Repetitive DNA sequences include retrotransposons in genomes of the Glomeromycota

Lineage-Specific Genes and Cryptic Sex: Parallels and Differences between Arbuscular Mycorrhizal Fungi and Fungal Pathogens

Arbuscular mycorrhizal fungi (AMF) live as obligate root symbionts on almost all land plants. They have long been regarded as ancient asexuals that have propagated clonally for millions of years. However, genomic studies in Rhizophagus irregularis and other AMF revealed many features indicative of sex. Surprisingly, comparative genomics of conspecific isolates of R. irregularis revealed an unexpected interstrain diversity, suggesting that AMF carry a high number of lineage-specific (LS) genes. Intriguingly, cryptic sex and LS genomic regions have previously been reported in a number of fungal pathogens of plants and humans. Here, we discuss these genomic similarities and highlight their potential relevance for AMF adaptation to the environment and for symbiotic functioning.

Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus

Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.

Structural features and mechanism of translocation of non-LTR retrotransposons in Candida albicans

A number of abundant mobile genetic elements called retrotransposons reverse transcribe RNA to generate DNA for insertion into eukaryotic genomes. Non-long-terminal repeat (non-LTR) retrotransposons represent a major class of retrotransposons, and transposons that move by target-primed reverse transcription lack LTRs characteristic of retroviruses and retroviral-like transposons. Yeast model systems in Candida albicans and Saccharomyces cerevisiae have been developed for the study of non-LTR retrotransposons. Non-LTR retrotransposons are divided into LINEs (long interspersed nuclear elements), SINEs (short interspersed nuclear elements), and SVA (SINE, VNTR, and Alu). LINE-1 elements have been described in fungi, and several families called Zorro elements have been detected from C. albicans. They are all members of L1 clades. Through a mechanism named target-primed reverse transcription (TPRT), LINEs translocate the new copy into the target site to initiate DNA synthesis primed by the 3′ OH of the broken strand. In this article, we describe some advances in the research on structural features and origin of non-LTR retrotransposons in C. albicans, and discuss mechanisms underlying their reverse transcription and integration of the donor copy into the target site.

New insights into nested long terminal repeat retrotransposons in Brassica species

Long terminal repeat (LTR) retrotransposons, one of the foremost types of transposons, continually change or modify gene function and reorganize the genome through bursts of dramatic proliferation. Many LTR-TEs preferentially insert within other LTR-TEs, but the cause and evolutionary significance of these nested LTR-TEs are not well understood. In this study, a total of 1.52Gb of Brassica sequence containing 2020 bacterial artificial chromosomes (BACs) was scanned, and six bacterial artificial chromosome (BAC) clones with extremely nested LTR-TEs (LTR-TEs density: 7.24/kb) were selected for further analysis. The majority of the LTR-TEs in four of the six BACs were found to be derived from the rapid proliferation of retrotransposons originating within the BAC regions, with only a few LTR-TEs originating from the proliferation and insertion of retrotransposons from outside the BAC regions approximately 5-23Mya. LTR-TEs also preferably inserted into TA-rich repeat regions. Gene prediction by Genescan identified 207 genes in the 0.84Mb of total BAC sequences. Only a few genes (3/207) could be matched to the Brassica expressed sequence tag (EST) database, indicating that most genes were inactive after retrotransposon insertion. Five of the six BACs were putatively centromeric. Hence, nested LTR-TEs in centromere regions are rapidly duplicated, repeatedly inserted, and act to suppress activity of genes and to reshuffle the structure of the centromeric sequences. Our results suggest that LTR-TEs burst and proliferate on a local scale to create nested LTR-TE regions, and that these nested LTR-TEs play a role in the formation of centromeres.

LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders

Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ~14 to ~120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders.

