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Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and(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)
Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically(More)
We report the sequencing at 131× coverage, de novo assembly and analyses of the genome of a female Tibetan wild boar. We also resequenced the whole genomes of 30 Tibetan wild boars from six major distributed locations and 18 geographically related pigs in China. We characterized genetic diversity, population structure and patterns of evolution. We searched(More)
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)
The ground tit (Parus humilis) is endemic to the Tibetan plateau. It is a member of family Paridae but it was long thought to be related to the ground jays because of their morphological similarities. Here we present the ground tit's genome and re-sequence two tits and one ground jay, to clarify this controversially taxonomic status and uncover its genetic(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)
The rapid expansion of intensively farmed vegetable fields has substantially contributed to the total N2O emissions from croplands in China. However, to date, the mechanisms underlying this phenomenon have not been completely understood. To quantify the contributions of autotrophic nitrification, heterotrophic nitrification, and denitrification to N2O(More)
The wetlands play an important role in carbon storage, especially at high latitudes, at which they store nearly one-third of global soil carbons. However, few studies have investigated the emissions of CO(2), CH(4) and N(2)O in the long-term, especially effects of freeze-thaw cycles on these gases emissions in freshwater marsh ecosystems. In this paper, we(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)