Molecular evolution and phylogeny of the RPB2 gene in the genus Hordeum

Background and Aims

It is known that the miniature inverted-repeat terminal element (MITE) preferentially inserts into low-copy-number sequences or genic regions. Characterization of the second largest subunit of low-copy nuclear RNA polymerase II (RPB2) has indicated that MITE and indels have shaped the homoeologous RPB2 loci in the St and H genome of Eymus species in Triticeae. The aims of this study was to determine if there is MITE in the RPB2 gene in Hordeum genomes, and to compare the gene evolution of RPB2 with other diploid Triticeae species. The sequences were used to reconstruct the phylogeny of the genus Hordeum.

Methods

RPB2 regions from all diploid species of Hordeum, one tetraploid species (H. brevisubulatum) and ten accessions of diploid Triticeae species were amplified and sequenced. Parsimony analysis of the DNA dataset was performed in order to reveal the phylogeny of Hordeum species.

Key Results

MITE was detected in the Xu genome. A 27–36 bp indel sequence was found in the I and Xu genome, but deleted in the Xa and some H genome species. Interestingly, the indel length in H genomes corresponds well to their geographical distribution. Phylogenetic analysis of the RPB2 sequences positioned the H and Xa genome in one monophyletic group. The I and Xu genomes are distinctly separated from the H and Xa ones. The RPB2 data also separated all New World H genome species except H. patagonicum ssp. patagonicum from the Old World H genome species.

Conclusions

MITE and large indels have shaped the RPB2 loci between the Xu and H, I and Xa genomes. The phylogenetic analysis of the RPB2 sequences confirmed the monophyly of Hordeum. The maximum-parsimony analysis demonstrated the four genomes to be subdivided into two groups.Key words: Molecular evolution, RPB2, Hordeum, transposable element, phylogeny     

The saprobic and fruiting abilities of the exotic forest pathogen Heterobasidion irregulare may explain its invasiveness

The North American fungal pathogen Heterobasidion irregulare is invading and threatening pine stands in Italy and is freely hybridizing with the native species Heterobasidion annosum. Susceptibility of native hosts has been excluded as a factor driving H. irregulare invasion. Here we tested whether H. irregulare and H. annosum differ in their ability to saprobically colonize pine wood, and whether saprobic growth is correlated to fruiting bodies production. When inoculated in pine logs, H. irregulare genotypes colonized a volume of wood significantly larger than H. annosum genotypes. Heterobasidion irregulare significantly exceeded H. annosum in all parameters used as metrics of fruiting body production, including number and size of fruiting bodies, and pores perimeter index (PPI), an index summarizing the amount of surface available for spore production. Number of fruiting bodies and PPI were significantly correlated with volume of wood colonized by Heterobasidion genotypes. Results may explain why H. irregulare has been reported to sporulate more abundantly than H. annosum and provide explanations for its high transmission potential in Italy. This knowledge implies that approaches to control the spread of H. irregulare should be aimed at limiting saprobic establishment of the fungus rather than focusing on identifying more tolerant tree species.     

3种同域分布的杓兰属植物的种子及杂交种子特征分析

杂交种子研究在一定程度上能说明是否存在杂种不活机制,在植物生殖隔离研究中具有重要意义。通过对同域分布的西藏杓兰(Cypripedium tibeticum)、黄花杓兰(C.flavum)和褐花杓兰(C.calcicola)的自交、异交、杂交种子的形态特征及活性进行分析,发现3种杓兰属植物两两之间均可产生杂交种子,且杂交种子活性较高,杂交种子与其他处理所得种子的外观、表面纹饰无显著性差异;种子宽度、种子长度、有胚率、着色率并没有比自交或异交种子显著低。这一结果表明这3种同域杓兰属植物种与种之间具有相当高的亲和性,它们之间不存在明显的杂种不活机制。黄花杓兰与西藏杓兰或褐花杓兰间的传粉者大小明显不同,黄花杓兰由丽蝇和熊蜂工蜂传粉,而西藏杓兰和褐花杓兰由体形较大的熊蜂蜂王传粉,传粉者隔离已使得它们之间的物种界限比较清晰,因此已经没有必要再产生杂种不活等其他隔离机制。而西藏杓兰与褐花杓兰的传粉者相同,又没有明显的杂种不活隔离机制,暗示它们之间有其他合子后隔离机制或应将其合并为一个种。     

