Genome survey sequencing (1.9X coverage) was generated for Moniliophthora perniciosa, the cause of witches’ broom disease on cacao plants. The sequence for this basidiomycete plant pathogen was published in BMC Genomics this week. The authors report a higher number of ROS metabolism and P450 genes. Evaluating whether these copy number differences are significantly different from other basidiomycete fungi and are lineage specific expansions will help determine if these families played a role in the adaptation of this plant pathogen.
This work provides an important stepping stone in understanding and eventually controlling this pathogen which is devastating cacao plantations. An associated review describes what we have and can learn about Witches’ broom disease.
Jorge MC Mondego, Marcelo F Carazzolle, Gustavo GL Costa, Eduardo F Formighieri, Lucas P Parizzi, Johana Rincones, Carolina Cotomacci, Dirce M Carraro, Anderson F Cunha, Helaine Carrer, Ramon O Vidal, Raissa C Estrela, Odalys Garcia, Daniela PT Thomazella, Bruno V de Oliveira, Acassia BL Pires, Maria Carolina S Rio, Marcos Renato R Araujo, Marcos H de Moraes, Luis AB Castro, Karina P Gramacho, Marilda S Goncalves, Jose P Moura Neto, Aristoteles Goes Neto, Luciana V Barbosa, Mark J Guiltinan, Bryan A Bailey, Lyndel W Meinhardt, Julio CM Cascardo, Goncalo AG Pereira (2008). A genome survey of Moniliophthora perniciosa gives new insights into Witches’ Broom Disease of cacao BMC Genomics, 9 (1) DOI: 10.1186/1471-2164-9-548
A paper (Park et al, BMC Genomics) from Fungal Bioinformatics Lab at Seoul University in South Korea describes their new “Fungal P450 Database”. The database contains sequence, names, and genome links for P450’s (or Cytochrome P450s) identified by similarity and phylogenetic classification from genome annotations. The group is using most of annotated genomes in GenBank (and I think some from elsewhere) of bacterial, fungi, animals, and plants.
I find the current nomenclature for this family of genes confusing but it has been I am sure a difficult job and wrangled to a large part by David Nelson (who also has a new paper on the CYPome of Aspergillus nidulans). I have found it difficult to follow the logic for naming these members, as it didn’t seem to be particularly phylogenetic at first, although I think that has improved. However, a stable and solid reference database is needed to for naming these gene members and for mapping new members in through straightforward analyses is an essential resource. Park et al have made great inroads to that end and it may indeed meet needs (I am cautious to say it is solved without more exploration or some sense of whether it is intended or will be taken up as just that sort of reference by the P450 community). It has seemed to me that a proper phylogenetic (or really, a phylogenomic) approach is essential for naming the P450 member genes as orthologous or paralogous members across multiple species. The group has defined their classes as clusters of homologs (e.g. Mg004 is Magnaporthe grisea gene in Cluster 9.1) and linked these also to the Nelson nomeclature (CYP68E1). By defining orthologous family members we can make more interpretations about how to transfer functional annotation in a truly phylogenomic context.
The overall family is so large and diverse (they report 4538 fungal P450s into 141 clusters/sub-families from 68 species) across many different species. The fungi tend to have very large families in some clades (e.g. some filamentous fungi) so I think this type of systematic and searchable system that will have stable identities for clusters is an essential resource. I know I’m going to try and give it a whirl. We have a couple of cool findings about changes in the P450 families in Basidiomycete Coprinopsis and related species comparisons that I hope we’ll be able to better interpret with this additional phylogenomic naming of gene family members.
Jongsun Park, Seungmin Lee, Jaeyoung Choi, Kyohun Ahn, Bongsoo Park, Jaejin Park, Seogchan Kang, Yong-Hwan Lee (2008). Fungal cytochrome P450 database BMC Genomics, 9 (1) DOI: 10.1186/1471-2164-9-402