might give diatoms originating from the Southern Ocean, a region typically depleted in cobalamin, a competitive advantage. Overall, we show that HGT is a prevalent mechanism that is actively used in diatoms to expand its adaptive capabilities.

The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms

“…In contrast to the wide expression of pleiotropic gene families, more than 200 families were identified showing significant enrichment for upregulation in one or a limited number of related conditions (Supplementary Note 5 and Supplementary Figs. [16][17][18][19]. Notably, many of these families were species or diatom-specific and responsive to either sexual reproduction, silica depletion, or bacterial interaction ( Fig.…”

“…5), 63% share similarity to proteins from other eukaryotes and 60% are functionally annotated. Application of a phylogeny-based horizontal gene transfer detection procedure identified 1741 genes of putative bacterial origin 16 . Assessing the accuracy and quality of S. robusta gene models revealed the successful recovery of 99% of core gene families conserved in Bacillariophyta (Supplementary Note 2, Supplementary Fig.…”

“…For a heat-shock transcription factor family (HSFs) expanded in diatoms 9 and showing pleiotropic expression in S. robusta, we identified that this expansion happened through tandem duplication in several diatoms (Fig. 2b) Ionotropic glutamate receptor (45) 8 Heat shock transcription factor family (120) 9 CAP superfamily (9) 10 Serine proteases, trypsin family, serine active site (87) 11 Protein kinase domain (85) 12 Activating transcription factor binding (45) 13 Voltage-dependent channel domain superfamily 1114 Phytochrome chromophore attachment domain 415 SGNH hydrolase superfamily (6) 16 Ricin B, lectin domain 3517 Unknown function (5) 18 HECT domain 1419 Cupredoxin 5 S. robusta NTF2-like tandem-enriched pleiotropic family had 19/ 68 copies annotated with the polyketide cyclase SnoaL-like domain. Enzymes for polyketide metabolism are absent in some protist lineages but expanded in others such as dinoflagellates and haptophytes, suggesting that the evolution of these compounds may have played an important role in their ecological success 23 .…”

An Insight into the Algal Evolution and Genomics

“…In the phylogeny-based HGT study on all sequenced diatoms genomes, 1979 genes were found to be of horizontal origin in diatoms. Furthermore, five vitamin B12 biosynthesis pathway genes were detected as HGT, imparting a competitive advantage to diatoms in cobalt depleted environment, as cobalt is essential co-factor for diatoms [46]. In an iron-scarce environment, diatoms have the ability to reduce their cellular iron requirement and replaces plastid-localized ferredoxin with flavodoxin, using flavin as co-factor.…”

Strategy for the Removal of Satellite Bacteria from the Cultivated Diatom

“…They are able to provide fundamentally novel information about water ecosystems and their functionality [7]. Since the evolutionary history of diatoms involves multiple endosymbioses and their associated genetic transfers, as well as horizontal gene transfers from bacteria [8,9], it is important to use axenic cultures for genomic [8,[10][11][12] and transcriptomic [13][14][15][16][17] studies.…”