Evolutionary history of the conifer root rot fungus Heterobasidion annosum sensu lato

We investigated two hypotheses for the origin of the root rot fungus Heterobasidion annosum species complex: (i) that geology has been an important factor for the speciation (ii) that co-evolutionary processes with the hosts drove the divergence of the pathogen species. The H. annosum species complex consists of five species: three occur in Europe, H. annosum s.s., Heterobasidion parviporum and Heterobasidion abietinum, and two in North America, Heterobasidion irregulare and Heterobasidion occidentale; all with different but partially overlapping host preferences. The evolution of the H. annosum species complex was studied using six partially sequenced genes, between 10 and 30 individuals of each species were analysed. Neighbour-joining trees were constructed for each gene, and a Bayesian tree was built for the combined data set. In addition, haplotype networks were constructed to illustrate the species relationships. For three of the genes, H. parviporum and H. abietinum share haplotypes supporting recent divergence and/or possible gene flow. We propose that the H. annosum species complex originated in Laurasia and that the H. annosum s.s./H. irregulare and H. parviporum/H. abietinum/H. occidentale ancestral species emerged between 45 and 60 Ma in the Palaearctic, well after the radiation of the host genera. Our data imply that H. irregulare and H. occidentale were colonizing North America via different routes. In conclusion, plate tectonics are likely to have been the main factor influencing Heterobasidion speciation and biogeography.     

Fitness of the parasitoid Diadegma insulare is affected by its host's food plants

The diamondback moth, Plutella xylostella (L.) is considered a specialist on Brassicaceae, but it is capable of expanding its food range by incorporation of non-brassicaceous plants into its diet. The use of a new food plant may change food availability and vulnerability of P. xylostella to its natural enemies, especially specialist parasitoids. In this laboratory study, we evaluated the bottom-up effects of two Brassicaceae viz. Brassica napus L. and Descurainia sophia (L.) Webb ex Prantl and two non-Brassicaceae viz. Tropaeolum majus L. and Cleome hassleriana Chodat on several fitness correlates of the specialist parasitoid, Diadegma insulare (Cresson) reared on P. xylostella larvae. Percentage of parasitism of host larvae by D. insulare varied among the plant species and was highest on T. majus and lowest on D. sophia. Values of several fitness correlates for D. insulare differed when the host was feeding on various plant species. Egg to adult development was fastest on B. napus followed by C. hassleriana, D. sophia and T. majus. Female wasps reared on C. hasseleriana lived the longest in absence of food. The response of D. insulare to potential food-plant expansion by its host P. xylostella is discussed.     

Contributions to the lichen flora of the Lakshadweep (Laccadive) Islands,India

Abstract:The first lichen records from the Lakshadweep (Laccadive) Islands are presented.Lithothelium insulare (Pyrenulaceae) is described as new and nine other taxa are reported. The poor lichen flora, dominated by pantropical species, is probably a result of the lack of natural habitats in this area.     

Natural enemies ofPlutella xylostella (Lep.: Plutellidae) on crucifers in Honduras

Three primary parasitoids in three genera were reared fromPlutella xylostella (L.) larvae and pupae collected in various crucifer producing regions of Honduras. The ichneumonidDiadegma insulare (Cresson) was by far the most abundant species. TwoSpilochalcis species, facultative hyperparasitoids attackingP. xylostella andD. insulare, were encountered as well as eleven species in nine genera of obligate hyperparasitoids attackingD. insulare. Three vespid predators are noted as predating on larvae.      

