为了探讨DNA条形码技术在蟹蛛科蜘蛛物种鉴定中的可行性,本研究基于线粒体COI基因序列,使用邻接法和贝叶斯法构建系统发育树,ABGD(automatic barcode gap discovery)软件对样本进行划分,对小五台山25种蟹蛛110个样本进行DNA条形码分子鉴...为了探讨DNA条形码技术在蟹蛛科蜘蛛物种鉴定中的可行性,本研究基于线粒体COI基因序列,使用邻接法和贝叶斯法构建系统发育树,ABGD(automatic barcode gap discovery)软件对样本进行划分,对小五台山25种蟹蛛110个样本进行DNA条形码分子鉴定.结果表明:邻接法和贝叶斯法构建的系统发育树聚类结果与ABGD软件划分结果以及形态分类鉴定结果相一致.据此笔者认为DNA条形码作为一种有效的分子鉴定工具可以应用到蟹蛛科蜘蛛物种鉴定中.展开更多
目的了解陕西省近年来发现的男男性行为人群(Men who have sex with men,MSM)中,艾滋病病毒(Human immunodeficiency virus,HIV)流行株的基因序列特征、亚型、流行现状和趋势,为艾滋病防治工作提供科学依据。方法对HIV感染者进行流行病...目的了解陕西省近年来发现的男男性行为人群(Men who have sex with men,MSM)中,艾滋病病毒(Human immunodeficiency virus,HIV)流行株的基因序列特征、亚型、流行现状和趋势,为艾滋病防治工作提供科学依据。方法对HIV感染者进行流行病学相关因素调查,无菌采集全血,分离血浆提取病毒核酸,应用套式反转录聚合酶链式反应(Nested reverse transcription-polymerase chain reaction,Nested RT-PCR)扩增gag、env和pol基因的部分片段,并对扩增产物进行测序,用Mega 5.0软件将测序结果与各亚型国际参考株比对,根据基因离散率和系统进化树分析确定基因型及其特征。结果 71份样本中成功获得51份PCR扩增阳性产物并得到相应序列。综合gag、env和pol基因离散程度和系统进化树分析发现,陕西省MSM人群中至少存在3种HIV-1基因亚型和重组毒株(即B亚型、CRF01_AE和CRF07_BC重组型)。其中CRF01_AE为主要流行株,共28例(54.9%),其次是CRF07_BC重组型20例(39.2%)和B亚型3例(5.9%),重组型占到了94.1%(48/51)。根据基因离散率,在三种不同基因片段中,以env基因变异程度最大,HIV-1B亚型、CRF07_BC和CRF01_AE重组型的组内离散率分别为(12.8%±1.2%)、(6.6%±0.6%)和(8.4%±0.7%)。结论首次在陕西省MSM人群HIV感染者中,发现至少存在HIV-1B亚型和CRF01_AE、CRF07_BC重组型,以CRF01_AE重组型为主。该人群显示多亚型且近期呈高度流行的趋势。加强对MSM人群的行为干预,控制HIV在MSM人群中的传播,将是今后陕西省艾滋病防治工作的重点之一。展开更多
The chloroplast and mitochondrion of red algae （Phylum Rhodophyta） may have originated from different endosymbiosis. In this study, we carried out phylogenomic analysis to distinguish their evolutionary lin-eages by...The chloroplast and mitochondrion of red algae （Phylum Rhodophyta） may have originated from different endosymbiosis. In this study, we carried out phylogenomic analysis to distinguish their evolutionary lin-eages by using red algal RNA-seq datasets of the 1 000 Plants （1KP） Project and publicly available complete genomes of mitochondria and chloroplasts of Rhodophyta. We have found that red algae were divided into three clades of orders, Florideophyceae, Bangiophyceae and Cyanidiophyceae. Taxonomy resolution for Class Florideophyceae showed that Order Gigartinales was close to Order Halymeniales, while Order Graci-lariales was in a clade of Order Ceramials. We confirmed Prionitis divaricata （Family Halymeniaceae） was closely related to the clade of Order Gracilariales, rather than to genus Grateloupia of Order Halymeniales as reported before. Furthermore, we found both mitochondrial and chloroplastic genes in Rhodophyta under negative selection （Ka/Ks〈1）, suggesting that red algae, as one primitive group of eukaryotic algae, might share joint evolutionary history with these two organelles for a long time, although we identified some dif-ferences in their phylogenetic trees. Our analysis provided the basic phylogenetic relationships of red algae, and demonstrated their potential ability to study endosymbiotic events.展开更多
The chloroplast and mitochondrion of brown algae （Class Phaeophyceae of Phylum Ochrophyta） may have originated from different endosymbiosis. In this study, we carried out phylogenomic analysis to distinguish their e...The chloroplast and mitochondrion of brown algae （Class Phaeophyceae of Phylum Ochrophyta） may have originated from different endosymbiosis. In this study, we carried out phylogenomic analysis to distinguish their evolutionary lineages by using algal RNA-seq datasets of the 1 000 Plants （1KP） Project and publicly available complete genomes of mitochondria and chloroplasts of Kingdom Chromista. We have found that there is a split between Class Phaeophyceae of Phylum Ochrophyta and the others （Phylum Cryptophyta and Haptophyta） in Kingdom Chromista, and identified more diversity in chloroplast genes than mitochondrial ones in their phylogenetic trees. Taxonomy resolution for Class Phaeophyceae showed that it was divided into Laminariales-Ectocarpales clade and Fucales clade, and phylogenetic positions of Kjellmaniella crassi-folia, Hizikia fusifrome and Ishige okamurai were confirmed. Our analysis provided the basic phylogenetic relationships of Chromista algae, and demonstrated their potential ability to study endosymbiotic events.展开更多
文摘为了探讨DNA条形码技术在蟹蛛科蜘蛛物种鉴定中的可行性,本研究基于线粒体COI基因序列,使用邻接法和贝叶斯法构建系统发育树,ABGD(automatic barcode gap discovery)软件对样本进行划分,对小五台山25种蟹蛛110个样本进行DNA条形码分子鉴定.结果表明:邻接法和贝叶斯法构建的系统发育树聚类结果与ABGD软件划分结果以及形态分类鉴定结果相一致.据此笔者认为DNA条形码作为一种有效的分子鉴定工具可以应用到蟹蛛科蜘蛛物种鉴定中.
