Genome-wide identification and evolution of <Emphasis Type="Italic">TC1</Emphasis>/<Emphasis Type="Italic">Mariner</Emphasis> in the silkworm (<Emphasis Type="Italic">Bombyx mori</Emphasis>) genome

TC1/Mariner transposons belong to class II transposable elements (TEs) that use DNA-mediated “cut and paste” mechanism to transpose, and they have been identified in almost all organisms. Although silkworm (Bombyx mori) has a large amount of TC1/Mariner elements, the genome wide information of this superfamily in the silkworm is unknown. In this study, we have identified 2670 TC1/Mariner (Bmmar) elements in the silkworm genome. All the TEs were classified into 22 families by means of fgclust, a tool of repetitive sequence classification, seven of which was first reported in this study. Phylogenetic and structure analyses based on the catalytic domain (DDxD/E) of transposase sequences indicated that all members of TC1/Mariner were grouped into five subgroups: Mariner, Tc1, maT, DD40D and DD41D/E. Of these five subgroups, maT rather than Mariner possessed most members of TC1/Mariner (51.23%) in the silkworm genome. In particular, phylogenetic analysis and structure analysis revealed that Bmmar15 (DD40D) formed a new basal subgroup of TC1/Mariner element in insects, which was referred to as bmori. Furthermore, we concluded that DD40D appeared to intermediate between mariner and Tc1. Finally, we estimated the insertion time for each copy of TC1/Mariner in the silkworm and found that most of members were dramatically amplified during a period from 0 to 1 mya. Moreover, the detailed functional data analysis showed that Bmmar1, Bmmar6 and Bmmar9 had EST evidence and intact transposases. These implied that TC1/Mariner might have potential transpositional activity. In conclusion, this study provides some new insights into the landscape, origin and evolution of TC1/Mariner in the insect genomes.     

Comparison of bioethanol production from cultivated versus wild <Emphasis Type="Italic">Gracilaria verrucosa</Emphasis> and <Emphasis Type="Italic">Gracilaria gigas</Emphasis>

The seaweed genus Gracilaria is a potential candidate for the production of bioethanol due to its high carbohydrate content. Gracilaria is abundant throughout the world and can be found in both wild and cultivated forms. Differences in the ecological factors such as temperature, salinity, and light intensity affecting wild and cultivated specimens may influence the biochemical content of seaweeds, including the carbohydrate content. This study aimed to investigate the proximate composition and potential bioethanol production of wild and cultivated G. gigas and G. verrucosa. Bioethanol was produced using separate hydrolysis fermentation (SHF), employing a combination of enzymatic and acid hydrolysis, followed by fermentation with Saccharomyces cerevisiae ATCC 200062. The highest carbohydrate content was found in wild G. gigas. The highest galactose and glucose contents (20.21 ± 0.32 and 9.70 ± 0.49 g L^?1, respectively), as well as the highest production of bioethanol (3.56 ± 0.02 g L^?1), were also found in wild G. gigas. Thus, we conclude that wild G. gigas is the most promising candidate for bioethanol production. Further research is needed to optimize bioethanol production from wild G. gigas. Domestication of wild G. gigas is a promising challenge for aquaculture to avoid overexploitation of this wild seaweed resource.     

Ectomycorrhizae of <Emphasis Type="Italic">Tuber huidongense</Emphasis> and <Emphasis Type="Italic">T. liyuanum</Emphasis> with <Emphasis Type="Italic">Castanea mollissima</Emphasis> and <Emphasis Type="Italic">Pinus armandii</Emphasis>

Tuber huidongense and T. liyuanum are common commercial white truffles in China that belong to the Rufum and Puberulum groups of the genus Tuber, respectively. Their mycorrhizae were successfully synthesized with two native trees—Castanea mollissima and Pinus armandii—under greenhouse conditions. The identities of the mycorrhizae were confirmed through internal transcribed spacer (ITS) sequence analyses, and their morphological characteristics were described. All of the obtained mycorrhizae have an interlocking pseudoparenchymatous mantle, which is a typical feature of truffle mycorrhizae. The mycorrhizae of T. huidongense on the two trees have hyaline branched emanating hyphae, similar to the documented mycorrhizae of the Rufum group. The unramified, spiky, and hyaline cystidia on the mycorrhizae of T. liyuanum with both C. mollissima and P. armandii further confirmed that this characteristic is constant for the mycorrhizae of the Puberulum group. The successful mycorrhizal syntheses on the two nut-producing trees will be of economic importance in the cultivation of the two truffles.     

