Browsing by Author "Xu, Lei"

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    Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies
    Sugawara, Masayuki; Epstein, Brendan; Badgley, Brian D.; Unno, Tatsuya; Xu, Lei; Reese, Jennifer; Gyaneshwar, Prasad; Denny, Roxanne; Mudge, Joann; Bharti, Arvind K.; Farmer, Andrew D.; May, Gregory D.; Woodward, Jimmy E.; Médigue, Claudine; Vallenet, David; Lajus, Aurélie; Rouy, Zoé; Martinez-Vaz, Betsy; Tiffin, Peter; Young, Nevin D.; Sadowsky, Michael J. (2013-02-20)
    Background The sinorhizobia are amongst the most well studied members of nitrogen-fixing root nodule bacteria and contribute substantial amounts of fixed nitrogen to the biosphere. While the alfalfa symbiont Sinorhizobium meliloti RM 1021 was one of the first rhizobial strains to be completely sequenced, little information is available about the genomes of this large and diverse species group. Results Here we report the draft assembly and annotation of 48 strains of Sinorhizobium comprising five genospecies. While S. meliloti and S. medicae are taxonomically related, they displayed different nodulation patterns on diverse Medicago host plants, and have differences in gene content, including those involved in conjugation and organic sulfur utilization. Genes involved in Nod factor and polysaccharide biosynthesis, denitrification and type III, IV, and VI secretion systems also vary within and between species. Symbiotic phenotyping and mutational analyses indicated that some type IV secretion genes are symbiosis-related and involved in nitrogen fixation efficiency. Moreover, there is a correlation between the presence of type IV secretion systems, heme biosynthesis and microaerobic denitrification genes, and symbiotic efficiency. Conclusions Our results suggest that each Sinorhizobium strain uses a slightly different strategy to obtain maximum compatibility with a host plant. This large genome data set provides useful information to better understand the functional features of five Sinorhizobium species, especially compatibility in legume-Sinorhizobium interactions. The diversity of genes present in the accessory genomes of members of this genus indicates that each bacterium has adopted slightly different strategies to interact with diverse plant genera and soil environments.
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    Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass
    Huang, Linkai; Feng, Guangyan; Yan, Haidong; Zhang, Zhongren; Bushman, Bradley Shaun; Wang, Jianping; Bombarely, Aureliano; Li, Mingzhou; Yang, Zhongfu; Nie, Gang; Xie, Wengang; Xu, Lei; Chen, Peilin; Zhao, Xinxin; Jiang, Wenkai; Zhang, Xinquan (2020-02)
    Orchardgrass (Dactylis glomerata L.) is an important forage grass for cultivating livestock worldwide. Here, we report an similar to 1.84-Gb chromosome-scale diploid genome assembly of orchardgrass, with a contig N50 of 0.93 Mb, a scaffold N50 of 6.08 Mb and a super-scaffold N50 of 252.52 Mb, which is the first chromosome-scale assembled genome of a cool-season forage grass. The genome includes 40 088 protein-coding genes, and 69% of the assembled sequences are transposable elements, with long terminal repeats (LTRs) being the most abundant. The LTRretrotransposons may have been activated and expanded in the grass genome in response to environmental changes during the Pleistocene between 0 and 1 million years ago. Phylogenetic analysis reveals that orchardgrass diverged after rice but before three Triticeae species, and evolutionarily conserved chromosomes were detected by analysing ancient chromosome rearrangements in these grass species. We also resequenced the whole genome of 76 orchardgrass accessions and found that germplasm from Northern Europe and East Asia clustered together, likely due to the exchange of plants along the 'Silk Road' or other ancient trade routes connecting the East and West. Last, a combined transcriptome, quantitative genetic and bulk segregant analysis provided insights into the genetic network regulating flowering time in orchardgrass and revealed four main candidate genes controlling this trait. This chromosome-scale genome and the online database of orchardgrass developed here will facilitate the discovery of genes controlling agronomically important traits, stimulate genetic improvement of and functional genetic research on orchardgrass and provide comparative genetic resources for other forage grasses.
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    Integration of small RNAs and transcriptome sequencing uncovers a complex regulatory network during vernalization and heading stages of orchardgrass (Dactylis glomerata L.)
    Feng, Guangyan; Xu, Lei; Wang, Jianping; Nie, Gang; Bushman, Bradley Shaun; Xie, Wengang; Yan, Haidong; Yang, Zhongfu; Guan, Hao; Huang, Linkai; Zhang, Xinquan (2018-10-03)
    Background Flowering is a critical reproductive process in higher plants. Timing of optimal flowering depends upon the coordination among seasonal environmental cues. For cool season grasses, such as Dactylis glomerata, vernalization induced by low temperature provides competence to initiate flowering after prolonged cold. We combined analyses of the transcriptome and microRNAs (miRNAs) to generate a comprehensive resource for regulatory miRNAs and their target circuits during vernalization and heading stages. Results A total of 3,846 differentially expressed genes (DEGs) and 69 differentially expressed miRNAs were identified across five flowering stages. The expression of miR395, miR530, miR167, miR396, miR528, novel_42, novel_72, novel_107, and novel_123 demonstrated significant variations during vernalization. These miRNA targeted genes were involved in phytohormones, transmembrane transport, and plant morphogenesis in response to vernalization. The expression patterns of DEGs related to plant hormones, stress responses, energy metabolism, and signal transduction changed significantly in the transition from vegetative to reproductive phases. Conclusions Five hub genes, c136110_g1 (BRI1), c131375_g1 (BZR1), c133350_g1 (VRN1), c139830_g1 (VIN3), and c125792_g2 (FT), might play central roles in vernalization response. Our comprehensive analyses have provided a useful platform for investigating consecutive transcriptional and post-transcriptional regulation of critical phases in D. glomerata and provided insights into the genetic engineering of flowering-control in cereal crops.
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    Los estudios hispánicos como puente: coordinación y análisis de la calidad de actividades didácticas colectivas de difusión de la narrativa oral China
    Giménez Doblas, Nicolás (Virginia Tech, 2021-09-29)
    A la fragmentación de la comunidad de la enseñanza y el aprendizaje de español se suma la ausencia de una metodología científica que analice la calidad de las actividades educativas y culturales que se realizan en este ámbito académico. De esta forma no se valora su margen de mejora, su impacto ni su pertinencia reales. Propongo en esta investigación un modelo de planificación, ejecución y evaluación cualitativa y cuantitativa que permita conocer el grado de excelencia en la gestión y la satisfacción de sus participantes y destinatarios. El ámbito en el que se ha llevado a cabo esta propuesta ha sido la Enseñanza Superior de la República Popular China, donde he trabajado siete años. Entre 2017 y 2020 he cofundado con mis alumnos y coordinado la iniciativa colectiva Puente con el objetivo de demostrar que los estudios hispánicos tienen el potencial de reducir el desconocimiento cultural y la falta de comunicación e integración de la comunidad educativa, y plantear una serie de objetivos en común. Las redes sociales, la difusión de la narrativa oral china y una actitud comunicativa han servido como elementos unificadores para la celebración de cinco actividades a nivel nacional con un fin didáctico, académico y divulgativo. La meta propuesta supone una innovación y un complemento a la enseñanza reglada en el análisis del complejo contexto previo local más allá del aula. Tanto la metodología utilizada como los resultados obtenidos pueden resultar de utilidad para futuros estudios vinculados con la organización de eventos de enseñanza y aprendizaje no solo de español, sino también de otras lenguas y en otros entornos educativos. Y, en especial, tienen el potencial de promover el acercamiento y el entendimiento ante el creciente clima de tensión internacional.