基于高通量测序的象山港海域黑鲷(Acanthopagrus schlegelii)食性分析

选取象山港黑鲷个体为研究对象,以18S rDNA为靶标,利用Illumina Miseq高通量测序方法研究黑鲷饵料生物组成特征,分析不同龄组黑鲷的食性异同。通过序列比对,共在黑鲷胃含物中鉴定出41个属中的62种饵料生物,分属9个门,其中节肢动物门（Arthropoda）、绿藻门（Chlorophyta）和软体动物门（Mollusca）是黑鲷饵料生物的优势组成门类。从饵料生物相对丰度和出现频率上分析,石莼（Ulva lactuca）、熊本牡蛎（Crassostrea sikamea）、胸刺水蚤（Centropages hamatus）、日本蟳（Charybdis japonica）、毛蚶（Scapharca subcrenata）和褐菖鲉（Sebastiscus marmoratus）是黑鲷的优势饵料物种,所占饵料生物总相对丰度的比重达60.90%。相似性分析检验（ANOSIM）结果显示：1至4龄黑鲷个体的饵料生物组成不存在显著性差异。与传统食性分析方法相比,高通量测序法在黑鲷饵料生物检测灵敏性上显现了较为明显的优势,保障黑鲷等重要物种的种群稳定对于该海域具有重要的生态和经济意义。     

基于高通量测序的不同虫态洋虫内共生微生物群落分析

【目的】为分析不同虫态下洋虫内共生微生物菌群组成情况,以成虫和幼虫两种虫态为研究对象。【方法】通过对洋虫内共生微生物提取及高通量测序分析,获得不同样品中微生物组成结构及变化情况。【结果】不同虫态下,随着生长发育的进行,洋虫体内细菌在丰度和多样性两个方面都有很大变化,成虫中的菌群数量相对较少,多样性较幼虫也明显降低。在几种特定微生物组成上不同虫态也存在着较大的差异,成虫中,漫游球菌属和乳酸菌菌属为优势菌属;幼虫体内乳酸菌菌属为优势菌属。真菌变化不明显,孢囊线黑粉酵母菌属为其优势菌属。【结论】研究结果将为后继洋虫生物资源的研究提供相关信息,为洋虫内共生微生物资源开发与利用提供理论依据。     

高通量测序技术在野生动物食性分析中的应用

食性研究是动物生态学颇受关注的一个重要内容,而食性分析方法由于受到技术和适用范围的限制,也在不断改进和更新。随着高通量测序技术的发展,该技术逐渐扩展到野生动物的食性分析,使食性分析的效率得到极大提升,并拓宽了食性分析的应用范围。尽管高通量测序应用于食性分析在数据量、灵敏度和分辨率方面的优势较为明显,但由于涉及到的步骤较多,受到的影响因素较为复杂,目前高通量测序应用于食性分析还属于研究比较薄弱的领域。概述了高通量测序技术应用于食性分析的基本流程,总结了该技术在食物组成分析、种内和种间食性关系、食物与栖息地、行为关系方面的研究动态,分析了PCR、污染和定量分析对该技术应用性的影响,提出了相应的解决对策和建议,并对其应用前景进行了展望。     

长江口强壮箭虫和肥胖箭虫的丰度变化对环境变暖的响应

根据1959年和2002年在长江口28°00′～32°00′N,122°00′～123°30′E海域4个季节8个航次海洋调查资料,分析强壮箭虫(Sagitta crassa)和肥胖箭虫(Sagitta enflata)丰度的平面分布和季节变化特征,并结合同步的温度资料分析不同生态类群的强壮箭虫和肥胖箭虫对环境变暖的响应.结果表明:长江口水域春、夏、秋3季强壮箭虫平均丰度均小于1.00 ind/m3,出现率低,无集群性.1959年冬季平均丰度达3.24 ind/m3,出现率较高,有明显的集群性,而2002年冬季平均丰度锐减为0.001 ind/m3,几无分布.肥胖箭虫夏季平均丰度、出现率和集聚强度明显高于其它季节.2002年夏季平均丰度达16.06 ind/m3,较1959年增加3.71 ind/m3,且分布区明显扩大.可见,暖温种强壮箭虫和暖水种肥胖箭虫对长江口海域变暖的响应不同,可作为长江口海洋变暖长期变化的重要指示种.     