Identification of <Emphasis Type="Italic">Pm58</Emphasis> from <Emphasis Type="Italic">Aegilops tauschii</Emphasis>

Key message

A novel powdery mildew-resistance gene, designated Pm58, was introgressed directly from Aegilops tauschii to hexaploid wheat, mapped to chromosome 2DS, and confirmed to be effective under field conditions. Selectable KASP? markers were developed for MAS.

Abstract

Powdery mildew caused by Blumeria graminis (DC.) f. sp. tritici (Bgt) remains a significant threat to wheat (Triticum aestivum L.) production. The rapid breakdown of race-specific resistance to Bgt reinforces the need to identify novel sources of resistance. The d-genome species, Aegilops tauschii, is an excellent source of disease resistance that is transferrable to T. aestivum. The powdery mildew-resistant Ae. tauschii accession TA1662 (2n?=?2x?=?DD) was crossed directly with the susceptible hard white wheat line KS05HW14 (2n?=?6x?=?AABBDD) followed by backcrossing to develop a population of 96 BC₂F₄ introgression lines (ILs). Genotyping-by-sequencing was used to develop a genome-wide genetic map that was anchored to the Ae. tauschii reference genome. A detached-leaf Bgt assay was used to screen BC₂F_4:6 ILs, and resistance was found to segregate as a single locus (χ?=?2.0, P value?=?0.157). The resistance gene, referred to as Pm58, mapped to chromosome 2DS. Pm58 was evaluated under field conditions in replicated trials in 2015 and 2016. In both years, a single QTL spanning the Pm58 locus was identified that reduced powdery mildew severity and explained 21% of field variation (P value?<?0.01). KASP? assays were developed from closely linked GBS-SNP markers, a refined genetic map was developed, and four markers that cosegregate with Pm58 were identified. This novel source of powdery mildew-resistance and closely linked genetic markers will support efforts to develop wheat varieties with powdery mildew resistance.

     

A preliminary integrated genetic map distinguishes every chromosome pair and locates essential genes related to abiotic adaptation of <Emphasis Type="Italic">Crassostrea angulata</Emphasis>/<Emphasis Type="Italic">gigas</Emphasis>

Background

The re-sequencing of C. angulata has revealed many polymorphisms in candidate genes related to adaptation to abiotic stress that are not present in C. gigas; these genes, therefore, are probably related to the ability of this oyster to retain high concentrations of toxic heavy metals. There is, in addition, an unresolved controversy as to whether or not C. angulata and C. gigas are the same species or subspecies. Both oysters have 20 metacentric chromosomes of similar size that are morphologically indistinguishable. From a genomic perspective, as a result of the great variation and selection for heterozygotes in C. gigas, the assembly of its draft genome was difficult: it is fragmented in more than seven thousand scaffolds.

Results

In this work sixty BAC sequences of C. gigas downloaded from NCBI were assembled in BAC-contigs and assigned to BACs that were used as probes for mFISH in C. angulata and C. gigas. In addition, probes of H3, H4 histone, 18S and 5S rDNA genes were also used. Hence we obtained markers identifying 8 out the 10 chromosomes constituting the karyotype. Chromosomes 1 and 9 can be distinguished morphologically. The bioinformatic analysis carried out with the BAC-contigs annotated 88 genes. As a result, genes associated with abiotic adaptation, such as metallothioneins, have been positioned in the genome. The gene ontology analysis has also shown many molecular functions related to metal ion binding, a phenomenon associated with detoxification processes that are characteristic in oysters. Hence the provisional integrated map obtained in this study is a useful complementary tool for the study of oyster genomes.

