‘Candidatus Phytoplasma australiense’ is the phytoplasma associated with Australian grapevine yellows, papaya dieback and Phormium yellow leaf diseases

Sequence comparisons and phylogenetic analysis of the 16S rRNA genes and the 16S/23S spacer regions of the phytoplasmas associated with Australian grapevine yellows, papaya dieback and Phormium yellow leaf diseases revealed minimal nucleotide differences between them resulting in the formation of a monophyletic group. Therefore, along with Australian grapevine yellows, the phytoplasmas associated with Phormium yellow leaf and papaya dieback should also be considered as Candidatus Phytoplasma australiense.     

Tomato dwarf leaf curl virus, a new bipartite geminivirus associated with tomatoes and peppers in Jamaica and mixed infection with tomato yellow leaf curl virus

Genomic characterization using nonradioactive probes, polymerase chain reaction with degenerate primers for whitefly transmitted geminiviruses and nucleotide sequencing were used to describe a new bipartite geminivirus, associated with dwarfing and leaf curling of tomatoes and peppers in Jamaica. Partial DNA-A and DNA-B clones were obtained. DNA sequence analysis showed that tomato and pepper samples have a similar geminivirus associated with them. Nucleotide sequence identity > 92% between the common regions of DNA-A and DNA-B confirmed the bipartite nature of the Jamaican geminivirus isolates. Nucleotide sequence comparisons of DNA-A and DNA-B with those of geminiviruses representing the major phylogenetic groups of Western Hemisphere geminiviruses showed the greatest similarity to potato yellow mosaic virus and members of the Abutilon mosaic virus cluster of geminiviruses. This new virus is given the name tomato dwarf leaf curl virus (TDLCV) because of the dwarfing and leaf curling symptoms associated with infected tomato plants. Polymerase chain reaction and Southern hybridization showed mixed infections of TDLCV with tomato yellow leaf curl virus from Israel in 16% of the field samples of tomatoes and peppers.     

红果型沙地云杉内生真菌多样性

了解沙地云杉植物内生真菌生态多样性,为沙地云杉内生真菌的种属鉴别和资源的开发利用提供科学的依据,并为下一步深入研究内生真菌代谢产物提供理论基础。对内蒙古自治区克什克腾旗白音敖包自然保护区的沙地云杉进行调查,采用组织分离法对沙地云杉的不同组织部位进行内生真菌分离,以形态学和分子生物学相结合的方法进行鉴定,选取其中60株进行扩增、测序和系统发育分析。从系统发育树可见,菌株聚为2个大分支,分别为子囊菌亚门和半知菌亚门,10个小分支对应7个科分属于10个属12种,其中链格孢属（Alternaria）与青霉属（Penicillium）为优势菌属,红果型沙地云杉内生真菌菌种资源较丰富。     

Evolutionary analysis of plant jacalin-related lectins (JRLs) family and expression of rice JRLs in response to Magnaporthe oryzae

Jacalin-related lectins (JRLs) are widely distributed carbohydrate-binding proteins in the plant kingdom, which play key roles in development and pathogen defense. In this study, we profiled evolutionary trajectory of JRLs family in 30 plant species and identified domain diversification and recombination leading to different responsive patterns of JRLs in rice during defense against rice blast. All of 30 plant species analyzed in our study have two types of JRLs by containing either a single jacalin or repeated jacalin domains, while chimeric jacalins exist in more than half of the species, especially in the Poaceae family. Moreover, Poaceae species have evolved two types of unique chimeric JRLs by fusing the jacalin domain(s) with dirigent or NB_ARC domain, some of which positively regulate plant immunity. Seven Poaceae-specific JRLs are found in the rice genome. We further found expression of rice JRLs, including four Poaceae-specific JRLs, are induced by Magnaporthe oryzae infections at either early or late infection stages. Overall, the results present the evolutionary trajectory of JRLs in plant and highlight essential roles of Poaceae specific JRLs against pathogen attacks in rice.     