Species of Heterobasidion host a diverse pool of partitiviruses with global distribution and interspecies transmission

We investigated the geographic occurrence and genetic diversity of partitiviruses among 247 Heterobasidion specimens representing seven species and originating from Europe, Asia, and North America. Based on sequence analysis, partitiviruses were relatively rare, and occurred only in about 5 % of the Heterobasidion isolates analyzed, constituting a minority (about 28 %) of all virus-infected [double-stranded RNA (dsRNA)-positive] isolates. Altogether ten virus strains were characterized in sequence: one complete genome sequence of 3893 bp, six complete RNA-dependent RNA polymerase sequences of 2000-2033 bp, and three partial polymerase sequences. Based on phylogenetic analysis, the virus strains were assigned into three putative partitivirus species: HetRV1 (Heterobasidion RNA virus 1), HetRV4, and HetRV5. Degenerate consensus primers were designed for RT-PCR detection of these virus species. HetRV1 occurred in five different Heterobasidion species, and resembled the previously described Heterobasidion annosum virus (HaV). Highly similar HetRV1 strains with 98 % nucleotide level similarity were found from H. parviporum (member of the H. annosum species complex) and H. australe (member of the H. insulare complex) growing in the same region in Bhutan. This observation suggests recent virus transmission between these taxonomically distant Heterobasidion species in nature. It was also shown that HetRV1 can be transmitted by mycelial contact between the H. annosum and H. insulare complexes. The two other virus species, HetRV4 and HetRV5, were closely related to the Amasya Cherry Disease-associated mycovirus, to Heterobasidion parviporum partitivirus Fr110B, and also to several plant-infecting alphacryptoviruses. These results are in accordance with the view of a close evolutionary relationship between partitiviruses of plants and fungi.     

Molecular evolution and genome divergence at <Emphasis Type="Italic">RPB2</Emphasis> gene of the St and H genome in <Emphasis Type="Italic">Elymus</Emphasis> species

Molecular evolution of the second largest subunit of low copy nuclear RNA polymerase II (RPB2) in allotetrploid StH genomic species of Elymus is characterized here. Our study first reported a 39-bp MITE stowaway element insertion in the genic region of RPB2 gene for all tetraploid Elymus St genome and diploid Pseudoroegneria spicata and P. stipifolia St genome. The sequences on 3′-end are highly conserved, with AGTA in all sequences but H10339 (E. fibrosis), in which the AGTA was replaced with AGAA. All 12 Stowaway-containing sequences encompassed a 9 bp conserved TIRs (GAGGGAGTA). Interestingly, the 5′-end sequence of GGTA which was changed to AGTA or deleted resulted in Stowaway excision in the H genome of Elymus sepcies, in which Stowaway excision did not leave footprint. Another two large insertions in all St genome sequences are also transposable-like elements detected in the genic region of RPB2 gene. Our results indicated that these three transposable element indels have occurred prior to polyploidization, and shaped the homoeologous RPB2 loci in St and H genome of Eymus species. Nucleotide diversity analysis suggested that the RPB2 sequence may evolve faster in the polyploid species than in the diploids. Higher level of polymorphism and genome-specific amplicons generated by this gene indicated that RPB2 is an excellent tool for investigating the phylogeny and evolutionary dynamics of speciation, and the mode of polyploidy formation in Elymus species.     

Virus Community Dynamics in the Conifer Pathogenic Fungus Heterobasidion parviporum Following an Artificial Introduction of a Partitivirus

Viruses infecting the conifer pathogenic fungus Heterobasidion annosum sensu lato are intracellular and spread via anastomosis contacts. In the laboratory, these viruses transmit readily even between somatically incompatible isolates, but their dispersal capacity in natural conditions has not been previously studied. We introduced a mycovirus to a heavily diseased forest site by inoculating Norway spruce stumps with heartrot decay using a mycelial suspension of Heterobasidion parviporum strain RT3.49C hosting the partitivirus strain HetRV4-pa1. The Heterobasidion population at the sample plot was screened for mycoviruses prior to and after the inoculation. Based on sequence analysis, the resident H. parviporum strains harbored six different strains of the virus species Heterobasidion RNA virus 6 (HetRV6) and one strain of HetRV4 prior to the inoculation. After three growth seasons, the inoculated H. parviporum host strain was not detected, but the introduced virus had infected two resident H. parviporum genets. The presence of a preexisting HetRV6 infection did not hinder spread of the introduced partitivirus but resulted in coinfections instead. The resident HetRV6 virus population seemed to be highly stable during the incubation period, while the single indigenous HetRV4 infection was not detected after the inoculation. In laboratory infection experiments, the introduced virus could be transmitted successfully into all of the resident H. parviporum genets. This study shows for the first time transmission of a Heterobasidion virus between somatically incompatible hosts in natural conditions.     

