Tag Archives: neurospora

Neurospora 2010 and upcoming fungal conferences

Don’t forget to register for Neurospora 2010 held at the beautiful Asilomar Conference center in Pacific Grove, CA held April 8-11, 2010. Get your filamentous fungi fix here!

Also save the date for some other important upcoming conferences you may consider attending

Other evolutionary and genomics meetings

Fungal genome assembly from short-read sequences

This is a research blog so I though I’d post some quick numbers we are seeing for de novo assembly of the Neurospora crassa genome using Velvet. The genome of N.crassa is about 40Mb and sequencing of several flow cells using Solexa/Illumina technology to see what kind of de novo reconstruction we’d get. I knew that this is probably insufficient for a very good assembly given what has been reported in the literature, but sometimes it is helpful to give it a try on local data.  Mostly this is a project about SNP discovery from the outset. I used a hash size of 21 in velvet with an early (2FC) and later (4FC) dataset. Velvet was run with a hashsize of 21 for these data based on some calculations and running it with different hash sizes to see the optimal N50.  Summary contig size numbers come from the commands using cndtools from Colin Dewey.

  faLen < contigs.fa | stats

2 flowcells (~10M reads @36bp/read or about 10X coverage of 40Mb genome)

            N = 199562
          SUM = 25463251
          MIN = 49
 1ST-QUARTILE = 87
       MEDIAN = 107.0
 3RD-QUARTILE = 146
          MAX = 5371
         MEAN = 127.59568956
          N50 = 130

4 flow cells  (~20M reads @36bp/read; or about 20X coverage of a 40Mb genome)

            N = 102437
          SUM = 38352075
          MIN = 41
 1ST-QUARTILE = 77.0
       MEDIAN = 153
 3RD-QUARTILE = 467
          MAX = 7189
         MEAN = 374.396702363
          N50 = 837

So that’s N50 of 837bp – for those used to seeing N50 on the order or 1.5Mb this is not great.  But from4 FC worth of sequencing which was pretty cheap.  This is a reasonably repeat-limited genome so we should get pretty good recovery if the seq coverage is high enough. Using Maq we can both scaffold the reads and recover a sufficient number of high quality SNPs for the mapping part of the project.

To get a better assembly one would need much deeper coverage as Daniel and Ewan explain in their Velvet paper and shown in Figure 4 (sorry, not open-access for 6 mo). Full credit: This sequence was from unpaired sequence reads from Illumina/Solexa Genomic sequencing done at UCB/QB3 facility on libraries prepared by Charles Hall in the Glass lab.

Podospora genome published

P.anserinaThe genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings.  The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons among filamentous Sordariomycete fungi. The authors primarily focused on comparative genomics of Podospora to Neurospora crassa, the next closest model filamentous species.  Within the Sordariomycetes there are now a very interesting collection of closely related species which can be useful for applying synteny and phylogenomics approaches.

The analyses in the manuscript focused on these differences between Neurospora and Podospora identifying some key differences in carbon utilization contrasting the coprophillic (Podospora) and plant saprophyte (Neurospora).  There are several observations of gene family expansions in the Podospora genome which could be interpreted as additional enzyme capacity to break down carbon sources that are present in dung.

The genome of Neurospora has be shaped by the action of the genome defense mechanisms like RIP that has been on interpretation of the reduced number of large gene families and paucity of transposons. The authors report a surprising finding that in their analysis that despite sharing orthologs of genes that are involved in several genome defense, they in fact find fewer repetitive sequences in Podospora while it still fails to have good evidence of RIP.

Overall, these data suggest that P. anserina has experienced a fairly complex history of transposition and duplications, although it has not accumulated as many repeats as N. crassaP. anserina possesses all the orthologues of N. crassa factors necessary for gene silencing, including RIP, meiotic MSUD and also vegetative quelling, a post transcriptional gene silencing mechanism akin to RNA interference

I think this data and observations interleaves nicely with the work our group is exploring on evolution of genome of several Neurospora species which have different mating systems. The fact that the gene components that play a role in MSUD and a RIP are found in Podpospora but yet the degree of RIP and the lack of any observed meiotic silencing suggests some interesting occurrences on the Neurospora branch to be explored.  The potentially different degrees of RIP efficiency and types of mating systems (heterothallic and pseudohomothallic) among the Neurospora spp may also provide a link to understanding how RIP evolved and its role on N. crassa evolution.