Conclusions

In this study 8 out of 10 chromosome pairs of Crassostrea angulata/gigas were identified using BAC clones as probes. As a result all chromosomes can now be distinguished. Moreover, FISH showed that H3 and H4 co-localized in two pairs of chromosomes different that those previously escribed. 88 genes were annotated in the BAC-contigs most of them related with Molecular Functions of protein binding, related to the resistance of the species to abiotic stress. An integrated genetic map anchored to the genome has been obtained in which the BAC-contigs structure were not concordant with the gene structure of the C. gigas scaffolds displayed in the Genomicus database.

     

Differentiation of the pollen size in five representatives of <Emphasis Type="Italic">Taraxacum</Emphasis> sect. <Emphasis Type="Italic">Palustria</Emphasis>

Measurements of the pollen size in 5 species of Taraxacum sect. Palustria at three levels of ploidy: 2n = 3x = 24 (T. paucilobum), 2n = 4x = 32 (T. vindobonense, T. trilobifolium), 2n = 5x = 40 (T. mendax) and one taxon of unknown number of chromosomes 2n = ? (T. portentosum) are presented in this paper. Obtained results indicate a lack of distinct positive correlation between the pollen size and ploidy in the studied group of plants. Distinct relationship was, however, found between ploidy and the range of pollen size and shape variability. Most variable were the pollen grains of triploid T. paucilobum and the least — those in pentaploid T. mendax. Ranges of pollen variability in tetraploid T. trilobifolium and T. vindobonense and in T. portentosum of unknown number of chromosomes showed intermediate values.     

Effect of light and temperature on the daily rhythm of adult eclosion in the blood-sucking mosquitoes <Emphasis Type="Italic">Aedes communis</Emphasis> De Geer and <Emphasis Type="Italic">Culex pipiens</Emphasis> L. (Diptera,Culicidae)

A comparative study on the effect of light and temperature on the daily rhythm of adult eclosion was carried out on the blood-sucking mosquitoes Aedes (Ochlerotatus) communis De Geer and Culex pipiens pipiens L. Two forms of C. p. pipiens were investigated: the autogenous form molestus occurring in the underground habitats (the urban mosquito), and the anautogenous form pipiens inhabiting mostly the above-ground biotopes. The study included both field observations and laboratory experiments. Under natural conditions (southern Karelia, 62°N) at optimal temperatures A. communis and C. p. p. f. pipiens demonstrated a bimodal eclosion rhythm with morning and evening peaks, whereas in C. p. p. f. molestus only an evening maximum was observed. The fraction of adults eclosing in the middle of the day increased at lower temperatures. In all the mosquitoes studied, the daily eclosion dynamics in the nature did not differ significantly between the variants with different levels of illumination, suggesting that temperature was the main factor regulating the eclosion rhythm. However, experiments with constant temperature showed that light also could influence the timing of eclosion. The responsiveness to light was different in two studied forms of C. p. pipiens. Under a constant temperature and light-dark cycles the rhythm became weak or disappeared completely in the mosquitoes from above-ground biotopes (A. communis and C. p. p. f. pipiens) but persisted in the urban mosquito. The effect of gradual twilight transitions was more prominent than that of switching the light on or off abruptly. The observed differences in the light and temperature dependence of the eclosion rhythm are discussed in relation to the ecological conditions in different habitats.     