Biosynthesis of fomannoxin in the root rotting pathogen Heterobasidion occidentale

Fomannoxin is a biologically active benzohydrofuran, which has been suggested to be involved in the pathogenicity of the root rotting fungus Heterobasidion annosum sensu lato. The biosynthesis of fomannoxin was investigated through an isotopic enrichment study utilizing [1-¹³C]glucose as metabolic tracer. ¹³C NMR spectroscopic analysis revealed the labeling pattern and showed that the isoprene building block originates from the mevalonic acid pathway, whereas the aromatic motif is formed via the shikimic acid route by elimination of pyruvate from chorismic acid. A natural product, 4-hydroxy-3-(3-methylbut-2-enyl)benzaldehyde (1), was isolated and characterized, and was suggested to be a key intermediate in the biosynthesis of fomannoxin and related secondary metabolites previously identified from the H. annosum fungal species complex.     

Host Plants Affect the Foraging Success of Two Parasitoids that Attack Light Brown Apple Moth Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae)

The light brown apple moth, Epiphyas postvittana is a key pest of wine grapes in Australia. Two parasitoids, Dolichogenidea tasmanica and Therophilus unimaculatus, attack the larval stage of this pest. D. tasmanica is dominant in vineyards, whereas T. unimaculatus is mainly active in native vegetation. We sought to understand why they differ in their use of habitats. Plants are a major component of habitats of parasitoids, and herbivore-infested plants influence parasitoid foraging efficiency by their architecture and emission of volatile chemicals. We investigated how different plant species infested by E. postvittana could affect the foraging success of the two parasitoid species in both laboratory and field experiments. Four common host-plant species were selected for this study. In paired-choice experiments to determine the innate foraging preferences for plants, both parasitoid species showed differences in innate search preferences among plant species. The plant preference of D. tasmanica was altered by oviposition experience with hosts that were feeding on other plant species. In a behavioral assay, the two parasitoid species allocated their times engaged in various types of behavior differently when foraging on different plant species. For both parasitoids, parasitism on Hardenbergia violacea was the highest of the four plant species. Significantly more larvae dropped from Myoporum insulare when attacked than from the other three host-plant species, which indicates that parasitism is also affected by interactions between plants and host insects. In vineyards, parasitism by D. tasmanica was significantly lower on M. insulare than on the other three host-plant species, but the parasitism rates were similar among the other three plant species. Our results indicate that plants play a role in the habitat preferences of these two parasitoid species by influencing their foraging behavior, and are likely to contribute to their distributions among habitats.     

Multiple virus infections on Heterobasidion sp.

Heterobasidion viruses have previously been shown to affect each other’s transmission and phenotypic effects on their hosts in a complex way. In this work, Heterobasidion parviporum strains hosting five coinfecting viruses simultaneously were constructed and used as donors in transmission experiments. They showed that viruses move more frequently between the mycelia of the same species than between the mycelia of H. parviporum and Heterobasidion annosum. One of the strains was used to show that coinfection of five viruses is relatively unstable in a natural environment and analyses of the growth rate and competitive ability of Heterobasidion strains hosting various virus combinations revealed that viral effects are not additive. The results also supported the view that the transmission of the promising virocontrol agent HetPV13-an1 may be enhanced by coinfecting viruses in the donor mycelium. However, its detrimental effects may be blocked by the presence of other viruses in the same mycelium.RepositoriesGenBank accession number MN058080.     

