Mycorrhizal Genomics Initiative – Year 3

July 31st, 2014 by Francis Martin Leave a reply »

In 2003, the Poplar Mesocosm Sequencing project was launched to sequence the genome of three Populus-associated fungi, the ectomycorrhizal (EM) basidiomycete Laccaria bicolor, the arbuscular mycorrhizal (AM) glomeromycete Rhizophagus irregularis (formerly Glomus intraradices), and the poplar leaf rust Melampsora larici-populina. The publication of the genome sequence of L. bicolor was a landmark event for the mycorrhizal community. It has been rapidly followed by the release of the genome of the iconic edible EM Tuber melanosporum, the Périgord black truffle and more recently, by the genome of Rhizophagus irregularis. These genomes have provided unprecedented knowledge about the structure and functioning of the mycorrhizal fungal species and their interactions with their host plants. Genome-wide transcript profilings have also led to the identification of master genes with crucial roles in symbiosis formation, such as those coding for Mycorrhiza-induced Small Secreted Proteins (MiSSPs) controling plant immunity and development.

An international effort, referred as to the Mycorrhiza 25 Genomes Project and then the Mycorrhizal Genomics Initiative (MGI), aiming to unearth the evolution and functioning of mycorrhizal symbioses through large-scale genome sequencing has been launched in 2011. As of writing, this initiative targets a set of 35 fungal species that are able to form various types of mycorrhizal symbioses, i.e., EM, arbuscular, ericoid and orchid mycorrhizae (see my previous posts ‘Mycorrhizal Genomics Initiative‘ and ‘Exploring the Mycorrhizal Genomes‘ ). Sequencing is carried out at JGI and Genoscope in the framework of the JGI Community Science Program, the 1000 Fungal Genomes Project and the TuberEvol project. Comparison of these genomes should facilitate the characterization of the genetic mechanisms that underpin the formation and evolution of ecologically-relevant mycorrhizal symbioses and characterization of genes selectively associated with particular symbiotic patterns.

The fungal species sequenced have been selected based on: (1) their phylogenetic position, (2) their ecological relevance, and (3) their ability to establish different types of mycorrhizal symbiosis. As of today, genomic sequences and gene repertoires are publicly available for 28 mycorrhizal fungi, including 24 ectomycorrhizal species, 3 ericoid species, 2 orchid mycorrhizal species and 1 arbuscular mycorrhizal species (see Table below & see the JGI MycoCosm Mycorrhizal Fungi portal.

Genomes of the sequenced mycorrhizal fungi range in size from about 36 Mb, as in the case of Rhizopogon vinicolor, to a 193 Mb, as in Tuber magnatum (Table). Repetitive DNA, mostly in the form of transposable elements (TE), is responsible for the bulk of the variation. A striking feature is the wide variation in repetitive DNA content (from 3.6 % for H. cylindrosporum to 58.3% for T. magnatum). Predicted gene contents range from about 7500 for T. melanosporum to ~28000 genes for Rhizophagus irregularis.

We are drafting a paper summarizing the main conclusions from the analysis of the first series of mycorrhizal genomes. Stay tune!

 

Species Genome size Gene #
1 Amanita muscaria Koide v1.01 40,699,759 18,153
2 Boletus edulis v1.01 46,637,611 16,933
3 Cenococcum geophilum 1.58 v2.01 177,557,160 14,748
4 Choiromyces venosus 120613-1 v1.01 126,035,033 17,986
5 Cortinarius glaucopus AT 2004 276 v2.01 63,450,306 20,377
6 Gyrodon lividus BX v1.01 43,048,674 11,779
7 Hebeloma cylindrosporum h7 v2.01 38,226,047 15,382
8 Laccaria amethystina LaAM-08-1 v1.01 52,197,432 21,066
9 Laccaria bicolor 81306 v1.01 50,950,722 17,791
10 Laccaria bicolor D101 v1.01 70,029,479 22,538
11 Laccaria bicolor S238N-H70 v1.01 57,049,857 19,903
12 Laccaria bicolor S238N-H82 v1.01 52,023,709 18,706
13 Laccaria bicolor S238N-H82xH70 v1.01 42,115,601 17,045
14 Laccaria bicolor v2.01 60,707,050 23,132
15 Meliniomyces bicolor E v2.03 82,384,847 18,619
16 Meliniomyces variabilis F v1.03 55,857,776 20,389
17 Morchella conica CCBAS932 v1.01 48,213,273 11,600
18 Oidiodendron maius Zn v1.03 46,426,256 16,703
19 Paxillus involutus ATCC 200175 v1.01 58,301,126 17,968
20 Paxillus rubicundulus Ve08.2h10 v1.01 53,011,005 22,065
21 Piloderma croceum F 1598 v1.01 59,326,866 21,583
22 Pisolithus microcarpus 441 v1.01 53,027,657 21,064
23 Pisolithus tinctorius Marx 270 v1.0 71,007,534 22,701
24 Rhizophagus irregularis DAOM 181602 v1.02 91,083,792 30,282
25 Rhizopogon vinicolor AM-OR11-026 v1.01 36,102,320 14,469
26 Scleroderma citrinum Foug A v1.01 56,144,862 21,012
27 Sebacina vermifera MAFF 305830 v1.04 38,094,242 15,312
28 Suillus brevipes v1.01 51,712,595 22,453
29 Suillus luteus UH-Slu-Lm8-n1 v1.01 37,014,302 18,316
30 Terfezia boudieri S1 v1.01 63,234,573 10,200
31 Tricholoma matsutake 945 v3.01 175,759,688 22,885
32 Tuber aestivum1 131,544,163 9,344
33 Tuber magnatum v1.01 192,781,443 9,433
33 Tuber melanosporum v1.01 124,945,702 7,496
34 Tulasnella calospora AL13/4D v1.04 62,392,858 19,659
35 Wilcoxina mikolae CBS 423.85 v1.01 117,288,895 13,093

 

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