<Emphasis Type="Italic">Talaromyces heiheensis</Emphasis> and <Emphasis Type="Italic">T. mangshanicus</Emphasis>, two new species from China

Two new species, Talaromyces heiheensis from rotten wood and T. mangshanicus isolated from soil, are illustrated and described as new to science in sections Trachyspermi and Talaromyces. The phylogenetic positions of the two new species inferred from the internal transcribed spacer, beta-tubulin, calmodulin and RNA polymerase II second largest subunit regions were carried out. Talaromyces heiheensis is phylogenetically closely related to T. albobiverticillius, T. rubrifaciens, T. solicola and T. erythromellis, and characterised by slow growth on Czapek yeast autolysate agar at 25 °C, orange conidia en masse on malt extract agar at 25 °C, biverticillate and terverticillate conidiophores, acerose phialides and subglobose to ellipsoidal, smooth-walled conidia. Talaromyces mangshanicus is related to T. kendrickii, T. qii and T. thailandensis, and characterised by slow-growing colonies with absent or sparse sporulation on CYA agar at 25 °C, conidia en masse greyish purple, purplish red soluble pigment on yeast extract agar (YES) at 25 °C, biverticillate conidiophores, ampulliform phialides and subglobose to ellipsoidal conidia with echinulate walls. They are distinguished from the known species in culture characteristics on four standard media, microscopic features and sequence data.     

Acaricidal active fractions from acetone extract of <Emphasis Type="Italic">Aloe vera</Emphasis> L. against <Emphasis Type="Italic">Tetranychus cinnabarinus</Emphasis> and <Emphasis Type="Italic">Panonychus citri</Emphasis>

This study aimed to isolate acaricidal active fractions from acetone extract of Aloe vera L. and investigate the toxicity of these fractions against Tetranychus cinnabarinus (T. cinnabarinus) and Panonychus citri (P. citri). Acetone extract of A. vera L. was isolated by immersing in acetone for 72 h, and diverse fractions were fractionated by column chromatography. The acaricidal activity of each fractions was evaluated by corrected mortality of T. cinnabarinus through slide-dip bioassay. The 8th and 13th fractions of acetone extract with good acaricidal activity were indentified by LC/MS, and the toxicity of these two fractions to T. cinnabarinus and P. citri was identified by regression analysis. Acetone extract of A. vera L. exhibited obvious acaricidal activity, from which a total of 18 fractions were isolated. The 8th and 13th fractions with strong acaricidal activity against T. cinnabarinus were identified to be 3-O-alpha-d-mannopyranosyl-d-mannopyranose (OAMM) and aloe emodin. When compared with spirodiclofen, both OAMM and aloe emodin exhibited higher toxicity to T. cinnabarinus, while only OAMM exhibited a higher toxicity to P. citri (P < 0.05). OAMM and aloe emodin isolated from acetone extract of A. vera L. exhibited obvious acaricidal activities against T. cinnabarinus and P. citri.     

Taxonomy and pathogenicity of <Emphasis Type="Italic">Leptographium</Emphasis> species associated with <Emphasis Type="Italic">Ips subelongatus</Emphasis> infestations of <Emphasis Type="Italic">Larix</Emphasis> spp. in northern China,including two new species

The larch bark beetle (Ips subelongatus), which occurs in larch plantations over a vast area of eastern Asia, infects both dying and fallen trees. When its population reaches a high density, the beetle may also infect healthy trees, resulting in tree decline and, eventually, death. Leptographium spp., in both their sexual and asexual states, are mainly associated with conifer-infesting bark beetles; some species are important tree pathogens. The aims of this study were to identify the Leptographium spp. associated with I. subelongatus infestations of Larix spp. in northern China and to examine their pathogenicity towards the tree. Morphological studies and phylogenetic approaches based on multilocus DNA sequence data (ITS2- partial r28S, partial β-tubulin, and EF-1α gene regions) showed that three Leptographium species occur in association with I. subelongatus in the areas investigated: Leptographium taigense, which is recorded in China for the first time, and two new species, namely L. innermongolicum sp. nov. and L. zhangii sp. nov. Leptographium innermongolicum is closely related to L. taigense, whereas L. zhangii belongs to the Grosmannia piceaperda species complex. The pathogenicity of these Leptographium species towards mature Larix spp. was tested by stem inoculation in forests. All inoculations only resulted in small lesions on the inner bark; therefore, the three Leptographium species were not considered to be pathogenic.     