Deceptive pollination of the Lady's Slipper Cypripedium tibeticum (Orchidaceae)

To test whether the nectarless flowers of Cypripedium tibeticum attract pollinators through mimicry like the allied species C. macranthos var. rebunense, pollination biology of C. tibeticum was investigated in western China. Although C. tibeticum was also pollinated by bumble bee queens, i.e. Bombus lepidus , B. lucorum and B. hypnorum , no special, rewarding model plants were found in the habitat. Field experimentation confirmed that the flowers were self-compatible but insects were required to transfer orchid pollen to the stigma. Both Bombus queens and workers were visitors, but queens were much more frequent than workers and only queens were effective pollinators. Floral functional morphology analysis showed that it was large queens rather than small workers that fitted well with the flowers of C. tibeticum. With the faint sweet-fruity scent, the minor floral fragrance compound, ethyl acetate, probably plays a role in attracting bumble bees by food deception. The dark flowers with the inflated, trap-like labellum are hypothesized to mimic the nest site of queens. Therefore, bumble bee queens tend to be attracted by C. tibeticum through nest site mimic combined with food deception. Considering that the co-blooming flowers of C. flavum are pollinated by the Bombus workers, and C. smithii pollinated by a queen, we suggest that using the same bumblebees with different body sizes as the pollinators is the main reproductive isolation between interfertile C. tibeticum and C. flavum, while C. tibeticum and C. smithii tend to hybridize naturally.     

Structural,Biochemical, and Computational Characterization of the Glycoside Hydrolase Family 7 Cellobiohydrolase of the Tree-killing Fungus Heterobasidion irregulare

Root rot fungi of the Heterobasidion annosum complex are the most damaging pathogens in temperate forests, and the recently sequenced Heterobasidion irregulare genome revealed over 280 carbohydrate-active enzymes. Here, H. irregulare was grown on biomass, and the most abundant protein in the culture filtrate was identified as the only family 7 glycoside hydrolase in the genome, which consists of a single catalytic domain, lacking a linker and carbohydrate-binding module. The enzyme, HirCel7A, was characterized biochemically to determine the optimal conditions for activity. HirCel7A was crystallized and the structure, refined at 1.7 Å resolution, confirms that HirCel7A is a cellobiohydrolase rather than an endoglucanase, with a cellulose-binding tunnel that is more closed than Phanerochaete chrysosporium Cel7D and more open than Hypocrea jecorina Cel7A, suggesting intermediate enzyme properties. Molecular simulations were conducted to ascertain differences in enzyme-ligand interactions, ligand solvation, and loop flexibility between the family 7 glycoside hydrolase cellobiohydrolases from H. irregulare, H. jecorina, and P. chrysosporium. The structural comparisons and simulations suggest significant differences in enzyme-ligand interactions at the tunnel entrance in the −7 to −4 binding sites and suggest that a tyrosine residue at the tunnel entrance of HirCel7A may serve as an additional ligand-binding site. Additionally, the loops over the active site in H. jecorina Cel7A are more closed than loops in the other two enzymes, which has implications for the degree of processivity, endo-initiation, and substrate dissociation. Overall, this study highlights molecular level features important to understanding this biologically and industrially important family of glycoside hydrolases.     

Natural occurrence in Argentina of a new fungal pathogen of cockroaches,Metarhizium argentinense sp. nov.

The aim of this study was to search for entomopathogenic fungi that infect wild cockroaches in forest ecosystems in two protected natural areas of Argentina. Two isolates of Metarhizium argentinense were obtained and identified from wild cockroaches (Blaberidae: Epilamprinae) through the use of morphological characteristics and molecular phylogenetic analyses. This novel species was found in Argentina and is a member of the Metarhizium flavoviride species complex. Phylogenetic analyses, based on sequence similarity analysis using internal transcribed spacer (ITS) and a set of four protein-coding marker sequences (EF1A, RPB1, RPB2 and BTUB), supported the status of this fungus as a new species. In addition, we tested the biological activity of the new species through assays against Blattella germanica nymphs and found that the two evaluated isolates were pathogenic. However, isolate CEP424 was more virulent and caused a confirmed mortality of 76 % with a median lethal time of 7.2 d. This study reports the southernmost worldwide location of a Metarhizium species that infects cockroaches and will help expand the knowledge of the biodiversity of pathogenic fungi of Argentine cockroaches.