鲩肠袋虫18S rDNA的扩增、测序与分析

研究测定了寄生于草鱼肠道的鲩肠袋虫的18S rDNA序列。鲩肠袋虫的18S rDNA基因序列包括1638个碱基。分别用3种分析方法(邻接法、最大简约法、贝叶斯法)构建了毛口亚纲的系统发育树,得到结果如下:均支持毛口亚纲为单系发生且内分前庭目、内毛目和澳大利亚枝3个类群(100%Bay、100%MP、100%NJ);均支持内毛目(100%Bay、98%MP、93%NJ)、澳大利亚枝(100%Bay、97%MP、99%NJ)的单系性和前庭目的并系性。3种构树方法都支持鲩肠袋虫与澳大利亚枝聚类(100%Bay、100%MP、100%NJ),而后与"内毛目+前庭目(部分)"构成姊妹群(100%Bay、85%MP、72%NJ);而结肠小袋纤毛虫与"澳大利亚枝+鲩肠袋虫"以及"内毛目+前庭目(部分)"分枝并列,共同构成毛口亚纲(100%Bay、100%MP、100%NJ)。这暗示了肠袋虫类群在系统发育上的并系性和其分类阶元的提升。     

基于Solexa高通量测序的唐古特红景天(Rhodiola algida)微卫星信息分析

利用所获得的Solexa高通量唐古特红景天转录组拼接EST序列进行微卫星位点的挖掘分析,期望为红景天属SSR标记的开发提供生物信息学依据。在得到的6552条EST序列中,三碱基最多,占总EST序列的41.50%;单核苷酸和二核苷酸重复类型的SSR含量相似,分别为27.76%和24.76%;二至六碱基微卫星分布密度与其对应的SSR含量成正比。在单核苷酸重复类型中,T和A重复类型最多,分别为总SSR的14.91%、12.70%,而G和C重复类型则很少;在二核苷酸重复类型中,AG重复类型最多,占总SSR的5.60%,GA和TC重复类型次之,分别为4.75%、4.72%;在三核苷酸重复类型中,GAA重复类型最多,为总SSR的1.85%,GAT次之,为1.79%,TTC、TCT、TCA、GGA、GCT、GAG重复类型间的SSR数相差不大;四、五、六核苷酸重复类型则很少。除五、六核苷酸重复类型外,其长度变化与其对应的重复类型碱基长度成反比;同种重复类型中,微卫星的长度与其对应的SSR数成反比。     

基于高通量测序的RNA修饰检测技术

转录后修饰广泛存在于各种RNA分子中,对RNA发挥功能至关重要.目前,RNA上的化学修饰已达到160余种(https://iimeb.genesilico.pl/modomies/),其中甲基化修饰是最常见的修饰类型.薄层层析、高效液相色谱及质谱等传统的检测方法对RNA修饰的鉴定和定量做出了重要贡献.然而,RNA修饰的...     

环境样本中微型和微微型浮游植物高通量测序的引物优化

分别以18Sr DNA的V4区和V9区为目标基因,采用高通量测序平台和生物信息学方法,分析海水样品中微型和微微型浮游植物多样性。利用在线分析软件对V4(F/R)、V9(F/R)和C4(F/R)3对引物的敏感性、特异性进行了评估和比较,发现自行设计的引物V4(F/R)对真核藻类的扩增特异性高于V9(F/R)和C4(F/R)。高通量测序结果显示,检测样品平均获得68834条原始序列,高质量数据占99%以上,获得基因注释的序列数达94%以上。3对引物V4(F/R)、V9(F/R)、C4(F/R)鉴定的平均微型/微微型浮游植物OTUs数分别为78、42、58,引物V4(F/R)鉴定效率相对较高,同时对细小微胞藻(Micromonas pusilla)、(金牛微球藻Ostreococcus tauri)、密球藻(Pycnococcus provasolii)、抑食金球藻(Aureococcus anophagefferens)、赤潮异弯藻(Heterosigma akashiwo)等优势种检出频率高于引物V9(F/R)。相对已发表的2对引物,设计的引物V4(F/R)对海洋微型和微微型藻类多样性检测更为高效。     