The fungal matrices of <Emphasis Type="Italic">Ophiostoma ips</Emphasis> hinder movement of the biocontrol nematode agent, <Emphasis Type="Italic">Deladenus siricidicola</Emphasis>, disrupting management of the woodwasp, <Emphasis Type="Italic">Sirex noctilio</Emphasis>

Deladenus (=?Beddingia) siricidicola (Tylenchida: Neotylenchidae) is the most effective biocontrol agent used against the invasive wood wasp, Sirex noctilio (Fabricius) (Hymenoptera: Siricidae). The nematodes feed and reproduce on the wood-inhabiting fungus, Amylostereum areolatum (Chaillet ex Fr.) Boidin (Russulales: Amylostereaceae) and parasitise larvae of S. noctilio. In the nematode biocontrol program, the nematodes are inoculated into herbicide-weakened ‘trap trees’. Recent declines in nematode parasitism of S. noctilio in Australia have coincided with an increased incidence of an exotic bark beetle, Ips grandicollis (Eichhoff) (Coleoptera: Curculionidae), attacking trap trees and vectoring a wood-inhabiting fungus, Ophiostoma ips (Rumbold) Nannfelt (Ophiostomatales: Ophiostomataceae), which may inhibit migration of the nematode within the tree to the detriment of S. noctilio biocontrol. Several in vitro and in vivo experiments were conducted to investigate the effect of fungal interactions on the ability of D. siricidicola to locate and reproduce on A. areolatum. Deladenus siricidicola showed preference to A. areolatum in the presence and absence of O. ips, but the presence of O. ips negatively affected the choice response and the number of eggs laid by the nematodes. Deladenus siricidicola was unable to survive and reproduce on O. ips. Results give a clearer understanding of the choice response of D. siricidicola in I. grandicollis infested trees, explaining the disruptive impact of bark beetles on biocontrol of S. noctilio, an effect that could extend from Australia to other important pine growing countries.     

<Emphasis Type="Italic">Diplazium</Emphasis> hybrids involving <Emphasis Type="Italic">D. plantaginifolium</Emphasis> and <Emphasis Type="Italic">D</Emphasis>. <Emphasis Type="Italic">ternatum</Emphasis> from Mexico and Central America

Here we evaluate the origins and relationships of Mexican and Central American Diplazium hybrids derived from crosses involving either D. plantaginifolium or D. ternatum. Based on study of live plants and herbarium specimens, we distinguish D. ×verapax from the similar D. riedelianum and present evidence that the former is a sterile hybrid derived from a cross between D. plantaginifolium and D. werckleanum. We also describe new hybrids, D. ×torresianum and D. ×subternatum from Mexico and northern Central America. Both involve D. ternatum as one parent. Diplazium. cristatum is the other putative parent of D. ×torresianum, and D. plantaginifolium is the second parent of D. ×subternatum. We also designate lectotypes for D. cordovense and D. dissimile.     

Role of Arabidopsis <Emphasis Type="Italic">ABF1</Emphasis>/<Emphasis Type="Italic">3</Emphasis>/<Emphasis Type="Italic">4</Emphasis> during <Emphasis Type="Italic">det1</Emphasis> germination in salt and osmotic stress conditions

Key message

Arabidopsis det1 mutants exhibit salt and osmotic stress resistant germination. This phenotype requires HY5, ABF1, ABF3, and ABF4.

Abstract

While DE-ETIOLATED 1 (DET1) is well known as a negative regulator of light development, here we describe how det1 mutants also exhibit altered responses to salt and osmotic stress, specifically salt and mannitol resistant germination. LONG HYPOCOTYL 5 (HY5) positively regulates both light and abscisic acid (ABA) signalling. We found that hy5 suppressed the det1 salt and mannitol resistant germination phenotype, thus, det1 stress resistant germination requires HY5. We then queried publically available microarray datasets to identify genes downstream of HY5 that were differentially expressed in det1 mutants. Our analysis revealed that ABA regulated genes, including ABA RESPONSIVE ELEMENT BINDING FACTOR 3 (ABF3), are downregulated in det1 seedlings. We found that ABF3 is induced by salt in wildtype seeds, while homologues ABF4 and ABF1 are repressed, and all three genes are underexpressed in det1 seeds. We then investigated the role of ABF3, ABF4, and ABF1 in det1 phenotypes. Double mutant analysis showed that abf3, abf4, and abf1 all suppress the det1 salt/osmotic stress resistant germination phenotype. In addition, abf1 suppressed det1 rapid water loss and open stomata phenotypes. Thus interactions between ABF genes contribute to det1 salt/osmotic stress response phenotypes.

