Molecular characterization of strawberry pathogen Gnomonia fragariae and its genetic relatedness to other Gnomonia species and members of Diaporthales

Gnomonia fragariae is a poorly studied ascomycete belonging to Diaporthales. Originally G. fragariae was considered a saprophyte occurring on dead tissues of strawberry plants. Recently this fungus was found in Latvia and Sweden, and it was proven to be the cause of severe root rot and petiole blight of strawberry. Thirteen isolates of this pathogen and several other Gnomonia species occurring on rosaceous hosts were characterized by molecular analysis using nucleotide sequences of partial LSU rRNA gene and the total ITS region. The homologous regions from relevant diaporthalean taxa available in the GenBank were also included and compared with the taxa sequenced in this study. Phylogenetic analyses revealed that G. fragariae, G. rubi, and Gnomonia sp. (CBS 850.79) were genetically different from G. gnomon, the type species of the genus, and other members of Gnomoniaceae. The analyses showed that G. fragariae and Hapalocystis were genetically very closely related, forming a phylogenetic clade, which is possibly presenting a new family in the Diaporthales. Morphological comparisons of the Gnomonia species on the basis of commonly used criteria for the taxonomy of Diaporthales, so far did not reveal any evident features for the polyphyletic status of Gnomonia.     

Multilocus sequence analysis of bradyrhizobia isolated from Aeschynomene species in Senegal

This study reports the multilocus sequence analysis (MLSA) of nine house-keeping gene fragments (atpD, dnaK, glnA, glnB, gltA, gyrB, recA, rpoB and thrC) on a collection of 38 Bradyrhizobium isolated from Aeschynomene species in Senegal, which had previously been characterised by several phenotypic and genotypic techniques, allowing a comparative analysis of MLSA resolution power for species delineation in this genus. The nifH locus was also studied to compare house-keeping and symbiotic gene phylogenies and obtain insights into the unusual symbiotic properties of these Aeschynomene symbionts. Phylogenetic analyses (maximum likelihood, Bayesian) of concatenated nine loci produced a well-resolved phylogeny of the strain collection separating photosynthetic bradyrhizobial strains (PB) from non-photosynthetic bradyrhizobial (NPB) ones. The PB clade was interpreted as the remains an expanding ancient species that presently shows high diversification, giving rise to potential new species. B. denitrificans LMG8443 and BTAi1 strains formed a sub-clade that was identified as recently emerging new species. Congruence analyses (by Shimodaira–Hasegawa (S–H) tests) identified three gene-fragments (dnaK, glnB and recA) that should be preferred for MLSA analyses in Bradyrhizobium genus. The nine loci or nifH phylogenies were not correlated with the unusual symbiotic properties of PB (nod-dependent/nod-independent). Advantages and drawbacks of MLSA for species delineation in Bradyrhizobium are discussed.     

三种厚朴叶绿体基因组的比较研究

为了深入发掘日本厚朴、厚朴、凹叶厚朴叶绿体基因组差异,筛选厚朴优良性状候选基因,开展三种厚朴的分子遗传研究,该文利用Illumina HiSeq高通量测序平台首次对日本厚朴叶绿体进行测序、组装,并与已有的厚朴、凹叶厚朴叶绿体基因组共同注释,获得三个物种叶绿体基因图谱,筛选出三个基因组中的差异基因,又与同科中11个亲缘物种进行叶绿体基因组比对,构建NJ遗传树。结果表明：(1)日本厚朴叶绿体基因组的Clean Reads为19 791 019,Q30为91.33%,组装后基因组全长160 051 bp, GC含量为39.2%,含tRNA 37个,rRNA 8个。(2)比对分析发现三种厚朴具有相似的IR、LSC和SSC结构,以及GC含量和tRNA数量,但编码基因种类和数量、内含子和外显子的数量和结构等存在差异。(3)日本厚朴的功能基因数目较厚朴、凹叶厚朴分别多6个和4个,主要分布于LSC区和IR区,涉及核糖体大亚基、核糖体小亚基和未知功能基因类群。(4)系统发育分析结果进一步显示日本厚朴与凹叶厚朴亲缘关系较近,其次是厚朴。该研究表明日本厚朴具有更丰富的叶绿体基因组结构、组成和变异特征,是其适...     

