Fungal Evolution Meets Fungal Genomics

Leigh, J.; Seif, Elias; Rodríguez-Ezpeleta, Naiara; Jacob, Yannick; Bf, Lang

doi:10.1201/9780203027356.ch12

Cited by 11 publications

(9 citation statements)

References 1 publication

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As the early eukaryotic world must have been exclusively unicellular, protists are the key to understanding the origin and evolution of multicellular eukaryotes. As we know today, close unicellular relatives of the multicellular animals, fungi and land plants are, respectively, choanoflagellates plus Ichthyosporea (4,5), nucleariids [(6–9); E.Steenkamp, S.Baldauf and B.F.Lang, unpublished data], and charophyte algae (10,11). Unfortunately, very few protist genome projects are underway and protist nuclear genomics data are often limited to one or a few standard genes.…”

Section: Introductionmentioning

confidence: 99%

TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)

O'Brien¹,

Koski

Zhang³

et al. 2007

Nucleic Acids Research

View full text Add to dashboard Cite

The TBestDB database contains ∼370 000 clustered expressed sequence tag (EST) sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and includes experimental information, consensus sequences, gene annotations and metabolic pathway predictions. Most of these ESTs have been generated by the Protist EST Program, a collaboration among six Canadian research groups. EST sequences are read from trace files up to a minimum quality cut-off, vector and linker sequence is masked, and the ESTs are clustered using phrap. The resulting consensus sequences are automatically annotated by using the AutoFACT program. The datasets are automatically checked for clustering errors due to chimerism and potential cross-contamination between organisms, and suspect data are flagged in or removed from the database. Access to data deposited in TBestDB by individual users can be restricted to those users for a limited period. With this first report on TBestDB, we open the database to the research community for free processing, annotation, interspecies comparisons and GenBank submission of EST data generated in individual laboratories. For instructions on submission to TBestDB, contact tbestdb@bch.umontreal.ca. The database can be queried at .

show abstract

Section: Introductionmentioning

confidence: 99%

TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)

O'Brien¹,

Koski

Zhang³

et al. 2007

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Accordingly, the occurrence of P2, P5, P7-10, and P12 in both T. deformans and A. nidulans possibly indicates that T. deformans is an ancestral fungus that branches at the base of the ascomycetes. Although it has been proposed to be related to Schizosaccharomyces species based on rRNA phylogenies (Nishida and Sugiyama 1993), it does not appear to be related based on either mtP-RNA structure or from mitochondrial protein sequences (Leigh et al 2003).…”

Section: Mitochondrial Rnase P Rnas In Ascomycete Fungimentioning

confidence: 99%

“…deformans has been grouped together with Schizosaccharomyces species in phylogenetic analyses (termed archiascomyetes, Nishida and Sugiyama 1993; for an alternative view, see Bullerwell et al 2003b;Leigh et al 2003), but the mtP-RNA secondary structure of T. deformans exhibits striking similarity only to the euascomyete A. nidulans (Fig. 2B).…”

Section: Fission Yeastsmentioning

confidence: 99%

Mitochondrial RNase P RNAs in ascomycete fungi: Lineage-specific variations in RNA secondary structure

Seif¹,

Forget²,

Martín³

et al. 2003

RNA

View full text Add to dashboard Cite

The RNA subunit of mitochondrial RNase P (mtP-RNA) is encoded by a mitochondrial gene (rnpB) in several ascomycete fungi and in the protists Reclinomonas americana and Nephroselmis olivacea. By searching for universally conserved structural elements, we have identified previously unknown rnpB genes in the mitochondrial DNAs (mtDNAs) of two fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces octosporus; in the budding yeast Pichia canadensis; and in the archiascomycete Taphrina deformans. The expression of mtP-RNAs of the predicted size was experimentally confirmed in the two fission yeasts, and their precise 5 and 3 ends were determined by sequencing of cDNAs generated from circularized mtP-RNAs. Comparative RNA secondary structure modeling shows that in contrast to mtP-RNAs of the two protists R. americana and N. olivacea, those of ascomycete fungi all have highly reduced secondary structures. In certain budding yeasts, such as Saccharomycopsis fibuligera, we find only the two most conserved pairings, P1 and P4. A P18 pairing is conserved in Saccharomyces cerevisiae and its close relatives, whereas nearly half of the minimum bacterial consensus structure is retained in the RNAs of fission yeasts, Aspergillus nidulans and Taphrina deformans. The evolutionary implications of the reduction of mtP-RNA structures in ascomycetes will be discussed.

show abstract

“…This term recognizes that such molecules appear to be circles in restriction and sequence analysis, whereas in vivo, the bulk of molecules consist of linear, multimeric head-to-tail concatemers (45). Other mitochondrial DNA topologies have been reported as well, including (i) single linear mtDNAs in some ascomycete and chytridiomycete fungi (reviewed in 14), in apicomplexa, chlorophytes, ciliates and golden algae (reviewed in 1); (ii) several (i.e., three) circular-mapping DNAs in the fungus Spizellomyces; (1; the multiple circles of angiosperm mtDNAs are not listed here because they are believed to derive from one master circle; see above); and (iii) at least two linear mitochondrial chromosomes in the chlorophyte Polytomella parva (46). Several mitochondrial chromosomes have been also found in the animal Dicyema, but their topology is unknown (47).…”

Section: Mitochondrial Genome Architecturementioning

confidence: 99%

“…Most chytridiomycete fungi encode highly reduced sets of only 7 -9 mitochondrial tRNAs. Additional differences in coding content include unidentified reading frames and plasmid-encoded polymerases, which are quite common in filamentous fungi (14).…”

Section: Fungal Mtdnasmentioning

confidence: 99%

Parallels in Genome Evolution in Mitochondria and Bacterial Symbionts

Burger

Lang

2003

IUBMB Life

View full text Add to dashboard Cite

SummaryMitochondria, the energy-producing organelles of the eukaryotic cell, originate from an endosymbiotic a-proteobacterium. These organelles are believed to have arisen only once in evolutionary history, but despite their common ancestry, mitochondrial DNAs vary extensively throughout eukaryotes in genome architecture and gene content. New insights into early mitochondrial genome evolution come from the investigation of primitive mitochondriate eukaryotes, as well as the comparison between mitochondria and intracellular bacterial symbionts. IUBMB Life, 55: 205-212, 2003

show abstract

Fungal Evolution Meets Fungal Genomics

Cited by 11 publications

References 1 publication

TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)

TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)

Mitochondrial RNase P RNAs in ascomycete fungi: Lineage-specific variations in RNA secondary structure

Parallels in Genome Evolution in Mitochondria and Bacterial Symbionts

Contact Info

Product

Resources

About