Senescence in Podospora

Another aspect of Podopsora biology that isn’t touched on, is the use of the fungus as a model for senescence.  The fungus exhibits maternal senescence which involves targeted changes in the mitochondria that leads to cell death.  The evolutionary and molecular basis for this process has been of interest to many research groups and the genome sequence can provide an additional toolkit for identifying the factors involved in the apoptosis process in this filamentous fungi. Whether it will help find a real link for aging research in other eukaryotes remains to be seen, but it is a good model system for some aspects of how aging and damage to mtDNA are linked.

Espagne, E., Lespinet, O., Malagnac, F., Da Silva, C., Jaillon, O., Porcel, B.M., Couloux, A., Aury, J., et al (2008). The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biology, 9(5), R77. DOI: 10.1186/gb-2008-9-5-r77

RIPing in an asexual fungus

ResearchBlogging.orgA.niger conidiophoreA paper in Current Genetics describes the discovery of Repeat Induced Polymorphism (RIP) in two Euriotiales fungi.  RIP has been extensively studied in Neurospora crassa and has been identified in other Sordariomycete fungi Magnaporthe, Fusiarium. This is not the first Aspergillus species to have RIP described as it was demonstrated in the biotech workhorse Aspergillus oryzae.  However, I think this study is the first to describe RIP in a putatively asexual fungus.  The evidence for RIP is only found in transposon sequences in the Aspergillus and Penicillium.  A really interesting aspect of this discovery is RIP is thought to only occur during sexual stage, but a sexual state has never been observed for these fungi.   Continue reading RIPing in an asexual fungus

Cryptococcus species deliniation

ResearchBlogging.org What delineates species boundaries in fungi? Much work has been done on biological and phylogenetic species concepts in fungi. Some concepts are reviewed in Taylor et al 2006 and in Taylor et al 2000, and applications can be seen in several pathogens such as Paraccocidiodies, Coccidioides, and the model filamentous (non-pathogenic) fungus Neurospora.

A paper in Fungal Genetics and Biology on species definitions in Cryptococcus neoformans from multi-locus sequencing seeks to provide additional treatment of the observed diversity. A large study of 117 Cryptococcus isolates were examined through multi-locus sequencing (6 loci) and identified two monophyletic lineages within C. neoformans varieties that correspond to var. neoformans and var. grubii. However within the C. gattii samples they identified four monophyletic groups consistent with deep divergences observed from whole genome trees for two strains of C. gattii, MLST, and AFLP studies. By first defining species, we can now test whether any of the species groups have different traits including prevalence in clinical settings and in nature.

BOVERS, M., HAGEN, F., KURAMAE, E., BOEKHOUT, T. (2007). Six monophyletic lineages identified within Cryptococcus neoformans and Cryptococcus gattii by multi-locus sequence typing. Fungal Genetics and Biology DOI: 10.1016/j.fgb.2007.12.004

Neurospora speciation through experimental evolution

ResearchBlogging.orgDettman, Anderson, and Kohn recently published a paper in BMC Evolutionary Biology on reproductive experimental evolution in two Neurospora crassa populations evolved under different selective conditions. This is a great study that complements work published last year in Nature on experimental evolution in Saccharomyces cerevisiae populations. Neurospora populations were evolved under high salt and low temperature and were started from either high diversity (interspecific crosses, N. crassa vs N. intermedia) or low diversity (intraspecific cross, two N. crassa isolates D143 (Louisiana, USA)and D69 (Ivory Coast)) as described in Figure 1. The experimentally evolved populations were then tested for asexual and sexual fitness (they were taken through complete meiotic cycle throughout the experiment to avoid insure there was selection on the sexual reproduction pathway.

Continue reading Neurospora speciation through experimental evolution

Neurospora alternative splicing

mitochondriaA quick link to a Neurospora paper in Genetics today entitled “Alternative Splicing Gives Rise to Different Isoforms of the Neurospora crassa Tob55 Protein That Vary in Their Ability to Insert ß-Barrel Proteins Into the Outer Mitochondrial Membrane”. The authors investigated alternative splicing of a gene found in the TOB complex on the outside of the mitochondria. They found reduced growth rate when a strain expressed only the the longest form of three isoforms and confirmed the protein expression of the three isoforms with mass spec.

Genomes on the horizon at JGI

Several more fungi are on the docket for sequencing at JGI through their community sequencing program. This includes

This complements an ever growing list of fungal genome sequences which is probably topping 80+ now not including the several dozen strains of Saccharomyces that are being sequenced at Sanger Centre and a separately funded NIH project to be sequenced at WashU.