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ARHGEF9 disruption in a female patient is associated with X linked mental retardation and sensory hyperarousal

Introduction: We identified a female patient with mental retardation and sensory hyperarousal. She has a de novo paracentric inversion of one X chromosome with completely skewed inactivation of the normal X chromosome. Objective: We aimed to identify whether a single gene or gene region caused her cognitive and behavioural impairment and that of others. Results:… [Read More]

IMG/M: a data management and analysis system for metagenomes

IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Department of Energys (DOE) Joint Genome Institute (JGI). IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system. IMG/M provides IMGs comparative data analysis tools extended to handle metagenome data, together with… [Read More]

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

Mycorrhizal symbioses – the union of roots and soil fungi – are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants(1,2). Boreal, temperate and montane forests all depend on ectomycorrhizae(1). Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the… [Read More]

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models…. [Read More]

Parallel evolution of truncated transfer RNA genes in arachnid mitochondrial genomes

The cloverleaf secondary structure of transfer RNA (tRNA) is highly conserved across all forms of life. Here, we provide sequence data and inferred secondary structures for all tRNA genes from 8 new arachnid mitochondrial genomes, including representatives from 6 orders. These data show remarkable reductions in tRNA gene sequences, indicating that T-arms are missing from… [Read More]

The genome of Polaromonas sp strain JS666: Insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium, and features of relevance to biotechnology

Polaromonas sp. strain JS666 can grow on cis-1,2-dichloroethene (cDCE) as a sole carbon and energy source and may be useful for bioremediation of chlorinated solvent-contaminated sites. Analysis of the genome sequence of JS666 (5.9 Mb) shows a bacterium well adapted to pollution that carries many genes likely to be involved in hydrocarbon and xenobiotic catabolism… [Read More]

The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates

Background: Welwitschia mirabilis is the only extant member of the family Welwitschiaceae, one of three lineages of gnetophytes, an enigmatic group of gymnosperms variously allied with flowering plants or conifers. Limited sequence data and rapid divergence rates have precluded consensus on the evolutionary placement of gnetophytes based on molecular characters. Here we report on the… [Read More]

Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae)

Background: The genus Cuscuta L. (Convolvulaceae), commonly known as dodders, are epiphytic vines that invade the stems of their host with haustorial feeding structures at the points of contact. Although they lack expanded leaves, some species are noticeably chlorophyllous, especially as seedlings and in maturing fruits. Some species are reported as crop pests of worldwide… [Read More]

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta

Background: Plastid genome content and protein sequence are highly conserved across land plants and their closest algal relatives. Parasitic plants, which obtain some or all of their nutrition through an attachment to a host plant, are often a striking exception. Heterotrophy can lead to relaxed constraint on some plastid genes or even total gene loss…. [Read More]