为了解生态基因组学的发展历程和研究热点,利用VOSviewer与CiteSpace可视化分析工具对2000-2019年Web of Science核心合集数据库生态基因组学研究领域的文献进行分析。结果表明,(1)生态基因组学研究的发文量呈现快速增长的趋势;(2)美国...为了解生态基因组学的发展历程和研究热点,利用VOSviewer与CiteSpace可视化分析工具对2000-2019年Web of Science核心合集数据库生态基因组学研究领域的文献进行分析。结果表明,(1)生态基因组学研究的发文量呈现快速增长的趋势;(2)美国、加拿大、德国、中国等国家的发文量较高,国家之间的合作较密切;(3)该领域的高产研究机构为加拿大英属哥伦比亚大学、加州大学戴维斯分校、中国科学院等;(4)该领域的高产作者有bernatchez,louis,nosil,patrik,feder,jeffrey;(5)“物种适应与进化”“物种间相互作用”“基因组学方法在生态学领域的应用”以及“差异基因的表达研究”是该研究领域的热点方向;(6)生态基因组学研究经历了“模式生物适应进化和变异”“进化和生态功能基因组学”“新一代基因测序技术”这些发展过程,未来会关注“物种形成过程中的基因组差异”“基因组学工具”等方面。展开更多
Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecula...Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecular ecology,quantitative genetics and genomics. Therefore,it is extremely necessary to select several versatile,low-cost,efficient and time-and labor-saving methods to develop a large panel of microsatellite markers. In this study,we used Zhikong scallop(Chlamys farreri) as the target species to compare the efficiency of the five methods derived from three strategies for microsatellite marker development. The results showed that the strategy of constructing small insert genomic DNA library resulted in poor efficiency,while the microsatellite-enriched strategy highly improved the isolation efficiency. Although the mining public database strategy is time-and cost-saving,it is difficult to obtain a large number of microsatellite markers,mainly due to the limited sequence data of non-model species deposited in public databases. Based on the results in this study,we recommend two methods,microsatellite-enriched library construction method and FIASCO-colony hybridization method,for large-scale microsatellite marker development. Both methods were derived from the microsatellite-enriched strategy. The experimental results obtained from Zhikong scallop also provide the reference for microsatellite marker development in other species with large genomes.展开更多
The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870s, an enormous number...The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870s, an enormous number of planktonic organisms have been described and studied. Plankton investigation has become one of the most important areas of aquatic ecological study, as well as a crucial component of aquatic environmental evaluation. Nonetheless, traditional investigations have mainly focused on morphospecies composition, abundances and dynamics, which primarily depend on morphological identification and counting under microscopes. However, for many species/groups, with few readily observable characteristics, morphological identification and counting have historically been a difficult task. Over the past decades, microbiologists have endeavored to apply and extend molecular techniques to address questions in microbial ecology. These culture-independent studies have generated new insights into microbial ecology. One such strategy, metagenome-based analysis, has also proved to be a powerful tool for plankton research. This mini-review presents a brief history of plankton research using morphological and metagenome-based approaches and the potential applications and further directions of metagenomic analyses in plankton ecological studies are discussed. The use of metagenome-based approaches for plankton ecological study in aquatic ecosystems is encouraged.展开更多
文摘为了解生态基因组学的发展历程和研究热点,利用VOSviewer与CiteSpace可视化分析工具对2000-2019年Web of Science核心合集数据库生态基因组学研究领域的文献进行分析。结果表明,(1)生态基因组学研究的发文量呈现快速增长的趋势;(2)美国、加拿大、德国、中国等国家的发文量较高,国家之间的合作较密切;(3)该领域的高产研究机构为加拿大英属哥伦比亚大学、加州大学戴维斯分校、中国科学院等;(4)该领域的高产作者有bernatchez,louis,nosil,patrik,feder,jeffrey;(5)“物种适应与进化”“物种间相互作用”“基因组学方法在生态学领域的应用”以及“差异基因的表达研究”是该研究领域的热点方向;(6)生态基因组学研究经历了“模式生物适应进化和变异”“进化和生态功能基因组学”“新一代基因测序技术”这些发展过程,未来会关注“物种形成过程中的基因组差异”“基因组学工具”等方面。
基金supported by ‘863’ Program (2006AA10A408 and 2006AA10A411), NSFC30571417, NYHYZX07-047, 2005DKA30470, 2006BAD09A10 and NCET-06-0594.
文摘Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecular ecology,quantitative genetics and genomics. Therefore,it is extremely necessary to select several versatile,low-cost,efficient and time-and labor-saving methods to develop a large panel of microsatellite markers. In this study,we used Zhikong scallop(Chlamys farreri) as the target species to compare the efficiency of the five methods derived from three strategies for microsatellite marker development. The results showed that the strategy of constructing small insert genomic DNA library resulted in poor efficiency,while the microsatellite-enriched strategy highly improved the isolation efficiency. Although the mining public database strategy is time-and cost-saving,it is difficult to obtain a large number of microsatellite markers,mainly due to the limited sequence data of non-model species deposited in public databases. Based on the results in this study,we recommend two methods,microsatellite-enriched library construction method and FIASCO-colony hybridization method,for large-scale microsatellite marker development. Both methods were derived from the microsatellite-enriched strategy. The experimental results obtained from Zhikong scallop also provide the reference for microsatellite marker development in other species with large genomes.
基金supported by the National Natural Science Foundation of China (Grant No. 30770298)
文摘The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870s, an enormous number of planktonic organisms have been described and studied. Plankton investigation has become one of the most important areas of aquatic ecological study, as well as a crucial component of aquatic environmental evaluation. Nonetheless, traditional investigations have mainly focused on morphospecies composition, abundances and dynamics, which primarily depend on morphological identification and counting under microscopes. However, for many species/groups, with few readily observable characteristics, morphological identification and counting have historically been a difficult task. Over the past decades, microbiologists have endeavored to apply and extend molecular techniques to address questions in microbial ecology. These culture-independent studies have generated new insights into microbial ecology. One such strategy, metagenome-based analysis, has also proved to be a powerful tool for plankton research. This mini-review presents a brief history of plankton research using morphological and metagenome-based approaches and the potential applications and further directions of metagenomic analyses in plankton ecological studies are discussed. The use of metagenome-based approaches for plankton ecological study in aquatic ecosystems is encouraged.
