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1. InvasionDB: A genome and gene database of invasive alien species
HUANG Cong, LANG Kun, QIAN Wan-qiang, WANG Shu-ping, CAO Xiao-mei, HE Rui, ZHAN An-ran, CHEN Meng-yao, YANG Nian-wan, LI Fei
Journal of Integrative Agriculture    2021, 20 (1): 191-200.   DOI: 10.1016/S2095-3119(20)63231-2
摘要280)      PDF    收藏

外来入侵物种是指被引入到其原产地范围以外的地区,并对当地的经济、生物多样性和生态环境造成了严重危害的物种。明确入侵性的遗传机制对于开发生态友好型的方法来防控外来入侵物种至关重要,同时,揭示外来物种的基因组特征有利于准确预测其入侵性潜能。然而,尽管已经有大量外来入侵物种的基因组被测序,但这些数据存放零散,缺少一个综合的外来入侵物种基因组数据管理与分析平台。因此,我们通过文献调研和数据库检索,收集了已完成基因组测序的外来入侵物种的组学相关数据,构建了InvasionDB数据库。该数据库包含131个外来入侵物种(100种入侵动物和31种入侵植物)的基因组和转录组数据,其中,76个物种的基因组被详细注释,并提供基因功能(包括Pfam、KEGG和NR注释信息)查询、序列比对和基因组可视化,以及全部数据下载功能。为了提供更多与入侵性相关的信息,我们进一步分析了19个与入侵昆虫的入侵性相关的基因家族,以及非编码RNAs(包括135494 个miRNAs, 89294 个rRNAs和2671941 个tRNAs)。因此,InvasionDB对于从基因组水平来研究外来入侵物种的入侵性,以及发展新的防控技术具有重要指导意义。


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2. Bioinformatic identification and analyses of the non-specific lipid transfer proteins in wheat
FANG Zheng-wu, HE Yi-qin, LIU Yi-ke, JIANG Wen-qiang, SONG Jing-han, WANG Shu-ping, MA Dong-fang, YIN Jun-liang
Journal of Integrative Agriculture    2020, 19 (5): 1170-1185.   DOI: 10.1016/S2095-3119(19)62776-0
摘要141)      PDF    收藏
Non-specific lipid transfer proteins (nsLTPs/LTPs) that can transport various phospholipids across the membrane in vitro are widespread in the plant kingdom, and they play important roles in many biological processes that are closely related to plant growth and development.  Recently, nsLTPs have been shown to respond to different forms of abiotic stresses.  Despite the vital roles of nsLTPs in many plants, little is known about the nsLTPs in wheat.  In this study, 330 nsLTP proteins were identified in wheat and they clustered into five types (1, 2, c, d, and g) by phylogenetic analysis with the nsLTPs from maize, Arabidopsis, and rice.  The wheat nsLTPs of type d included three subtypes (d1, d2, and d3) and type g included seven subtypes (g1–g7).  Genetic structure and motif pattern analyses showed that members of each type had similar structural composition.  Moreover, GPI-anchors were found to exist in non-g type members from wheat for the first time.  Chromosome mapping revealed that all five types were unevenly and unequally distributed on 21 chromosomes.  Furthermore, gene duplication events contributed to the proliferation of the nsLTP genes.  Large-scale data mining of RNA-seq data covering multiple growth stages and numerous stress treatments showed that the transcript levels of some of the nsLTP genes could be strongly induced by abiotic stresses, including drought and salinity, indicating their potential roles in mediating the responses of the wheat plants to these abiotic stress conditions.  These findings provide comprehensive insights into the nsLTP family members in wheat, and offer candidate nsLTP genes for further studies on their roles in stress resistance and potential for improving wheat breeding programs.
 
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3. Programmed cell death, antioxidant response and oxidative stress in wheat flag leaves induced by chemical hybridization agent SQ-1
WANG Shu-ping, ZHANG Gai-sheng, SONG Qi-lu, ZHANG Ying-xin, LI Ying, GUO Jia-lin, CHEN Zheng, NIU Na, MA Shou-cai, WANG Jun-wei
Journal of Integrative Agriculture    2016, 15 (1): 76-86.   DOI: 10.1016/S2095-3119(14)60977-1
摘要2101)      PDF    收藏
Male sterility induced by a chemical hybridization agent (CHA) is an important tool for utilizing crop heterosis. Leaves, especially the flag leaves, as CHA initial recipients play a decisive role in inducing male sterility. To investigate effects of different treatment times of CHA-SQ-1 used, morphological, biochemical and physiological responses of wheat flag leaves were detected in this study. CHA induced programmed cell death (PCD) as shown in terminal deoxynucleotidyl transferase-mediated dUTP nick end-labelling (TUNEL) and DNA laddering analysis. In the early phase, CHA-SQ-1 triggered organelle changes and PCD in wheat leaves accompanied by excess production of reactive oxygen species (O2 -. and H2O2) and down-regulation of the activities of superoxide dismutase (SOD), catalase (CAT) and guaiacol peroxidase (POD). Meanwhile, leaf cell DNAs showed ladder-like patterns on agarose gel, indicating that CHA-SQ-1 led to the activation of the responsible endonuclease. The oxidative stress assays showed that lipid peroxidation was strongly activated and photosynthesis was obviously inhibited in SQ-1-induced leaves. However, CHA contents in wheat leaves gradually reduced along with the time CHA-SQ-1 applied. Young flags returned to an oxidative/antioxidative balance and ultimately developed into mature green leaves. These results provide explanation of the relations between PCD and anther abortion and practical application of CHA for hybrid breeding.
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