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RNA-Seq, a method using next generation sequencing technologies to sequence the transcriptome, facilitates genome-wide analysis of splice junction sites. In this paper, we introduce SOAPsplice, a robust tool to detect splice junctions using RNA-Seq data without using any information of known splice junctions. SOAPsplice uses a novel two-step approach(More)
To date, occurrence and stimulation of different nitrification pathways in acidic soils remains unclear. Laboratory incubation experiments, using the acetylene inhibition and 15N tracing methods, were conducted to study the relative importance of heterotrophic and autotrophic nitrification in two acid soils (arable (AR) and coniferous forest) in subtropical(More)
An in situ 15N tracing study was conducted to investigate the characteristics of soil mineral nitrogen (N) production and conservation in acid forest soils of subtropical China. The six experimental soils were strongly acidic (pH ranged from 4.1 to 4.7), except for one soil, from an orange orchard which had a higher pH (5.7) due to lime application. Total(More)
Colobines are a unique group of Old World monkeys that principally eat leaves and seeds rather than fruits and insects. We report the sequencing at 146× coverage, de novo assembly and analyses of the genome of a male golden snub-nosed monkey (Rhinopithecus roxellana) and resequencing at 30× coverage of three related species (Rhinopithecus bieti,(More)
Amending vegetable soils with organic materials is increasingly recommended as an agroecosystems management option to improve soil quality. However, the amounts of NO, N2O, and N2 emissions from vegetable soils treated with organic materials and frequent irrigation are not known. In laboratory-based experiments, soil from a NO 3 − -rich (340 mg N kg−1)(More)
The potential denitrification (PD) rate, NO, N2O, and N2 emission were determined after treatment with 50 mg NO3 −−N kg−1 soil using the acetylene inhibition method, and meanwhile abundance of four denitrifying genes (i.e., narG, nirK, norB, nosZ) was also investigated in subtropical soils of China. Soil samples were collected from conifer forest (C), shrub(More)
Biological soil disinfestation (BSD) is an effective and environmentally friendly way to suppress soil-borne pathogens. Although it is increasingly used in USA, the Netherlands and Japan, its precise mechanism has not been well quantified so far. Quantitative real-time PCR, denaturing gradient gel electrophoresis and high performance liquid chromatography(More)
Continuous vegetable cultivation in greenhouses can easily induce soil degradation, which considerably affects the development of sustainable vegetable production. Recently, the reductive soil disinfestation (RSD) is widely used as an alternative to chemical soil disinfestations to improve degraded greenhouse vegetable soils. Considering the importance of(More)
In China, atmospheric deposition of NO3 − is increasing rapidly. However, information on how microbial N cycling in forest soils may respond to increasing deposition of NO3 − is currently lacking. Determination of process- and pool-specific N transformation rates can provide additional insights into the controls on the production and consumption of(More)
For understanding the effects of nitrification ability on nitrogen (N) use efficiency and N losses via denitrification in paddy soils under flooding conditions, six paddy soils with different nitrification activities were sampled from various sites of China and a pot experiment was conducted. Rice plants at tillering stage were transplanted into pots and(More)