Prosthecium species with Stegonsporium anamorphs on Acer

Data from microscopic morphology, single-spore cultures, and DNA analyses of teleomorphs and anamorphs support the recognition of five species of Prosthecium with Stegonsporium anamorphs on Acer: P. acerinum sp. nov., the teleomorph of S. acerinum; P. acerophilum comb. nov., formerly known as Dictyoporthe acerophila; P. galeatum comb. nov., originally described as Massaria galeata; P. opalus sp. nov.; and P. pyriforme sp. nov., the teleomorph of S. pyriforme s. str. The morphology of both type specimens and freshly collected material was investigated. The teleomorphs have brown ellipsoidal ascospores with five distosepta and often a longitudinal distoseptum. The anamorphs of all species described here belong to Stegonsporium; their connection to the Prosthecium teleomorphs was demonstrated by morphology and DNA sequences of single spore cultures derived from both ascospores and conidia. The anamorphs and teleomorphs of all five Prosthecium species are described and illustrated by LM images, and a key to these species is provided. As perceived from this work, S. pyriforme is restricted to Europe and does not occur in North America, whereas S. acerinum is restricted to North America, not found in Europe. The host associations given in the literature are revised and evidence is provided that only A. opalus, A. pseudoplatanus, and A. saccharum are confirmed hosts of Prosthecium with Stegonsporium anamorphs. Molecular phylogenetic analyses of tef1, ITS rDNA, and partial nuLSU rDNA sequences confirm that the species with Stegonsporium anamorphs are closely related to P. ellipsosporum, the generic type species. Stilbospora macrosperma is confirmed as the anamorph of P. ellipsosporum by DNA data of single spore isolates obtained from both ascospores and conidia.     

A revision of the Verticillium fungicola species complex and its affinity with the genus Lecanicillium

Verticillium fungicola, the type species of Verticillium sect. Albo-erecta, and related taxa were studied using morphological and molecular techniques. Sequences of the ITS region and SSU rDNA suggest that V. fungicola is very close to members of the genus Lecanicillium and unrelated to other species that were originally accommodated in the same section. New combinations in Lecanicillium are proposed for Verticillium fungicola and its var. flavidum at species rank, L. f. var. aleophilum is retained as a variety. These taxa can be distinguished from each other by optimum and maximum temperatures for growth, in addition to ITS sequence differences. Morphologically, L. flavidum is also distinct by repeated branching of the conidiophores, whereas the two varieties of L. fungicola have a simple conidiophore axis.     

A new Sparassis species from Spain described using morphological and molecular data

Sparassis miniensis, collected in Pinus pinaster forests in Galicia (northwest Iberian Peninsula) is described as a new species, based on morphological and molecular data. Sparassis miniensis is morphologically distinct from all other species in the genus Sparassis based on scattered flabellae, which are strongly laciniated, azonate, and arise from an orange to rose-purplish base. The sporadic presence of clamp connections is restricted to subhymenial hyphae. Molecular data from LSU-rDNA, ITS and partial gene coding RNA polymerase subunit II (rpb2) suggest a close relationship between the new species S. miniensis and S. brevipes, another European species producing large fruiting bodies but with entire flabellae and no clamp connections.     

Re-consideration of Peronospora farinosa infecting Spinacia oleracea as distinct species, Peronospora effusa

Downy mildew is probably the most widespread and potentially destructive global disease of spinach (Spinacia oleracea). The causal agent of downy mildew disease on various plants of Chenopodiaceae, including spinach, is regarded as a single species, Peronospora farinosa. In the present study, the ITS rDNA sequence and morphological data demonstrated that P. farinosa from S. oleracea is distinct from downy mildew of other chenopodiaceous hosts. Fifty-eight spinach specimens were collected or loaned from 17 countries of Asia, Europe, Oceania, North and South America, which all formed a distinct monophyletic group. No intercontinental genetic variation of the ITS rDNA within Peronospora accessions causing spinach downy mildew disease was found. Phylogenetic trees supported recognition of Peronospora from spinach as a separate species. Microscopic examination also revealed morphological differences between Peronospora specimens from Spinacia and P. farinosa s. lat. specimens from Atriplex, Bassia, Beta, and Chenopodium. Consequently, the name Peronospora effusa should be reinstated for the downy mildew fungus found on spinach. Here, a specimen of the original collections of Peronospora effusa is designated as lectotype.     

