Reference species for fungi

Reference fungi data

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 species cannot 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 levels include e.g. bony and cartilaginous fishes, segmented worms, amphibians, reptiles, birds and mammals - the familiar, very broad categories. I.e. a reference species list of animals, divided along class levels, might include zebrafish, african claw frog, the fruit fly, humans, the raven, the oyster etc. etc. Even though they are all fungi, our reference species are no more similar to each other than the former.

 

Reference species

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	162425	Subphylum Pezizomycotina; Class Eurotiomycetes
Bipolaris oryzae	BIPOR	101162	Subphylum Pezizomycotina; Class Dothideomycetes
Neurospora crassa	NEUCR	5141	Subphylum Pezizomycotina; Class Sordariomycetes
Saccharomyces cerevisiae	SACCE	4932	Subphylum Saccharomycotina
Schizosaccharomyces pombe	SCHPO	4896	Subphylum Taphrinomycotina
Phylum Basidiomyceta
Coprinopsis cinerea	COPCI	5346	Subphylum Agaricomycotina; Class Agaricomycetes
Cryptococcus neoformans	CRYNE	5207	Subphylum Agaricomycotina; Class Tremellomycetes
Puccinia Graminis	PUCGR	5297	Subphylum Pucciniomycotina
Ustilago maydis	USTMA	5270	Subphylum Ustilaginomycotina
Wallemia mellicola	WALME	1708541	Subphylum Wallemiales incertae sedis

 

Entrez

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]

 

Tax ID

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

4896
4932
5141
5270
5297
5346
5207
101162
162425
1708541

 

Trees

Text tree, based on the NCBI Taxonomy Common Tree

Dikarya
 |
 +--Basidiomycota
 |   |
 |   +-Agaricomycotina
 |   |  +-Wallemia mellicola
 |   |  +-Coprinopsis cinerea
 |   |  +-Cryptococcus 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

 

Strains

Genome sequencing is done from a single, defined strain of a species and several genomes from different strains of the same species may be deposited in the database. This may be a problem, since the annotation level is not the same for all of them, and there may be many strains. If you work with an organism at the strain-level, make sure you know which one is considered the "reference" in the field.

Species	Strain	tax ID
Aspergillus nidulans	Aspergillus nidulans FGSC A4	227321
Bipolaris oryzae	Bipolaris oryzae ATCC 44560	930090
Neurospora crassa	Neurospora crassa OR74A	367110
Saccharomyces cerevisiae	Saccharomyces cerevisiae S288C	559292
Schizosaccharomyces pombe	Schizosaccharomyces pombe 972h-	284812
Coprinopsis cinerea	Coprinopsis cinerea okayama7#130	240176
Cryptococcus neoformans	Cryptococcus neoformans var. neoformans JEC21	214684
Puccinia Graminis	Puccinia Graminis f. sp. tritici CRL 75-36-700-3	418459
Ustilago maydis	Ustilago maydis 521	237631
Wallemia mellicola	Wallemia mellicola CBS 633.66	671144

Note that the tax-IDs for the species and strains are indeed different!

 

R Code

A vector of binomial species names.

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

A data frame of binomial species and TaxIDs.

refTaxa <- data.frame(
              ID = as.integer(c(162425,
                                101162,
                                5141,
                                4932,
                                4896,
                                5346,
                                5207,
                                5297,
                                5270,
                                1708541)),
              species = c("Aspergillus nidulans",
                          "Bipolaris oryzae",
                          "Neurospora crassa",
                          "Saccharomyces cerevisiae",
                          "Schizosaccharomyces pombe",
                          "Coprinopsis cinerea",
                          "Cryptococcus neoformans",
                          "Puccinia Graminis",
                          "Ustilago maydis",
                          "Wallemia mellicola"),
              stringsAsFactors = FALSE)

A data frame of the genome-sequenced strains in which the Mbp1 orthologues are annotated.

library(jsonlite)
taxa <- fromJSON('[
  { "ID" : 227321,
  "species" : "Aspergillus nidulans FGSC A4"},
  { "ID" : 930090,
  "species" : "Bipolaris oryzae ATCC 44560"},
  { "ID" : 367110,
  "species" : "Neurospora crassa OR74A"},
  { "ID" : 559292,
  "species" : "Saccharomyces cerevisiae S288C"},
  { "ID" : 284812,
  "species" : "Schizosaccharomyces pombe 972h-"},
  { "ID" : 240176,
  "species" : "Coprinopsis cinerea okayama7#130"},
  { "ID" : 214684,
  "species" : "Cryptococcus neoformans var. neoformans JEC21"},
  { "ID" : 418459,
  "species" : "Puccinia graminis f. sp. tritici CRL 75-36-700-3"},
  { "ID" : 237631,
  "species" : "Ustilago maydis 521"},
  { "ID" : 671144,
  "species" : "Wallemia mellicola CBS 633.66"}
  ]
')
taxa
ID                                          species
# 1  227321                     Aspergillus nidulans FGSC A4
# 2  930090                      Bipolaris oryzae ATCC 44560
# 3  367110                          Neurospora crassa OR74A
# 4  559292                   Saccharomyces cerevisiae S288C
# 5  284812                  Schizosaccharomyces pombe 972h-
# 6  240176                 Coprinopsis cinerea okayama7#130
# 7  214684    Cryptococcus neoformans var. neoformans JEC21
# 8  418459 Puccinia graminis f. sp. tritici CRL 75-36-700-3
# 9  237631                              Ustilago maydis 521
# 10 671144                    Wallemia mellicola CBS 633.66

 

Mbp1 orthologues

RBMs to MBP1_SACCE

name	Originally...	RefSeqID	UniProtID
MBP1_ASPNI	AN3154	XP_660758	Q5B8H6
MBP1_BIPOR	COCMIDRAFT_338	XP_007682304	W6ZM86
MBP1_NEUCR	Swi4	XP_955821	Q7RW59
MBP1_SACCE	Mbp1	NP_010227	P39678
MBP1_SCHPO	Res2	NP_593032	P41412
MBP1_COPCI		XP_001837394	A8NYC6
MBP1_CRYNE		XP_569090	Q5KMQ9
MBP1_PUCGR	PGTG_08863	XP_003327086	E3KED4
MBP1_USTMA	UMAG_11222	XP_011392621	A0A0D1DP35
MBP1_WALME		XP_006957051	I4YGC0

 

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 ] 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.