尼氏单极虫(粘体门,双壳目)重描述及基于18S rDNA系统地位分析

采用常规细胞学方法与18S rDNA序列比较的方法,对采自于重庆市嘉陵江段的粘孢子虫,尼氏单极虫Thelohanellus nikolskii进行了形态学和分子生物学的研究,此为首次在我国长江流域检获尼氏单极虫。本文在补充了尼氏单极虫中国种群18S rDNA序列信息的分析、比较基础上,探讨了该虫与相邻种属的系统关系,佐证了其分类学位置。     

武汉单极虫(粘体门,双壳目)的重描述及基于18S rDNA序列系统发育分析

通过光镜、扫描电镜和18S rDNA序列对比,对寄生于异育银鲫Carassius auratus gibelio体表的粘孢子虫进行了形态学和分子生物学研究,鉴定其为武汉单极虫Thelohanellus wuhanensis,并发现了形态学新特征:膜状鞘的起始位置不同,且仅包围孢子后部;壳瓣底部内侧具“V”形褶皱;一片壳瓣前端有突起结构;缝脊直,突出明显;测得极丝全长为158.5 ～179.2 (170.7 ±5.7) μm.经18S rDNA序列对比,与T.wuhanensis[HQ613410]的相似率为99.87％.系统发育分析表明,单极虫与碘泡虫具有非常近的亲缘关系,将单极虫属与碘泡虫属二者归属于碘泡科的分类方法更合理.     

Dynamic analysis of phytoplankton community characteristics in Daya Bay, China

Daya Bay is a large bay along the southern coast of China. The composition, abundance, community structure and diversity of phytoplankton in Daya Bay were investigated to assess its status in different seasons in 2002, and a total of 48 genera and 114 species of phytoplankton were identified. The cell abundance of phytoplankton varied from 5.79 × 10⁴ cells/m³ to 5.37 × 10⁶ cells/m³ with an average of 1.14×10⁶ cells/m³. The largest community was Bacillariophyta containing 84 taxa, and its average abundance was 1.08 × 10⁶ cells/m³. Annual abundance variations show a typical one-peak cycle, with the highest peak recorded during summer and the lowest recorded during autumn. The ecotypes of phytoplankton were mostly alongshore warm-water species; however, marine warm-water species and eurytopic species during winter and autumn are more abundant than during the other seasons. The dominant species were diverse and varied with seasons. The species diversity index of phytoplankton in Daya Bay was low during summer, especially near the nuclear power station (NPS) and the aquaculture farms during summer and autumn. Community structure and cell abundance were categorized in relation to monsoon, current and anthropological activities. It is presented that the temperature and hydrodynamics in conjunction with the pattern of nutrients (DIN, DIP and N/P) availability and depletion affect the composition, abundance, community structure, community succession and diversity of phytoplankton.     