地黄内生放线菌的分离及地黄轮纹病拮抗菌Streptomyces folium leaf-16的新种鉴定

药用植物内生放线菌具有合成天然活性化合物的潜力,放线菌新种是寻找新型抗生素先导化合物的一个重要来源。【目的】挖掘药用植物地黄内生放线菌资源,并对地黄轮纹病拮抗菌株leaf-16进行新种鉴定。【方法】本研究采用五步消毒法分离河南道地药材地黄的内生放线菌,以地黄轮纹病原真菌草茎点霉(Phoma herbarum)为指示菌,采用平板对峙法筛选对该病菌有抑制作用的菌株,16S rRNA基因测序发现一株抗地黄轮纹病的放线菌新种leaf-16。通过形态、生理生化、细胞壁化学组分和分子生物学等特征对菌株leaf-16进行多相分类学鉴定。【结果】经平板对峙实验得到8株抗地黄轮纹病的放线菌,其中菌株leaf-16经16S rRNA基因测序、形态比较、生理生化、化学组分和分子生物学以及DNA-DNA杂交分析,确定菌株leaf-16为1株链霉菌新种,并命名为Streptomyces folium。【结论】菌株leaf-16为1株链霉菌新种,具有抑制地黄轮纹病原真菌的活性,为进一步分离新型抗地黄轮纹病的生物制剂奠定物质基础。     

三种锦鸡儿属植物水力结构特征及其干旱适应策略

水分胁迫是干旱半干旱区限制植物生长的主要因素。以干旱半干旱区的3种锦鸡儿属植物为研究对象,从生态适应策略角度来分析3种锦鸡儿植物产生生态分离的原因。对三种锦鸡儿属植物茎干叶片的显微结构、生理功能(导水率、光合速率以及水分利用效率)进行测定,并统计了3种锦鸡儿植株的形态特征,如一、二级枝的直径、长度、末端叶面积。结果表明:三种锦鸡儿属植物都能形成较小的导管直径来适应旱生环境,但是在导水结构上又表现出一定的差异性。中间锦鸡儿的导管直径最小,次脉密度和最大净光合速率最大;柠条锦鸡儿的导管直径、叶片厚度和比叶重(LMA)最大。小叶锦鸡儿在导水率下降50%时的水势(P_(50))最大,水分胁迫时极易发生栓塞,但正是由于导管的栓塞降低了水分运输效率,使其在旱生环境中能够通过减少水分的供应来降低水分的丧失,从而保证自身生长的水分需求;而中间锦鸡儿则主要通过减小导管直径来适应旱生环境;柠条锦鸡儿的水分利用效率最高,抗栓塞能力最强,抗旱性最好,同时柠条锦鸡儿可以通过减少蒸腾面积来减少水分的丧失。植物的导管直径大小、叶片厚度、LMA、叶脉密度对植物导水速率、光合速率等生理功能都有一定的影响。     

Genomic distribution of retrotransposons 297, 1731, copia, mdg1 and roo in the Drosophila melanogaster species subgroup

The intragenomic distribution of five retrotransposon families (297, 1731, copia, mdg1 and roo) in the species of the melanogaster complex was studied by comparing results of the Southern blotting technique in males and females with those of in situ hybridization. The degree of structural polymorphism of each family in the different species was also investigated by restriction enzyme analysis. It was found that genomic distribution is a trait that depends on the family and species. The distribution of roo is mainly euchromatic in the four species and 1731 is heterochromatic, but the distribution of families 297, copia and mdg1 is markedly different in the melanogaster and simulans clades. These families were mainly euchromatic in D. melanogaster but heterochromatic in its sibling species. In the simulans clade most copia and mdg1 elements are located on chromosome Y. Differences in genomic distribution are unrelated with structural conservation. The relation of intragenomic distribution to phylogeny, transpositional activity and the role of the host genome are discussed.     

