Reference species for fungi

Reference fungi

Explanation and definition for the "reference species" we use for the course.

Many bioinformatics procedures depend on the comparison of sequences between species. To make good use of evolutionary information, we should choose species that span the breadth of observations, and that are not biased towards a particular branch of the phylogenetic tree. To keep procedures manageable, the number of speciescannot be "too large". For fungi, we make use of recent phylogenetic studies that establish the branching order of the entire kingdom, and we choose ten representatives for clades at the Class or subphylum level. To illustrate the "class"level, for animals the class level contains e.g. bony and cartilaginous fishes, amphibians, reptiles, birds and mammals.

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To select a set of diverse species, the whole set of names of genome-sequenced fungi was loaded into the NCBI's Common Taxonomic Tree tree tool. Then ten representative species were manually selected as being well distributed across the tree. The selected species are:

Name	BICODE	tax ID	Classification
Phylum Ascomycota
Aspergillus nidulans	ASPNI	00000	Subphylum Pezizomycotina; Class Eurotiomycetes
Bipolaris oryzae	BIPOR	00000	Subphylum Pezizomycotina; Class Dothideomycetes
Neurospora crassa	NEUCR	00000	Subphylum Pezizomycotina; Class Sordariomycetes
Saccharomyces cerevisiae	SACCE	00000	Subphylum Saccharomycotina
Schizosaccharomyces pombe	SCHPO	00000	Subphylum Taphrinomycotina
Phylum Basidiomyceta
Coprinopsis cinerea	COPCI	00000	Subphylum Agaricomycotina; Class Agaricomycetes
Cryptococcus neoformans	CRYNE	00000	Subphylum Agaricomycotina; Class Tremellomycetes
Puccinia Graminis	PUCGR	00000	Subphylum Pucciniomycotina
Ustilago maydis	USTMA	00000	Subphylum Ustilaginomycotina
Wallemia mellicola	WALME	00000	Subphylum Wallemiales incertae sedis

 

Entrez selection code, e.g. for BLAST searches

"Wallemia mellicola"[organism] OR
"Puccinia Graminis"[organism] OR
"Ustilago maydis"[organism] OR
"Cryptococcus neoformans"[organism] OR
"Coprinopsis cinerea"[organism] OR
"Schizosaccharomyces pombe"[organism] OR
"Aspergillus nidulans"[organism] OR
"Neurospora crassa"[organism] OR
"Bipolaris oryzae"[organism] OR
"Saccharomyces cerevisiae"[organism]

 

Taxonomy IDs, e.g. for the NCBI taxonomy browser

4896
4932
5141
5270
5297
5346
40410
101162
162425
1708541

 

Text tree, based on the NCBI Taxonomy Common Tree

Dikarya
 |
 +--Basidiomycota
 |   |
 |   +-Agaricomycotina
 |   |  +-Wallemia mellicola
 |   |  +-Coprinopsis cinerea
 |   |  +-Cryptococcus neoformans var. neoformans
 |   |
 |   +-Puccinia graminis
 |   +-Ustilago maydis
 |
 +--Ascomycota
     |
     +-Schizosaccharomyces pombe
     |
     +-saccharomyceta
        +-Saccharomyces cerevisiae
        |
        +-leotiomyceta
           +-Aspergillus nidulans
           +-Neurospora crassa
           +-Bipolaris oryzae

 

Phylip tree format, e.g. to plot cladograms

(
(
'Wallemia mellicola':4,
'Puccinia graminis':4,
'Ustilago maydis':4,
(
'Coprinopsis cinerea':4,
'Cryptococcus neoformans':4
)Agaricomycotina:4
)Basidiomycota:4,
(
(
(
'Aspergillus nidulans':4,
'Bipolaris oryzae':4,
'Neurospora crassa':4
)leotiomyceta:4,
'Saccharomyces cerevisiae':4
)saccharomyceta:4,
'Schizosaccharomyces pombe':4
)Ascomycota:4
)Dikarya:4;

 

Cladogram, drawn with the Phylip program retree

                 ┌──────────── Schizosaccharomyces pombe
                 │  
                 │                          ┌───────────── Aspergillus nidulans
   ┌─────────────+                          │  
   │             │             ┌────────────+───────────── Bipolaris oryzae
   │             │             │            │  
   │             └─────────────+            └───────────── Neurospora crassa
   │                           │  
 ──+                           └──────────── <span style="background-color:#EEEEBB;">Saccharomyces cerevisiae</span>
   │  
   │                           ┌──────────── Cryptococcus neoformans
   │             ┌─────────────+  
   │             │             └───────────── Coprinopsis cinerea
   │             │  
   └─────────────+───────────── Ustilago maydis
                 │  
                 ├───────────── Puccinia graminis
                 │  
                 └───────────── Wallemia mellicola

 

Rcode

REFspecies <- c("Aspergillus nidulans",
                "Bipolaris oryzae",
                "Coprinopsis cinerea",
                "Cryptococcus neoformans",
                "Neurospora crassa",
                "Puccinia graminis",
                "Saccharomyces cerevisiae",
                "Schizosaccharomyces pombe",
                "Ustilago maydis",
                "Wallemia mellicola"
)

 

Further reading and resources

Ebersberger et al. (2012) A consistent phylogenetic backbone for the fungi. Mol Biol Evol 29:1319-34. (pmid: 22114356)

[ PubMed ] [ DOI ] Abstract The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses.