系统发育多样性和系统发育结构在岛屿植物群落保护中的意义：以福建沿海19个岛屿为例

为了探讨福建沿海岛屿植物多样性的形成与维持机制,本研究在福建近岸有居民岛屿前期调查资料的基础上,补充部分无居民岛屿植物多样性及环境和人口密度调查数据,从物种多样性和系统发育多样性两方面比较了19个岛屿植物多样性及其影响因素。结果表明,岛屿面积是影响植物物种丰富度(species richness, SR)和Faith系统发育多样性(phylogenetic diversity, PD)最重要的因素,纬度和年均降水量也有一定影响。19个岛屿系统发育结构倾向于聚集,植物群落的构建可能主要受到环境因素和人类活动干扰影响。地理距离对岛屿间植物群落系统发育β多样性的变化影响不显著。建议对PD较高的东山岛、粗芦岛、南日岛、湄洲岛、厦门岛、平潭岛、三都岛进行重点保护,并结合实际情况针对各岛屿功能定位制定保护和开发利用方案。本研究可以为多层次的多样性评价指标应用于岛屿植物多样性评估以及群落构建机制分析提供参考,也可以为岛屿生物多样性保护策略的制定提供理论依据。     

Endogenous viral elements in algal genomes

Endogenous viral elements （EVEs） are host-genomic fragments originated from viral genomes. They have been found universally in animal and plant genomes. Here we carried out a systematic screening and analy-sis of EVEs in algal genomes and found that EVEs commonly exist in algal genomes. We classified the EVE fragments into three categories according to the length of EVE fragments. Due to the probability of sequence similarity by chance, we ignored the potential function of medium-length EVE fragments. However, long-length EVE fragments probably had capability to encode protein domains or even entire proteins, and some short-length EVE fragments had high similarity with host＇s siRNA sequences and possibly served functions of small RNAs. Therefore, short and long EVE fragments might provide regulomic and proteomic novelty to the host＇s metabolism and adaptation. We also found several EVE fragments shared by more than 3 algal genomes. By phylogenetic analysis of the shared EVEs and their corresponding species, we found that the integration of viral fragments into host genomes was an ancient event, possibly before the divergence of Chlorophytes and Ochrophytes. Our findings show that there is a frequent genetic flow from viruses to algal genomes. Moreover, study on algal EVEs shed light on the virus-host interaction in large timescale and could also help us understand the balance of marine ecosystems.     

Phylogenomic analysis of transcriptomic sequences of mitochondria and chloroplasts of essential brown algae (Phaeophyceae) in China

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.     

16S rRNA is a better choice than COI for DNA barcoding hydrozoans in the coastal waters of China

Identification of hydrozoan species is challenging, even for taxonomic experts, due to the scarcity of distinct morphological characters and phenotypic plasticity. DNA barcoding provides an efficient method for species identification, however, the choice between mitochondrial cytochrome c oxidase subunit I（COI） and large subunit ribosomal RNA gene（16S） as a standard barcode for hydrozoans is subject to debate. Herein, we directly compared the barcode potential of COI and 16S in hydrozoans using 339 sequences from 47 pelagic hydrozoan species. Analysis of Kimura 2-parameter genetic distances（K2P） documented the mean intraspecific/interspecific variation for COI and 16S to be 0.004/0.204 and 0.003/0.223, respectively. An obvious ＂barcoding gap＂ was detected for all species in both markers and all individuals of a species clustered together in both the COI and 16S trees. These results suggested that the species within the studied taxa can be efficiently and accurately identified by COI and 16S. Furthermore, our results confirmed that 16S was a better phylogenetic marker for hydrozoans at the genus level, and in some cases at the family level. Considering the resolution and effectiveness for barcoding and phylogenetic analyses of Hydrozoa, we strongly recommend 16S as the standard barcode for hydrozoans.     

Biological identification and determination of optimum growth conditions for four species of Navicula

Four species in the genus Navicula were isolated using the serial dilution method. Based on scanning electron microscopy(SEM) and sequence comparisons of two segments of genes(small ribosomal subunit and large subunit of Rubisco), the species were identified as Navicula perminuta, N. pseudacceptata, N. vara, and N. rhynchocephala. Based on phylogenetic analysis and culture trials, there was a close relationship between N. perminuta and N. vara. Growth of these species was evaluated using measurements of optical density at 680 nm(OD680) under various environmental factors. Results showed that the optimum culture conditions were 25℃, 50–100 μmol photons m-2 s-1, pH 8.0, and salinities from 25 to 30. However, the favorable salinity for N. perminuta was surprisingly high at 35. Nutrient requirement analysis demonstrated that growth of Navicula depended on the availability of SiO32-. Their relative growth rates(RGR) peaked at the highest tested level(0.25 mmol/L). The optimal concentrations of NO3- and PO43- were 3.6 mmol/L and 0.18 mmol/L, respectively. Culture of these Navicula species for abalone or sea cucumber aquaculture should take these factors into consideration.     

中国15种海参的分子系统发育和骨片演化的分析

基于线粒体16S rRNA基因部分序列,对我国15种海参的分子系统发育进行了分析.结果表明,片段长度约为570bp,A+T的平均含量为54.7％.15种海参的遗传距离在0.041（花刺参与糙剌参）至0.327(红腹海参与花刺参)之间,不同海参种类间的遗传距离差别很大.NJ和MP聚类分析方法一致,符合传统的形态学分类结果...     

湘江长沙段污染沉积物中微生物群落结构与污染物关联性的研究

采用ICP-AES测试方法及PCA和PCR-RFLP分析技术,研究了湘江长沙段污染沉积物中微生物群落结构（主要是古细菌群落结构）与污染物的关联性。结果表明：（1）三个取样区域的不同污染物的污染程度呈现出明显的差异性;（2）所取样点的微生物群落结构主要分布在广古菌门（Euryarchaeota）和泉古菌门（Crenarc...     

中国金线鱼属鱼类分类研究进展

<正>金线鱼属(Nemipterus)隶属于硬骨鱼纲(Osteichthyes)、鲈形目(Perciformes)、金线鱼科(Nemipteridae),主要分布于印度洋和太平洋的热带、亚热带海域。金线鱼肉质鲜美、营养丰富,是我国东南沿海的重要经济鱼类,是南海北部区域最主要的渔获种类之一[1],有巨大的资源开发潜力和     

沙冬青根瘤菌结瘤基因nodA PCR-RFLP分析

 利用结瘤基因nodA PCR-RFLP和nodA PCR产物序列分析技术,对36株分离自沙冬青根瘤菌菌株的共同结瘤基因nodA进行了遗传类型和系统发育关系分析。试验结果表明,36株根瘤菌nodA PCR-RFLP分析显示在80%的相似水平上聚为两个类群5个亚群;选取不同基因型代表菌株的nodA进行序列测定和系统发育关系分析表明,测试菌株CCNWNX0117、CCNWNX0068、CCNWNX0083、CCNWNX0062、CCNWNX0058与中慢生根瘤菌聚在一起,系统发育地位相近;测试菌株CCNWNX0089、CCNWNX0081、CCNWNX0064与中华根瘤菌聚在一起,有较高的序列相似性。本研究中nodA基因所揭示的沙冬青根瘤菌遗传多样性和系统发育关系说明沙冬青根瘤菌nodA基因遗传多样性较高,宿主结瘤范围较宽。     

辽宁海城小孤山披毛犀化石的古DNA分析

从采自辽宁省海城县小孤山晚更新世披毛犀化石样品中成功地获得了1 080 bp细胞色素b基因序列,调用Genbank中已发表的披毛犀序列及5种现生犀牛的同源序列,以马作为外类群,采用邻接法(NJ法)和最大似然法(ME法)构建系统发育树,结果均显示披毛犀与现生苏门答腊犀亲缘关系最近,且辽宁省海城县小孤山样品处于披毛犀分支的根部;对披毛犀样品进行基因分异度分析结果表明,小孤山的披毛犀样品具有较高的基因分异度,为探讨披毛犀的起源、迁徙及演化等问题提供了重要的分子依据.