Conserved meiotic machinery in Glomus spp., a putatively ancient asexual fungal lineage

Arbuscular mycorrhizal fungi (AMF) represent an ecologically important and evolutionarily intriguing group of symbionts of land plants, currently thought to have propagated clonally for over 500 Myr. AMF produce multinucleate spores and may exchange nuclei through anastomosis, but meiosis has never been observed in this group. A provocative alternative for their successful and long asexual evolutionary history is that these organisms may have cryptic sex, allowing them to recombine alleles and compensate for deleterious mutations. This is partly supported by reports of recombination among some of their natural populations. We explored this hypothesis by searching for some of the primary tools for a sustainable sexual cycle—the genes whose products are required for proper completion of meiotic recombination in yeast—in the genomes of four AMF and compared them with homologs of representative ascomycete, basidiomycete, chytridiomycete, and zygomycete fungi. Our investigation used molecular and bioinformatic tools to identify homologs of 51 meiotic genes, including seven meiosis-specific genes and other “core meiotic genes” conserved in the genomes of the AMF Glomus diaphanum (MUCL 43196), Glomus irregulare (DAOM-197198), Glomus clarum (DAOM 234281), and Glomus cerebriforme (DAOM 227022). Homology of AMF meiosis-specific genes was verified by phylogenetic analyses with representative fungi, animals (Mus, Hydra), and a choanoflagellate (Monosiga). Together, these results indicate that these supposedly ancient asexual fungi may be capable of undergoing a conventional meiosis; a hypothesis that is consistent with previous reports of recombination within and across some of their populations.

Symbiosis-related plant genes modulate molecular responses in an arbuscular mycorrhizal fungus during early root interactions

To gain further insight into the role of the plant genome in arbuscular mycorrhiza (AM) establishment, we investigated whether symbiosis-related plant genes affect fungal gene expression in germinating spores and at the appressoria stage of root interactions. Glomus intraradices genes were identified in expressed sequence tag libraries of mycorrhizal Medicago truncatula roots by in silico expression analyses. Transcripts of a subset of genes, with predicted functions in transcription, protein synthesis, primary or secondary metabolism, or of unknown function, were monitored in spores and germinating spores and during interactions with roots of wild-type or mycorrhiza-defective (Myc-) mutants of M. truncatula. Not all the fungal genes were active in quiescent spores but all were expressed when G. intraradices spores germinated in wild-type M. truncatula root exudates or when appressoria or arbuscules were formed in association with wild-type M. truncatula roots. Most of the fungal genes were upregulated or induced at the stage of appressorium development. Inactivation of the M. truncatula genes DMI1, DMI2/MtSYM2, or DMI3/MtSYM13 was associated with altered fungal gene expression (nonactivation or inhibition), modified appressorium structure, and plant cell wall responses, providing first evidence that cell processes modified by symbiosis-related plant genes impact on root interactions by directly modulating AM fungal activity.

Spatial monitoring of gene activity in extraradical and intraradical developmental stages of arbuscular mycorrhizal fungi by direct fluorescent in situ RT-PCR

Gene expression profiling based on tissue extracts gives only limited information about genes associated with complex developmental processes such as those implicated in fungal interactions with plant roots during arbuscular mycorrhiza development and function. To overcome this drawback, a direct fluorescent in situ RT-PCR methodology was developed for spatial mapping of gene expression in different presymbiotic and symbiotic structures of an arbuscular mycorrhizal fungus. Transcript detection was optimized by targeting the LSU rRNA gene of Glomus intraradices and monitoring expression of a stearoyl-CoA-desaturase gene that is consistently expressed at high levels in spores, hyphae, arbuscules and vesicles. This method was further validated by localizing expression of fungal peptidylprolyl isomerase and superoxide dismutase genes, which are expressed to different extents in fungal structures. Direct fluorescent in situ RT-PCR offers new perspectives for the sensitive analysis of fungal developmental processes that occur during functional differentiation in symbiotic arbuscular mycorrhiza interactions.

Communities, populations and individuals of arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi in the phylum Glomeromycota are found globally in most vegetation types, where they form a mutualistic symbiosis with plant roots. Despite their wide distribution, only relatively few species are described. The taxonomy is based on morphological characters of the asexual resting spores, but molecular approaches to community ecology have revealed a considerable unknown diversity from colonized roots. Although the lack of genetic recombination is not unique in the fungal kingdom, arbuscular mycorrhizal fungi are probably ancient asexuals. The long asexual evolution of the fungi has resulted in considerable genetic diversity within morphologically recognizable species, and challenges our concepts of individuals and populations. This review critically examines the concepts of species, communities, populations and individuals of arbuscular mycorrhizal fungi.