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.

Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1

“…Thomas A. Richards et al defined 14 candidate plant-fungi HGT events by phylogenomic analysis, nine of which showed an infrequent pattern of HGT between plants and fungi, and some kind of genes were involved in transport of the sugar L-fucose and other functions [79]. Meng Li et al identified 19 fungal genes that had been transferred between fungi and bacteria/plants, which suggests that HGT might have played a role in the evolution and symbiotic adaptation of this arbuscular mycorrhizal fungus [80]. However, due to the incomplete assembly of the sydowii H-1.…”

A mycorrhizae-like gene regulates stem cell and gametophore development in mosses

“…This sequence relatedness between land plants and Mucoromycota might have resulted from several scenarios, including differential gene losses and organellar origin. On the other hand, it is also likely that PpMACRO2 was acquired from mycorrhizae-like fungi by the common ancestor of land plants 63 . This second scenario is not only consistent with the common belief that physical association, such as symbiosis, often facilitates horizontal gene transfer (HGT), but also supported by the amino acid residues uniquely shared by Mucoromycota and bryophyte sequences.…”

Verification of the phenylpropanoid pinoresinol biosynthetic pathway and its glycosides in Phomopsis sp. XP-8 using 13C stable isotope labeling and liquid chromatography coupled with time-of-flight mass spectrometry

“…Horizontal gene transfer (HGT) has long been recognized as an important force in the evolution of organisms (30). HGT occurs among different bacteria and plays important roles in the adaptation of microorganisms to different hosts or environmental conditions (31). More and more evidence for gene transfer between distantly related eukaryotic groups has been presented (30).…”