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Draft Genome Sequence of the Basidiomycete White-Rot Fungus Phlebia centrifuga.
Genome Announc. 2018 Apr 05; 6(14):
Publication Type
Journal Article
Miia R Mäkelä
Mao Peng
Zoraide Granchi
Thomas Chin-A-Woeng
Rosa Hegi
Sake I van Pelt
Steven Ahrendt
Robert Riley
Matthieu Hainaut
Bernard Henrissat
Igor V Grigoriev
Ronald P de Vries
Kristiina S Hildén
Author Affiliation
Department of Microbiology, University of Helsinki, Helsinki, Finland.
Genome Announc. 2018 Apr 05; 6(14):
Publication Type
Journal Article
Here, we report the genome sequence of wood-decaying white-rot fungus Phlebia centrifuga strain FBCC195, isolated from Norway spruce (Picea abies) in Finnish Lapland. The 34.66-Mb genome containing 13,785 gene models is similar to the genome length reported for other saprobic white-rot species.
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PubMed ID
29622620 View in PubMed
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Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.
BMC Genomics. 2016;17(1):267
Publication Type
Marijke J van Baren
Charles Bachy
Emily Nahas Reistetter
Samuel O Purvine
Jane Grimwood
Sebastian Sudek
Hang Yu
Camille Poirier
Thomas J Deerinck
Alan Kuo
Igor V Grigoriev
Chee-Hong Wong
Richard D Smith
Stephen J Callister
Chia-Lin Wei
Jeremy Schmutz
Alexandra Z Worden
BMC Genomics. 2016;17(1):267
Publication Type
Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these unicellular eukaryotes are important for marine ecology and for understanding Viridiplantae evolution and diversification.
We generated evidence-based Micromonas gene models using proteomics and RNA-Seq to improve prasinophyte genomic resources. First, sequences of four chromosomes in the 22 Mb Micromonas pusilla (CCMP1545) genome were finished. Comparison with the finished 21 Mb genome of Micromonas commoda (RCC299; named herein) shows they share =8,141 of ~10,000 protein-encoding genes, depending on the analysis method. Unlike RCC299 and other sequenced eukaryotes, CCMP1545 has two abundant repetitive intron types and a high percent (26 %) GC splice donors. Micromonas has more genus-specific protein families (19 %) than other genome sequenced prasinophytes (11 %). Comparative analyses using predicted proteomes from other prasinophytes reveal proteins likely related to scale formation and ancestral photosynthesis. Our studies also indicate that peptidoglycan (PG) biosynthesis enzymes have been lost in multiple independent events in select prasinophytes and plants. However, CCMP1545, polar Micromonas CCMP2099 and prasinophytes from other classes retain the entire PG pathway, like moss and glaucophyte algae. Surprisingly, multiple vascular plants also have the PG pathway, except the Penicillin-Binding Protein, and share a unique bi-domain protein potentially associated with the pathway. Alongside Micromonas experiments using antibiotics that halt bacterial PG biosynthesis, the findings highlight unrecognized phylogenetic complexity in PG-pathway retention and implicate a role in chloroplast structure or division in several extant Viridiplantae lineages.
Extensive differences in gene loss and architecture between related prasinophytes underscore their divergence. PG biosynthesis genes from the cyanobacterial endosymbiont that became the plastid, have been selectively retained in multiple plants and algae, implying a biological function. Our studies provide robust genomic resources for emerging model algae, advancing knowledge of marine phytoplankton and plant evolution.
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PubMed ID
27029936 View in PubMed
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