Silicon distribution in meadow steppe and typical steppe of northern China and its implications for phytolith carbon sequestration

Silicon (Si) not only plays an important role in plant growth but also contributes significantly to the long‐term terrestrial carbon sink in the form of phytoliths. This study investigated Si content of 184 plant species in meadow steppe and typical steppe of northern China to examine the influential factors of Si distribution and evaluate the potential phytolith carbon sequestration of these grasslands. Our results indicated that the average Si content generally decreased in the following order of Equisetopsida > Monocotyledoneae > Dicotyledoneae. Within angiosperms, although most Si accumulator plants were commelinid monocots, many eudicots also accumulated abundant Si in their above‐ground tissues. The Si content of plant above‐ground parts in typical steppe (6.53 ± 2.88 g/kg) was significantly higher than that in meadow steppe (2.15 ± 0.92 g/kg). The estimated phytolith‐occluded carbon (PhytOC) production flux in typical steppe (0.81 ± 0.36 kg CO₂ ha^?1 year^?1) was higher than that in meadow steppe (0.54 ± 0.23 kg CO₂ ha^?1 year^?1). This study demonstrates that plant phylogeny influences the Si content of individual species, whereas grassland type with different mean annual precipitation and mean annual temperature may significantly affect the abundance of high Si species. We conclude that increasing the abundance of grass species with high Si content in meadow steppe and appropriate grazing and fertilizer application in typical steppe will enhance the phytolith carbon sequestration in grasslands of northern China.     

Pythium yorkensis sp. nov., a potential soybean pathogen from southeastern Pennsylvania,USA

Biodiversity surveys of natural as well as agricultural ecosystems commonly reveal novel isolates. A new species, Pythium yorkensis sp. nov., is reported here, isolated from field soil during a survey of oomycete diversity in symptomless soybean across southeastern Pennsylvania. Molecular data from both mitochondrial and nuclear loci support a unique phylogenetic position for the isolates collected, and morphological features distinguish this new species from close relatives in Pythium clade J. Pathogenicity assays suggest that this new species may be a potential agricultural pathogen, as isolates were mildly aggressive on soybean. This study highlights the continued need for culture‐based surveys in collaboration with high‐throughput sequence‐based approaches for environmental sampling.     

Phylogenetic position and nucleotide diversity of Fusarium oxysporum f. sp. vanillae worldwide based on translation elongation factor 1α sequences

Fusarium oxysporum f. sp. vanillae is considered the most important fungus affecting vanilla crops around the world, causing rot on vanilla roots and stems. Previous studies showed that the ability to infect vanilla plants is a polyphyletic trait among strains of the Fusarium oxysporum species complex (FOSC). The same studies proposed a single origin for F. oxysporum f. sp. vanillae isolates sampled from Mexico, the centre of origin and distribution of vanilla. The aim of this work was to test the hypothesis of the monophyletic origin of a wider sample of isolates of F. oxysporum f. sp. vanillae infecting Mexican vanilla and estimate nucleotide diversity of pathogen isolates from the main vanilla‐producing countries. Sequence data for the TEF1α gene from 106 isolates was assembled. The phylogenetic analyses suggest that some Mexican isolates of F. oxysporum f. sp. vanillae belong in two well‐supported clades, mixed with isolates from Madagascar, Indonesia, Réunion and Comoros. The phylogenetic position of other Indonesian and Mexican isolates is unresolved. Estimations of nucleotide diversity showed that the population from Mexico is genetically more diverse than the other three populations from Madagascar, Indonesia and Réunion. The results support a polyphyletic origin of vanilla‐infecting isolates of F. oxysporum worldwide, and also reject the proposition that Mexican isolates have a single origin. The phylogenetic optimizations over the strict consensus tree of the ability to infect vanilla plants suggest that pathogenic strains around the world are the product of multiple shifts of pathogenesis and dispersion events.     