Phylogenetic analysis of the genus Kribbella based on the gyrB gene: proposal of a gyrB-sequence threshold for species delineation in the genus Kribbella

Given the advances in molecular biology, many microbial taxonomists feel that a sequencing based method should be developed that can replace DNA-DNA hybridisation for species delineation. The potential of the gyrB gene to be used for phylogenetic studies has been investigated within a number of actinobacterial genera, including Gordonia, Micromonospora and the whorl-forming Streptomyces species. This study aimed to determine whether the gyrB gene can discriminate between type strains of the genus Kribbella. Previous studies, in the genus Micromonospora, have found that a gyrB-based genetic distance of 0.014 correlates to a DNA relatedness of 70% and that those strains with a genetic distance of greater than 0.014 are likely to be distinct species. In this study, the gyrB-based genetic distances between Kribbella type strains were found to range from 0.0164 to 0.1495, supporting the use of the 0.014 genetic-distance value as the threshold for species delineation within this genus. Phylogenetic analysis based on the gyrB gene had improved resolution (longer branch lengths) compared to that based on the 16S rRNA gene sequence. Based on this study, the gyrB gene can be used to distinguish between Kribbella type strains. Furthermore, it is proposed that a 390-nucleotide sequence of the gyrB gene of a Kribbella isolate is sufficient to assess whether it is likely to represent a new species, before time and effort is invested in polyphasic taxonomic characterisation of the isolate.     

Natural variation of ascospore and conidial germination by Fusarium verticillioides and other Fusarium species

Fusarium verticillioides and other Fusarium species were examined for their spore germination phenotypes. In general, germinating spores of F. verticillioides formed germ tubes that immediately penetrated into agar. Such invasive germination was the predominant growth phenotype among 22 examined field isolates of F. verticillioides from a broad range hosts and locations. However, two of the field isolates were unique in that they formed conidial germ tubes and hyphae that grew along the surface of agar before penetration eventually occurred. Conidia of 22 other Fusarium species were assessed for their germination phenotypes, and only some strains of F. annulatum, F. fujikuroi, F. globosum, F. nygamai, and F. pseudoanthophilum had the surface germination phenotype (21 % of the strains assessed). Sexual crosses and segregation analyses involving one of the F. verticillioides surface germination strains, NRRL 25059, indicated a single locus, designated SIG1 (surface vs. invasive germination), controlled the germ tube growth phenotypes exhibited by both conidia and ascospores. Perfect correlation was observed between an ascospore germination phenotype and the germination phenotype of the conidia produced from the resulting ascospore-derived colony. Recombination data suggested SIG1 was linked (7 % recombination frequency) to FPH1, a recently described locus necessary for enteroblastic conidiogenesis. Corn seedling blight assays indicated surface germinating strains of F. verticillioides were less virulent than invasively germinating strains. Assays also indicated pathogenicity segregated independently of the FPH1 locus. Invasive germination is proposed as the dominant form of spore germination among Fusarium species. Furthermore, conidia were not necessary for corn seedling disease development, but invasive germination may have enhanced the virulence of conidiating strains.     

Morphological and molecular studies on Garra imberba and its related species in China

Garra imberba is widely distributed in China. At the moment, both Garra yiliangensis and G. hainanensis are treated as valid species, but they were initially named as a subspecies of G. pingi, a junior synonym of G. imberba. Garra alticorpora and G. nujiangensis also have similar morphological characters to G. imberba, but the taxonomic statuses and phylogenetic relationships of these species with G. imberba remains uncertain. In this study, 128 samples from the Jinshajiang, Red, Nanpanjiang, Lancangjiang, Nujiang Rivers as well as Hainan Island were measured while 1 mitochondrial gene and 1 nuclear intron of 24 samples were sequenced to explore the phylogenetic relationship of these five species. The results showed that G. hainanensis, G. yiliangensis, G. alticorpora and G. imberba are the same species with G. imberba being the valid species name, while G. nujiangensis is a valid species in and of itself.     

