Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

Abstract

Horizontal gene transfer (HGT) is the transfer of genetic material across species boundaries and has been a driving force in prokaryotic evolution. HGT involving eukaryotes appears to be much less frequent, and the functional implications of HGT in eukaryotes are poorly understood. We test the hypothesis that parasitic plants, because of their intimate feeding contacts with host plant tissues, are especially prone to horizontal gene acquisition. We sought evidence of HGTs in transcriptomes of three parasitic members of Orobanchaceae, a plant family containing species spanning the full spectrum of parasitic capabilities, plus the free-living Lindenbergia Following initial phylogenetic detection and an extensive validation procedure, 52 high-confidence horizontal transfer events were detected, often from lineages of known host plants and with an increasing number of HGT events in species with the greatest parasitic dependence. Analyses of intron sequences in putative donor and recipient lineages provide evidence for integration of genomic fragments far more often than retro-processed RNA sequences. Purifying selection predominates in functionally transferred sequences, with a small fraction of adaptively evolving sites. HGT-acquired genes are preferentially expressed in the haustorium-the organ of parasitic plants-and are strongly biased in predicted gene functions, suggesting that expression products of horizontally acquired genes are contributing to the unique adaptive feeding structure of parasitic plants.

Keywords: HGT; genomic transfer; parasitism; phylogenomics; validation pipeline.

Fig. 1.

Three models for phylogenomic identification of HGTs and further examination of the preliminary-screened HGT candidates. (Scheme 1) Parasitic genes (P) are nested inside donor clades (D). (Scheme 2) Parasitic gene group outside of the donor clade. (Scheme 3) Only one node of donor sequence is sister to parasite genes. In this study, donor refers to distantly related monocot and rosid sequences. Ancestral node is defined to be composed of exclusively parasitic and donor sequences. In A1, at least two nodes within the ancestral node (including the ancestral) are required to have BS ≥ 50; in A2, both the ancestral node and node 1 are required to have BS ≥ 50. In scheme 2 (B), the ancestral node and at least one node within the ancestral node are required to have BS ≥ 50. In scheme 3 (C), only the node that supports the grouping of the parasitic gene and donor sequence is required to have BS ≥ 50. “Non-DPs” refers to nonparasitic, nondonor sequences. (D) A total of 192 HGT orthogroup trees from the initial screening were classified into low-, medium-, and high-confidence categories based on a scoring scheme (SI Appendix, Table S1). Gray colors represent the HGT orthogroups identified in the monocots; darker gray colors represent the rosids. (E) The number of HGT candidate orthogroups manually curated as true HGTs (light gray); artifacts resulting from insufficient taxon sampling, frame shift errors, or tree inaccuracies (white); or fungal or host contamination (dark gray). The 42 “true” HGT orthogroups all fit scheme 1 of A.

Fig. 2.

RAxML-based maximum likelihood (ML) trees supporting HGT, donor families, and recipient taxa inferred from the 42 HGT set. Orthogroup tree (12835) supports a grass-derived Pong-like TE in S. hermonthica. HGT sequence is labeled with “H” and vertically inherited sequences with “V.” The species abbreviations are shown in SI Appendix, Fig. S1. (B) A hypothetical tree illustrates the color-coding system for each angiosperm lineage represented in A and Fig. 3. (C) Mapping of parasitic recipient taxa onto inferred donor family (x axis). Each genus in HGT recipient is followed with a three-letter code used in D. Total number of HGT orthogroups inferred from each donor family is placed on top of each bar. Numbers within each bar represent number of orthogroups; the number of singletons is not shown due to space limitations (SI Appendix, Table S9). (D) Number of HGT orthogroups supports transfers from shared and unique parasitic genera. Ale, Alectra; Lin, Lindenbergia; Oro, Orobanche; Phe, Phelipanche; Str, Striga; Tri, Triphysaria.

Fig. 3.

Genomic horizontal transfer of a tRNAHis guanylyltransferase from Frave (Fragaria) (or its ancestor) to Phelipanche. (A) A coding-sequence (CDS) tree by RAxML from represented species across angiosperm lineages. D, inferred donor (in Fragaria); H, the parasitic HGT gene; V, vertical parasitic gene; VR, related sequence of the vertical parasitic gene (in Mimulus). Seventy-four percent represents the CDS similarity between the HGT gene and its inferred donor. (B) Gene structure with four selected introns for the four sequences (H, D, V, and VR). Yellow and green bars represent coding sequence; the vertical dashed lines represent the intron positions; the boxes represent introns. At least four conserved intron positions were shown on the gene structure; the third intron was lost in the HGT gene, and the fourth intron on the graph (which is the seventh intron of the Mimulus gene) showed strong sequence similarity between the HGT gene and its donor (marked by red intron boxes with length within). (C) The phylogeny of the seventh intron (marked red in B) from genes on the CDS tree: the HGT gene groups with its donor supported by 98% BS, whereas the vertically inherited gene groups with a close relative (Mimulus sequence). The intron sequence similarity between the HGT (HGT) gene and its donor (D) is 51%, and the intron sequence similarity between the vertical gene (V) and its vertical relative (VR) is 21%. (D) The number of HGT orthogroups that support 25 genomic transfers in 24 HGT orthogroups containing introns in the CDS region (dark blue) and 2 HGT orthogroups containing introns in the UTR region (pink). The remaining orthogroups contain 15 HGT orthogroups (24 transfers) with insufficient genomic data to infer presence of introns (white) and one orthogroup containing HGT gene without introns (light blue).

Fig. 4.

Heat map showing the expression of HGT transgenes in P. aegyptiaca. Expression is shown with FPKM-transformed z scores to ensure even signal intensity across stages. Rows represent HGT genes, with their identified domain shown on the right; columns represent stages (below) or tissues (above). Haustorial and interface tissues are colored in green. Genes were clustered on the left to show similarity.