DOI: 10.5061/dryad.pb68n
title: Data from: Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients

description: Background: Hoplolaimina plant-parasitic nematodes (PPN) are a lineage of
 animals with many documented cases of horizontal gene transfer (HGT). In a
 recent study, we reported on three likely HGT candidate genes in the
 soybean cyst nematode Heterodera glycines, all of which encode secreted
 candidate effectors with putative functions in the host plant. Hg-GLAND1
 is a putative GCN5-related N-acetyltransferase (GNAT), Hg-GLAND13 is a
 putative invertase (INV), and Hg-GLAND16 is a putative chorismate mutase
 (CM), and blastp searches of the non-redundant database resulted in
 highest similarity to bacterial sequences. Here, we searched nematode and
 non-nematode sequence databases to identify all the nematodes possible
 that contain these three genes, and to formulate hypotheses about when
 they most likely appeared in the phylum Nematoda. We then performed
 phylogenetic analyses combined with model selection tests of alternative
 models of sequence evolution to determine whether these genes were
 horizontally acquired from bacteria. Results: Mining of nematode sequence
 databases determined that GNATs appeared in Hoplolaimina PPN late in
 evolution, while both INVs and CMs appeared before the radiation of the
 Hoplolaimina suborder. Also, Hoplolaimina GNATs, INVs and CMs formed
 well-supported clusters with different rhizosphere bacteria in the
 phylogenetic trees, and the model selection tests greatly supported models
 of HGT over descent via common ancestry. Surprisingly, the phylogenetic
 trees also revealed additional, well-supported clusters of bacterial
 GNATs, INVs and CMs with diverse eukaryotes and archaea. There were at
 least eleven and eight well-supported clusters of GNATs and INVs,
 respectively, from different bacteria with diverse eukaryotes and archaea.
 Though less frequent, CMs from different bacteria formed supported
 clusters with multiple different eukaryotes. Moreover, almost all
 individual clusters containing bacteria and eukaryotes or archaea
 contained species that inhabit very similar niches. Conclusions: GNATs
 were horizontally acquired late in Hoplolaimina PPN evolution from
 bacteria most similar to the saprophytic and plant-pathogenic
 actinomycetes. INVs and CMs were horizontally acquired from bacteria most
 similar to rhizobacteria and Burkholderia soil bacteria, respectively,
 before the radiation of Hoplolaimina. Also, these three gene groups appear
 to have been frequent subjects of HGT from different bacteria to numerous,
 diverse lineages of eukaryotes and archaea, which suggests that these
 genes may confer important evolutionary advantages to many taxa. In the
 case of Hoplolaimina PPN, this advantage likely was an improved ability to
 parasitize plants.
description: Figure
 S1Raw
 Maximum Likelihood phylogenetic tree of the GCN5-related
 N-acetyltransferase (GNAT) superfamily and newly identified GNATs similar
 to Hoplolaimina homologs. Branches for each GNAT family are color-coded
 accordingly. Bootstrap support values are indicated at corresponding
 nodes, and those that support monophyly of each GNAT family are oversized
 in red font. Names and organisms found to contain each GNAT family are
 indicated to the right with brackets around the respective leaves.
 Sequence identifications are provided in parentheses at each
 leaf.Figure
 S2Detailed Maximum
 Likelihood phylogenetic tree of the FAM7 GNATs including Hoplolaimina
 homologs. Branches for each phylogenetic group are color-coded according
 to their taxonomy. Bootstrap support values are indicated at corresponding
 nodes, and those that support possible horizontal gene transfer (HGT)
 events are oversized in red font. Organism names are indicated to the
 right with brackets around the respective leaves. Sequence identifications
 are provided in parentheses at each leaf.Figure
 S3Detailed Maximum
 Likelihood phylogenetic tree of INVs similar to Hoplolaimina homologs.
 Branches for each phylogenetic group are color-coded according to their
 taxonomy. Bootstrap support values are indicated at corresponding nodes,
 and those that support possible horizontal gene transfer (HGT) events are
 oversized in red font. Organism names are indicated to the right with
 brackets around the respective leaves. Sequence identifications are
 provided in parentheses at each leaf.Figure
 S4Detailed Maximum
 Likelihood phylogenetic tree of CMs similar to Hoplolaimina homologs.
 Branches for each phylogenetic group are color-coded according to their
 taxonomy. Bootstrap support values are indicated at corresponding nodes,
 and those that support possible horizontal gene transfer (HGT) events are
 oversized in red font. Organism names are indicated to the right with
 brackets around the respective leaves. Sequence identifications are
 provided in parentheses at each leaf. Note that the Nacobbus aberrans leaf
 is colored red to indicate its possible neofunctionalization from the
 other Hoplolaimina homologs (see supplementary text, Additional file
 5).Figure
 S5Detailed Maximum
 Likelihood phylogenetic tree of initially poorly clustered FAM7 GNATs.
 Branches for each phylogenetic group are color-coded according to their
 taxonomy. Bootstrap support values are indicated at corresponding nodes,
 and those that support possible horizontal gene transfer (HGT) events are
 oversized in red font. Organism names are indicated to the right with
 brackets around the respective leaves. Sequence identifications are
 provided in parentheses at each leaf.