[Show abstract][Hide abstract] ABSTRACT: Saprotrophy on plant biomass is a recently developed nutrition strategy for Trichoderma. However, the physiology and evolution of this new nutrition strategy is still elusive. We report the deep sequencing and
analysis of the genome of Trichoderma longibrachiatum, an efficient cellulase producer. The 31.7-Mb genome, smallest among the sequenced Trichoderma species, encodes fewer nutrition-related genes than saprotrophic T. reesei (Tr), including glycoside hydrolases and nonribosomal peptide synthetase–polyketide synthase. Homology and phylogenetic analyses
suggest that a large number of nutrition-related genes, including GH18 chitinases, β-1,3/1,6-glucanases, cellulolytic enzymes,
and hemicellulolytic enzymes, were lost in the common ancestor of T. longibrachiatum (Tl) and Tr. dN/dS (ω) calculation indicates that all the nutrition-related genes analyzed are under purifying selection. Cellulolytic enzymes,
the key enzymes for saprotrophy on plant biomass, are under stronger purifying selection pressure in Tl and Tr than in mycoparasitic species, suggesting that development of the nutrition strategy of saprotrophy on plant biomass has
increased the selection pressure. In addition, aspartic proteases, serine proteases, and metalloproteases are subject to stronger
purifying selection pressure in Tl and Tr, suggesting that these enzymes may also play important roles in the nutrition. This study provides insights into the physiology
and evolution of the nutrition strategy of Trichoderma.
Full-text · Article · Jan 2014 · Genome Biology and Evolution
[Show abstract][Hide abstract] ABSTRACT: Here, we report the draft genome sequence of Antarctic sea ice bacterium Glaciecola punicea ACAM 611T, the type species of the genus Glaciecola. A blue-light-absorbing proteorhodopsin gene is present in the 3.08-Mb genome. This genome sequence can facilitate the study
of the physiological metabolisms and ecological roles of sea ice bacteria.
Full-text · Article · Jun 2012 · Journal of bacteriology
[Show abstract][Hide abstract] ABSTRACT: There are over 30 species in the marine bacterial genus Pseudoalteromonas. However, our knowledge about this genus is still limited. We sequenced the genomes of type strains of seven species in the
genus, facilitating the study of the physiology, adaptation, and evolution of this genus.
Full-text · Article · May 2012 · Journal of bacteriology
[Show abstract][Hide abstract] ABSTRACT: The cycloprodigiosin biosynthetic gene cluster has not been reported. We sequenced the genome of a cycloprodigiosin-producing
bacterial strain, Pseudoalteromonas rubra ATCC 29570T. Analysis revealed a probable cycloprodigiosin biosynthetic cluster, providing a good model for the study of cycloprodigiosin
synthesis and regulation.
Full-text · Article · Mar 2012 · Journal of bacteriology
[Show abstract][Hide abstract] ABSTRACT: Yu et al. (Polar Biol. 32:1539-1547, 2009) isolated 199 Pseudoalteromonas strains from Arctic sea ice. We sequenced the genomes of six of these strains, which are affiliated to different Pseudoalteromonas species based on 16S rRNA gene sequences, facilitating the study of physiology and adaptation of Arctic sea ice Pseudoalteromonas strains.
Full-text · Article · Feb 2012 · Journal of bacteriology
[Show abstract][Hide abstract] ABSTRACT: Glaciecola nitratireducens strain FR1064T was isolated from seawater and described as a new species by Baik et al. in 2006. The genome size is about 1.01 to 1.26 Mb
smaller than two reported Glaciecola genomes, indicating the gain or loss of large genome segments in the evolution of Glaciecola strains.
Full-text · Article · Dec 2011 · Journal of bacteriology