文摘目的了解陕西省近年来发现的男男性行为人群(Men who have sex with men,MSM)中,艾滋病病毒(Human immunodeficiency virus,HIV)流行株的基因序列特征、亚型、流行现状和趋势,为艾滋病防治工作提供科学依据。方法对HIV感染者进行流行病学相关因素调查,无菌采集全血,分离血浆提取病毒核酸,应用套式反转录聚合酶链式反应(Nested reverse transcription-polymerase chain reaction,Nested RT-PCR)扩增gag、env和pol基因的部分片段,并对扩增产物进行测序,用Mega 5.0软件将测序结果与各亚型国际参考株比对,根据基因离散率和系统进化树分析确定基因型及其特征。结果 71份样本中成功获得51份PCR扩增阳性产物并得到相应序列。综合gag、env和pol基因离散程度和系统进化树分析发现,陕西省MSM人群中至少存在3种HIV-1基因亚型和重组毒株(即B亚型、CRF01_AE和CRF07_BC重组型)。其中CRF01_AE为主要流行株,共28例(54.9%),其次是CRF07_BC重组型20例(39.2%)和B亚型3例(5.9%),重组型占到了94.1%(48/51)。根据基因离散率,在三种不同基因片段中,以env基因变异程度最大,HIV-1B亚型、CRF07_BC和CRF01_AE重组型的组内离散率分别为(12.8%±1.2%)、(6.6%±0.6%)和(8.4%±0.7%)。结论首次在陕西省MSM人群HIV感染者中,发现至少存在HIV-1B亚型和CRF01_AE、CRF07_BC重组型,以CRF01_AE重组型为主。该人群显示多亚型且近期呈高度流行的趋势。加强对MSM人群的行为干预,控制HIV在MSM人群中的传播,将是今后陕西省艾滋病防治工作的重点之一。
基金The National Natural Science Foundation of China under contract Nos 31140070,31271397 and 41206116the algal transcrip-tome sequencing was supported by 1KP Project(www.onekp.com)
文摘The chloroplast and mitochondrion of red algae （Phylum Rhodophyta） may have originated from different endosymbiosis. In this study, we carried out phylogenomic analysis to distinguish their evolutionary lin-eages by using red algal RNA-seq datasets of the 1 000 Plants （1KP） Project and publicly available complete genomes of mitochondria and chloroplasts of Rhodophyta. We have found that red algae were divided into three clades of orders, Florideophyceae, Bangiophyceae and Cyanidiophyceae. Taxonomy resolution for Class Florideophyceae showed that Order Gigartinales was close to Order Halymeniales, while Order Graci-lariales was in a clade of Order Ceramials. We confirmed Prionitis divaricata （Family Halymeniaceae） was closely related to the clade of Order Gracilariales, rather than to genus Grateloupia of Order Halymeniales as reported before. Furthermore, we found both mitochondrial and chloroplastic genes in Rhodophyta under negative selection （Ka/Ks〈1）, suggesting that red algae, as one primitive group of eukaryotic algae, might share joint evolutionary history with these two organelles for a long time, although we identified some dif-ferences in their phylogenetic trees. Our analysis provided the basic phylogenetic relationships of red algae, and demonstrated their potential ability to study endosymbiotic events.
基金The National Natural Science Foundation of China under contract Nos 31140070,31271397 and 41206116the algal transcrip-tome sequencing was supported by 1KP Project(www.onekp.com)
文摘The chloroplast and mitochondrion of brown algae （Class Phaeophyceae of Phylum Ochrophyta） may have originated from different endosymbiosis. In this study, we carried out phylogenomic analysis to distinguish their evolutionary lineages by using algal RNA-seq datasets of the 1 000 Plants （1KP） Project and publicly available complete genomes of mitochondria and chloroplasts of Kingdom Chromista. We have found that there is a split between Class Phaeophyceae of Phylum Ochrophyta and the others （Phylum Cryptophyta and Haptophyta） in Kingdom Chromista, and identified more diversity in chloroplast genes than mitochondrial ones in their phylogenetic trees. Taxonomy resolution for Class Phaeophyceae showed that it was divided into Laminariales-Ectocarpales clade and Fucales clade, and phylogenetic positions of Kjellmaniella crassi-folia, Hizikia fusifrome and Ishige okamurai were confirmed. Our analysis provided the basic phylogenetic relationships of Chromista algae, and demonstrated their potential ability to study endosymbiotic events.
