Horizontal Gene Transfer From Bacteria and Plants to the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis

Abstract

Arbuscular mycorrhizal fungi (AMF) belong to Glomeromycotina, and are mutualistic symbionts of many land plants. Associated bacteria accompany AMF during their lifecycle to establish a robust tripartite association consisting of fungi, plants and bacteria. Physical association among this trinity provides possibilities for the exchange of genetic materials. However, very few horizontal gene transfer (HGT) from bacteria or plants to AMF has been reported yet. In this study, we complement existing algorithms by developing a new pipeline, Blast2hgt, to efficiently screen for putative horizontally derived genes from a whole genome. Genome analyses of the glomeromycete Rhizophagus irregularis identified 19 fungal genes that had been transferred between fungi and bacteria/plants, of which seven were obtained from bacteria. Another 18 R. irregularis genes were found to be recently acquired from either plants or bacteria. In the R. irregularis genome, gene duplication has contributed to the expansion of three foreign genes. Importantly, more than half of the R. irregularis foreign genes were expressed in various transcriptomic experiments, suggesting that these genes are functional in R. irregularis. Functional annotation and available evidence showed that these acquired genes may participate in diverse but fundamental biological processes such as regulation of gene expression, mitosis and signal transduction. Our study suggests that horizontal gene influx through endosymbiosis is a source of new functions for R. irregularis, and HGT might have played a role in the evolution and symbiotic adaptation of this arbuscular mycorrhizal fungus.

Keywords: arbuscular mycorrhizal fungi; endobacteria; eukaryotic evolution; horizontal gene transfer; symbiosis.

Figure 1

Similarity plot of R. irregularis bacteria- and plant-like proteins. Circles represent relative bit scores of R. irregularis proteins. The x axis is the best bit score produced by BLASTP against bacteria/plants (first hit's taxonomy group). The y axis is the best bit score generated by BLASTP against second hit's taxonomy group (which contains all sequences not belonging to first hit's taxonomy group and fungi). To get the relative bit score, actual bit score is divided by bit score of the query sequence BLASTP against itself.

Figure 2

Molecular phylogeny of YbaK/prolyl-tRNA synthetases. Protein sequence of the fungus Wickerhamomyces ciferrii (XP_011275603.1) is used as the outgroup. Numbers beside branches represent bootstrap values from maximum likelihood and Bayesian analyses, respectively. Asterisks indicate values lower than 50%. Scale bars represent substitution numbers per amino-acid site. Bacterial and fungal sequences are colored in orange and blue, respectively.

Figure 3

Molecular phylogenies of genes horizontally transferred between plants and fungi (including R. irregularis). Fungal and plant sequences were shown in blue and green, respectively. Subtrees containing sequences from the same taxonomic clade were condensed. Numbers beside branches represent bootstrap values from maximum likelihood and Bayesian analyses, respectively. Asterisks indicate values lower than 50%. Scale bars represent the number of amino acid substitutions per site. Detailed molecular phylogenies for these genes were displayed in Supplementary Figures 14–20.

Figure 4

(A) Molecular phylogeny of the MULE transposase family. Fungal sequences were obtained from BLASTP output (E-value cutoff: 1) and keyword search result. Numbers beside branches represent bootstrap values from maximum likelihood and Bayesian analyses, respectively. Asterisks indicate values lower than 50%. Scale bar represents substitution numbers per amino-acid site. Fungal sequences are colored in blue. (B) Circular visualization of the transposase genes mapped on the different scaffolds of R. irregularis. Scaffold accession numbers are indicated beside the scaffold bars. The scaffold IDs assigned by Chen et al. (2018) are indicated in parentheses. The sequences maintaining syntenic relationship are linked by lines. Green links: synteny blocks of the transposase genes; Red links: synteny blocks of other segments. The histograms in the middle represent the number of mapped RNA-seq reads.

Figure 5

Gene ontology classification of the 18 genes (gene families) recently acquired by Rhizophagus.