     

Circadian rhythm of activity as a factor of reproductive isolation in closely related species of sand-desert tenebrionid beetles (Coleoptera,Tenebrionidae)

The results of long-term studies of the circadian rhythms of activity in Trigonoscelis gigas and T. sublaevicollis, typical and abundant representatives of the tenebrionid fauna in the Kara Kum desert are given. T. gigas and T. sublaevicollis are omni-seasonal species: their adults are observed on the sand surface from spring till late autumn. They spend their resting period in soil. Adults of both species are similar in morphology, ecology, and behavior, strongly differing in the circadian rhythm pattern. T. gigas are active only at twilight, whereas T. sublaevicollis are characterized by nocturnal activity. Therefore, inhabiting the same habitat, T. gigas and T. sublaevicollis never meet each other under natural conditions, independently of the season and weather. Hence, the circadian rhythm of activity can serve as a reliable mechanism of reproductive isolation in closely related tenebrionid species.     

Horizontal transfer of the C-termini of <Emphasis Type="Italic">tccC</Emphasis> genes in <Emphasis Type="Italic">Photorhabdus</Emphasis> and <Emphasis Type="Italic">Xenorhabdus</Emphasis>

The high molecular weight insecticidal toxin complexes (Tcs), including four toxin-complex loci (tca, tcb, tcc and tcd), were first identified in Photorhabdus luminescens W14. Each member of tca, tcb or tcc is required for oral toxicity of Tcs. However, the sequence sources of the C-termini of tccC3, tccC4, tccC6 and tccC7 are unknown. Here, we performed a whole genome survey to identify the orthologs of Tc genes, and found 165 such genes in 14 bacterial genomes, including 40 genes homologous to tccC1-7 in P. luminescens TT01. The sequence sources of the C-termini of tccC2-6 were determined by sequence analysis. Further phylogenetic investigations suggested that the C-termini of 6 tccC genes experienced horizontal gene transfer events.     

Acaricidal property of the essential oil from <Emphasis Type="Italic">Lippia gracilis</Emphasis> against <Emphasis Type="Italic">Tetranychus urticae</Emphasis> and a natural enemy, <Emphasis Type="Italic">Neoseiulus californicus</Emphasis>, under greenhouse conditions

The essential oil from the leaves of Lippia gracilis was investigated for fumigant and residual activity against Tetranychus urticae (Acari: Tetranychidae) and Neoseiulus californicus (Acari: Phytoseiidae). The results were compared to eugenol, Ortus^® and Azamax^®, as positive controls. Gas chromatography (GC) and GC/mass spectrometry analysis enabled the identification of 28 compounds, accounting for 99.1?±?0.6% of the essential oil. The major constituents were carvacrol (61%), p-cymene (11%) and thymol (11%). Mites were more susceptible to the oil in fumigant tests than in residual tests. Among the components, thymol and β-caryophyllene had the greatest fumigant and residual toxicity against T. urticae, respectively. The role of selected constituents (carvacrol, p-cymene, thymol, limonene, β-pinene, 1,8-cineole, terpinolene and β-caryophyllene) in the acaricidal properties of the L. gracilis essential oil is also discussed. Fumigant and residual effects of Lippia oil were more selective than eugenol with regard to a natural enemy of T. urticae, Neoseiulus californicus. Experiments under greenhouse conditions demonstrated greater toxicity of the Lippia oil in comparison to the positive control at 24, 48 and 72 h after treatment. The results suggest that Lippia oil is a good candidate for the formulation of a botanical acaricide for the integrated management of T. urticae.