通讯机构：
[Boulos Chalhoub] I;[Wei Hua; Hanzhong Wang] T;Institut National de Recherche Agronomique (INRA), Unité de Recherche en Génomique Végétale (URGV), UMR1165, Organization and Evolution of Plant Genomes (OEPG), 2 rue Gaston Crémieux, 91057 Evry, France<&wdkj&>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
摘要：
Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi-winter oilseed rape cultivar 'ZS11' and its comprehensive genomic comparison with the genomes of the winter-type cultivar 'Darmor-bzh' as well as two progenitors. The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11'. Within a short evolutionary period (similar to 6700years ago), semi-winter-type 'ZS11' and the winter-type 'Darmor-bzh' maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to Darmor-bzh', both two subgenomes of 'ZS11' are closely related to its progenitors, and the 'ZS11' genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi-winter-type 'ZS11' underwent potential genomic introgressions with B. rapa (A(r)). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization-responsive flowering time in 'ZS11' was first experienced HE, and then underwent genomic introgression event with A(r), which potentially has led to genetic differences in controlling vernalization in the semi-winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi-winter oilseed rape in Asia. Significance Statement We generated a high-quality reference genome sequence of semi-winter Brassica napus. Our BAC-to-BAC strategy was effective in the assembly of repetitive regions. The main phenotypic difference between semi-winter and winter B. napus morphotypes is the vernalization requirement. Here, we found that a key gene controlling the vernalization-responsive flowering time was altered in the semi-winter type ZS11' through both homoeologous exchanges and genomic introgression with B. rapa.
摘要：
With the massive data generated by the Human Microbiome Project, how to transform such data into useful information and knowledge remains challenging. Here, with currently available sequencing information (reference genomes and metagenomes), we have developed a comprehensive microarray, HuMiChip2, for strain-level identification and functional characterization of human microbiomes. HuMiChip2 was composed of 29,467 strain-specific probes targeting 2063 microbial strains/species and 133,924 sequence- and group-specific probes targeting 157 key functional gene families involved in various metabolic pathways and host-microbiome interaction processes. Computational evaluation of strain-specific probes suggested that they were not only specific to mock communities of sequenced microorganisms and metagenomes from different human body sites but also to non-sequenced microbial strains. Experimental evaluation of strain-specific probes using single strains/species and mock communities suggested a high specificity of these probes with their corresponding targets. Application of HuMiChip2 to human gut microbiome samples showed the patient microbiomes of alcoholic liver cirrhosis significantly (p < 0.05) shifted their functional structure from the healthy individuals, and the relative abundance of 21 gene families significantly (p < 0.1) differed between the liver cirrhosis patients and healthy individuals. At the strain level, five Bacteroides strains were significantly (p < 0.1) and more frequently detected in liver cirrhosis patients. These results suggest that the developed HuMiChip2 is a useful microbial ecological microarray for both strain-level identification and functional profiling of human microbiomes.
摘要：
This paper estimates carbon emissions from agricultural production in China's Hunan Province during the period from 1998 to 2012. It also analyzes trends in the development of agricultural carbon emissions and the decoupling relationship between carbon emissions and the agricultural output of Hunan. In this study, emissions from two key segments of the agricultural sector were quantified: (1) crop production and (2) livestock and poultry production (singular). A combined method of principal component analysis (PCA), multiple regression analysis, and decoupling analysis was employed to assess the drivers of agricultural carbon emissions. This showed that there was a weak and unstable decoupling relationship between agricultural carbon emissions and their output value during the period of study. The PCA revealed that two main factors-urbanization rate and nitrogen fertilization per acre-explained 92.51 % of the variation in the 11 factors that affected carbon emissions from crops. Also, two main factors (i.e., agriculture per capita GDP and the ratio of beef production to total livestock production) explained 86.27 % of the variation in nine factors that affected carbon emissions from the livestock and poultry industry. Using the PCA scores as independent variables, a multiple regression analysis of carbon emissions from the crop industry and the livestock and poultry industry showed the following patterns. (1) Theoretically, given a 10 % reduction in nitrogen fertilization per acre, crop carbon emissions would decrease by 519 units. If the rate of urbanization were to increase by 1 %, crop carbon emissions would increase by 83 units; (2) similarly, a 1 % reduction in the beef: total livestock and poultry production ratio would reduce carbon emissions from that industry by 329 units, and with "agricultural per capita GDP'' growth of 1 unit, those emissions would increase by 0.354 units. The results of this study contribute to evaluating the sustainability of agricultural production in the region, and they provide a foundation of knowledge for future development of related agricultural mitigation policy and low-carbon agricultural technology.