四川卧龙国家级自然保护区马先蒿属一新种——熊猫马先蒿

熊猫马先蒿(Pedicularis pandania)是在四川卧龙国家级自然保护区发现的马先蒿属一新种。该新种属于互生叶类群,其基生叶成丛,花冠属于短管有喙型,且下唇将喙包裹住,花管在近萼端发生约180度的扭旋使得花冠下唇在侧上方,这一特征明显区别于其他国产马先蒿物种。分子系统发育分析结果表明,熊猫马先蒿是Clade 7 成员,虽然与火焰系、假欧氏系、喙齿系、拟蕨系和长喙系等成员构成姐妹关系,但熊猫马先蒿的花冠形态特征明显区别于近缘物种。     

Phylogenetic relationship of Alexandrium tamiyavanichii (Dinophyceae) to other Alexandrium species based on ribosomal RNA gene sequences

The phylogenetic relationship of the thecate PSP-toxin producing dinoflagellate Alexandrium tamiyavanichii Balech to other species of Alexandrium was studied based on nucleotide sequences of the ITS1, ITS2, 5.8S, 18S and 28S subunits of the ribosomal RNA gene. These are the first such sequences available for A. tamiyavanichii, which is one of the producers of paralytic shellfish poisoning toxins in tropical waters. Based on the nucleotide sequences of the 28S, 18S and 5.8S subunits of the rRNA gene, A. tamiyavanichii grouped together with A. tamarense, A. catenella and A. fundyense. More interestingly, A. tamiyavanichii was most closely affiliated to A. tamarense isolates from Thailand. This result reaffirmed conclusions from previous studies that, for the A. tamarense/fundyense/catenella species complex, geographical origin rather than morphology seems to determine genetic relatedness. Results of this study also suggest that A. tamiyavanichii most probably belongs to the same species complex. Ribosomal RNA gene sequences do not separate the PSP toxin producing from the non-producing species of Alexandrium.     

Evolution of Tom, 297, 17.6 and rover retrotransposons in Drosophilidae species

LTR retrotransposons are the most abundant transposable elements in Drosophila and are believed to have contributed significantly to genome evolution. Different reports have shown that many LTR retrotransposon families in Drosophila melanogaster emerged from recent evolutionary episodes of transpositional activity. To contribute to the knowledge of the evolutionary history of Drosophila LTR retrotransposons and the mechanisms that control their abundance, distribution and diversity, we conducted analyses of four related families of LTR retrotransposons, 297, 17.6, rover and Tom. Our results show that these elements seem to be restricted to species from the D. melanogaster group, except for 17.6, which is also present in D. virilis and D. mojavensis. Genetic divergences and phylogenetic analyses of a 1-kb fragment region of the pol gene illustrate that the evolutionary dynamics of Tom, 297, 17.6 and rover retrotransposons are similar in several aspects, such as low codon bias, the action of purifying selection and phylogenies that are incongruent with those of the host species. We found an extremely complex association among the retrotransposon sequences, indicating that different processes shaped the evolutionary history of these elements, and we detected a very high number of possible horizontal transfer events, corroborating the importance of lateral transmission in the evolution and maintenance of LTR retrotransposons.     

Romellia is congeneric with Togninia, and description of Conidiotheca gen. nov. for one species of this genus with polysporous asci

During a continued survey of fungi accommodated in the Calosphaeriales, we observed that the genus Romellia is morphologically heterogeneous. Historically, four species were placed in the genus. Romellia was introduced for taxa with globose, dark, superficial, papillate perithecia, a paraphysate centrum, and octosporous asci containing eight allantoid, hyaline ascospores. The type species, R. vibratilis, was revised in our study, and its freshly collected material was cultured. The anamorph obtained in vitro matches the generic concept of the hyphomycete genus Phaeoacremonium, the anamorph of Togninia. The phylogenies inferred from newly obtained sequences of LSU rDNA, β-tubulin, and actin of R. vibratilis revealed that the species is congeneric with Togninia (Togniniaceae) and represents a good species. Revision of type and herbarium material of other Romellia species confirmed they are not congeneric with Togninia. Romellia tympanoides possesses immersed, subglobose perithecia with sessile asci containing eight ascospores, which during maturation produce ascoconidia filling the entire ascus. This maturation process represents a new kind of apparent polyspory known in the ascomycetes. We introduce a new genus, Conidiotheca, and a new combination for R. tympanoides. The species is compared with the genera Barrina and Tympanis. The relationships of two other Romellia species, R. ambigua and R. cornina, lie with Wegelina and Jattaea of the Calosphaeriales.