Dynamic analysis of phytoplankton community characteristics in Daya Bay, China

Daya Bay is a large bay along the southern coast of China. The composition, abundance, community structure and diversity of phytoplankton in Daya Bay were investigated to assess its status in different seasons in 2002, and a total of 48 genera and 114 species of phytoplankton were identified. The cell abundance of phytoplankton varied from 5.79 × 10⁴ cells/m³ to 5.37 × 10⁶ cells/m³ with an average of 1.14×10⁶ cells/m³. The largest community was Bacillariophyta containing 84 taxa, and its average abundance was 1.08 × 10⁶ cells/m³. Annual abundance variations show a typical one-peak cycle, with the highest peak recorded during summer and the lowest recorded during autumn. The ecotypes of phytoplankton were mostly alongshore warm-water species; however, marine warm-water species and eurytopic species during winter and autumn are more abundant than during the other seasons. The dominant species were diverse and varied with seasons. The species diversity index of phytoplankton in Daya Bay was low during summer, especially near the nuclear power station (NPS) and the aquaculture farms during summer and autumn. Community structure and cell abundance were categorized in relation to monsoon, current and anthropological activities. It is presented that the temperature and hydrodynamics in conjunction with the pattern of nutrients (DIN, DIP and N/P) availability and depletion affect the composition, abundance, community structure, community succession and diversity of phytoplankton.     

基于高通量测序的慈竹笋转录组分析与基因功能注释

慈竹是我国四川当地的优势丛生竹种之一,其纤维长度和质量较优异,是造纸、纺织等工业的良好原料。本文利用Illumina Hi SeqTM 2000平台,对10、50、100和150 cm高的慈竹笋进行转录组分析,共得到69.28 M条读长(Reads),经从头拼接、组装和聚类后得到111 137条非重复序列基因Unigene,其中共有63 094条注释到COG、GO、KEGG、Swiss-Prot和Nr数据库中。这些Unigene不仅具有一般的功能,如转录和信号转导等,还涉及到蔗糖转运与代谢、次级代谢产物及细胞壁的生物合成等方面。不同高度慈竹笋的纤维素合成酶基因存在差异表达,发现了可能调控慈竹生长发育以及纤维素和木质素生物合成的相关基因,为慈竹品种改良提供一定的理论基础。     

大亚湾大型底栖动物的群落结构

利用2004年3月、5月、9月和12月的大型底栖动物定量采样数据,对大亚湾大型底栖动物的群落结构进行研究.结果表明,大亚湾大型底栖动物大致可分为3个群落,分别分布于湾顶及湾中大部分海域、湾中部和湾口海域,湾中部海域群落的变化较为显著.大型底栖动物整体群落结构的季节变化总体较小,但雨季对大型底栖动物群落的影响较大,存在较明显的干湿季差异.大亚湾海域生态环境受到明显的扰动,处于扰动状态中的大型底栖动物群落稳定性较差;湾顶和湾中大部分海域内的群落Ⅰ,为大亚湾的主体群落,以软体动物为主,种类组成单一、季节变化小,以小鳞帘蛤Veremolpa micra和粗帝汶蛤Timoclea scabra 为特征种.该群落的稳定性最差,处于较强烈的扰动之中;稳定分布于湾口的群落Ⅲ稳定性最好,未受到扰动,以多毛类为主,种类组成较为复杂、变化较大;湾中部海域大型底栖动物群落结构变化较为复杂,主要变化区域为马鞭州附近海域.该群落系经强烈的人为扰动后,经次生演替而形成的新群落,其种类组成的季节变化非常显著,各季的种类几乎完全不同,群落的独立性和抗干扰能力均较弱;与1980's相比,大亚湾大部分区域内大型底栖动物基本保持了原有的群落,但群落稳定性大幅下降,群落的分布范围和种类组成发生较大程度的改变,主体群落组成呈明显的简单化趋势.在人类活动影响下,湾内同一区域内群落完全演替、湾中部海域出现新的群落.     

Composition and distribution of ciliates inner and outer of Daya Bay, China

Daya Bay was undergoing eutrophication process by increased nutrient loading, and the changes in nutrients have strongly influenced the phytoplankton community structure. Ciliates are common component of planktonic community, what role do ciliates play in Daya Bay was still unknown. In this study, ciliates were enumerated and identified from the inner and outer Daya Bay during three seasons. Thirty-one species belong to 16 genera of ciliates were recorded, and Cyclotrichida, Strombidiida, Tintinnida were most common. In spring, ciliates abundance of D2 was lower than D1 and D3, abundance in the surface of D1 and D3 were higher than in the bottom, while D2 showed the opposite character. The lowest ciliate abundance was found in the E1 in summer. In fall, Ciliates abundance of D3 was lower than in fall, and abundance in the surface was lower than in the bottom, which was different compared to in spring. Different hydrographic character was shown between the surface (high temperature, low salinity and nutrients) and bottom layer (low temperature, high salinity and nutrients) at E1 in summer. Ciliate abundance had no significant variation between the surface and bottom at E1 in summer, but ciliates community structure changed a lot.     