5科11种鱼类ITS1特征分析及其在系统分类研究中的适用性

为了探讨ITS1作为分子标记用于鱼类系统演化的适用性,实验选取鲈形目5科11种鱼类为研究对象,包括尖吻鲈科、射水鱼科、军曹鱼科、剑鱼科和鲹科。通过克隆和测序等技术共获得了348条ITS1序列,长度范围为442~661 bp;通过对所有序列的长度、变异位点数量、GC含量、核苷酸多样性及单倍型多样性指数等遗传特征比较分析发现,11种鱼类ITS1序列无论是在种内还是在种间,长度和序列都表现出较为明显的多态性。特别是在军曹鱼中,70条克隆的长度范围为648~661 bp,但有一条序列存在55 bp缺失,结合该序列的GC含量,二级结构和最小自由能,推断该序列为假基因。以鮣为外类群,基于核糖体ITS1序列构建的邻接树显示在物种种类水平上,不同个体的克隆都按种类聚支,ITS1可以用于该类群物种的区分;在属级水平上,ITS1将11属鱼类完全区分开,能够用于属级水平的区分;在科级水平上,虽然鲹科分为2支的分子结果和形态分类存在差异,但ITS1构建的系统关系与线粒体分子标记构建的系统进化树相似。研究表明,核糖体ITS1可以作为一种有效的分子标记用于研究鱼类的系统分类研究,并且不同的分类阶元其解析能力不同,这将为鱼类核糖体的研究提供科学依据。     

中国达氏鳇野生群体和两个养殖群体的线粒体遗传多样性分析

达氏鳇(Huso dauricus)是黑龙江流域土著鲟,近几十年来野生资源急剧下降,被确定为濒危物种之一。本研究采用线粒体DNA的Cyt b基因和D-loop区域的多态性信息评估了黑龙江抚远段野生群体、北京房山国家级鲟鱼原种场的保种群体及浙江衢州国家级鲟鱼良种场的繁殖群体等3个达氏鳇群体的遗传多样性水平。所有测试个体在Cyt b基因位点的核苷酸水平上没有检测到多样性,均具有相同的Cyt b单倍型,而在D-loop区域中发现了9种单倍型,对于D-loop区,单倍型多样性(H_d)达到0.593,但核苷酸多样性(π)仅为0.00213。在8尾野生个体中检测到6种D-loop单倍型,2个养殖群体共计58尾个体共计检出5种D-loop单倍型个体。分析结果显示:野生达氏鳇群体遗传多样性极低,历史上可能经历过严重的遗传瓶颈,同时达氏鳇人工繁殖过程中每批次可能只有极少个体参与了繁殖。此外,基于Cyt b基因部分序列的分析结果提示,达氏鳇与其他太平洋鲟类的亲缘关系较近,而与欧鳇(Huso huso)关系较远,传统上鳇属(Huso)的分类地位得不到有效的分子生物学数据支持。     

南极鱼类DNA条形码及分子系统进化研究

本文采用COI基因兼并引物对15种36个南极鱼类DNA进行扩增测序,并结合Gen Bank已有序列进行联配分析,对南极鱼2科22属43种共97条COI基因片段(539 bp)进行序列比较和系统发生关系研究,探索了DNA条形码技术在辅助鱼类物种鉴定和分类中的适应性与可行性。结果分析表明,43种南极鱼科和鳄冰鱼科的鱼类COI基因的平均碱基组成为T:31.9%、G:18.3%、A:22.2%和C:27.6%,具有明显的碱基偏倚性。南极鱼类的种间平均距离为0.157,种内平均遗传距离为0.002,种间平均遗传距离是种内平均距离的79倍;系统分析结果显示,除南极小带腭鱼(Cryodraco antarcticus)和罗斯海小带腭鱼(Cryodraco atkinsoni)外,其余的鱼类皆能够形成独立的分支,且与形态学分支一致。由此可见,DNA条形码对南极鱼亚目鳄冰鱼科和南极鱼科鱼类能够进行有效的物种鉴定,基于COI基因所建的NJ(neighbor-joining)树对物种分类具有较为准确的辨识力。系统发生关系表明,DNA条形码可以对除南极小带腭鱼(Cryodraco antarcticus)和罗斯海小带腭鱼(Cryodraco atkinsoni)外的南极鱼物种进行鉴定,不仅可以作为形态学的辅助手段为南极鱼分类系统的必要补充和佐证,并且可以用于探讨南极鱼类近缘种的系统发育关系。