遥感技术在大亚湾区域土地利用类型监测中的应用

文章综合利用了Landsat系列卫星不同传感器(MSS、TM、ETM )的遥感资料对1979至2004年20多年间的大亚湾周边的植被陆地、非植被陆地以及水域等土地利用类型的相关变化进行了定量监测与评估。遥感监测结果表明,在过去的二十多年间,大亚湾周边植被覆盖总体保持相对稳定,但非植被陆地由1991年的5.1%左右上升到2004年的10.5%左右,水体面积也相应降低了5%左右,表现出“人进水退”的总体变化格局,该变化特征与该区域过去的环境政策、经济活动发展历程有关。通过将人类对区域环境影响的方式、力度和土地利用类型的变化建立一种对应关系,可以预测以后的开发建设活动对土地利用类型的影响,并应用到区域环境影响评价中去。     

Composition and distribution of ciliates inner and outer of Daya Bay, China

Daya Bay was undergoing eutrophication process by increased nutrient loading, and the changes in nutrients have strongly influenced the phytoplankton community structure. Ciliates are common component of planktonic community, what role do ciliates play in Daya Bay was still unknown. In this study, ciliates were enumerated and identified from the inner and outer Daya Bay during three seasons. Thirty-one species belong to 16 genera of ciliates were recorded, and Cyclotrichida, Strombidiida, Tintinnida were most common. In spring, ciliates abundance of D2 was lower than D1 and D3, abundance in the surface of D1 and D3 were higher than in the bottom, while D2 showed the opposite character. The lowest ciliate abundance was found in the E1 in summer. In fall, Ciliates abundance of D3 was lower than in fall, and abundance in the surface was lower than in the bottom, which was different compared to in spring. Different hydrographic character was shown between the surface (high temperature, low salinity and nutrients) and bottom layer (low temperature, high salinity and nutrients) at E1 in summer. Ciliate abundance had no significant variation between the surface and bottom at E1 in summer, but ciliates community structure changed a lot.     

大亚湾人工鱼礁海域浮游植物的群落特征

近年来,随着大亚湾沿岸城镇社会经济的快速发展和人类活动的增加,大亚湾海域生态环境日益恶化。人工鱼礁是修复、改善和优化海洋生态环境,保护和增殖渔业资源最有效的措施之一。根据投礁前、后大亚湾大辣甲南人工鱼礁海域浮游植物垂直拖网调查结果,初步分析了大亚湾人工鱼礁区浮游植物的群落特征。结果表明:投礁后,浮游植物的平均丰度呈逐年递增趋势,礁区内的平均丰度明显高于同期对照海区;浮游植物的多样性指数和均匀度都比投礁前有了明显增加。上述结果表明,投放人工鱼礁有助于改善海域生态环境和提高水域的初级生产力水平。     

Commercial high-throughput sequencing and its applications in DNA analysis

DNA sequences can be used for the analysis of genetic variation and gene function. The high-throughput sequencing techniques that have been developed over the past three years can read as many as one billion bases per run, and are far less expensive than the traditional Sanger sequencing method. Therefore, the high-throughput sequencing has been applied extensively to genomic analyses, such as screening for mutations, construction of genomic methylation maps, and the study of DNA-protein interactions. Although they have only been available for a short period, high-throughput sequencing techniques are profoundly affecting many of the life sciences, and are opening out new potential avenues of research. With the highly-developed commercial high-throughput sequencing platforms, each laboratory has the opportunity to explore this research field. Therefore, in this paper, we have focused on commercially-popular high-throughput sequencing techniques and the ways in which they have been applied over the past three years.