First report of Pectobacterium aroidearum causing soft rot on leaf mustard in China.

Leaf mustard (Brassica juncea [L.] Czern. et Coss.) is widely planted in China as an important leaf vegetable. In March 2022, water-soaked and mushy rot symptoms were observed on leaf mustard plants in the field of Zhaotong (27.85°N; 105.05°E), Yunnan, China. The incidence of symptomatic leaf mustard was approximately 10%. The isolation of the causal agent followed the method of Peng et al. (2023). Briefly, infected tissues from four diseased plants were mixed and teased apart, and homogenized by vortex shaking. The bacterial suspension was diluted and spread on nutrient agar (NA). About 10 single colonies exhibiting different colony morphologies were picked and purified separately by successive streaking. A pinprick method was used for pathogenicity tests with an inoculum concentration of 108 CFU/ml (Singh et al. 2013). Among 10 isolates, only strain YKX exhibited soft rot symptoms on detached mustard leaves. In addition, ten two-month-old leaf mustard plants grown in the greenhouse were used for in vivo pathogenicity tests. Briefly, sterilized pins were dipped in the bacterial suspension, and then leaf mustard petioles were pricked with these pins. After inoculation, each plant was kept in a plastic bag for 12 hours to maintain high humidity. As expected, strain YKX caused obvious rot symptoms on eight plants at 1-2 days post-inoculation while the control group including two plants treated with sterile water showed no symptoms. The colonies of strain YKX on NA were white, roughly circular, and convex. For a preliminary identification, total DNA was extracted and used as the template in PCR amplification of 16S rDNA with the universal PCR primer pair 27F/1492R (Weisburg et al. 1991). The quality-filtered DNA sequence (871 bp) showed 100% query coverage and 99.47% identity to the 16S rDNA sequences of type strain Pectobacterium aroidearum SCRI 109T (GenBank: NR_159926) found in the NCBI rRNA/ITS database. Whole-genome sequencing of strain YKX was then performed using the Illumina and Nanopore sequencing platforms by Tsingke Biotechnology Co., Ltd. (Beijing, China). A single contig (GenBank: CP129239) with a length of approximately 4.9 Mb was obtained by de novo hybrid assembly using Unicycler v0.5.0 (Wick et al. 2017). The quality of the genomic data was evaluated by BUSCO v5.4.7 (Manni et al. 2021) against the gammaproteobacteria_odb10 dataset. A BUSCO complete score of 99.5% indicated high assembly quality. The genome sequence of strain YKX was uploaded to the Type Strain Genome Server for a genome-based taxonomic analysis (Meier-Kolthoff et al. 2022). The distance-based phylogeny showed that strain YKX and P. aroidearum L6 (GenBank: CP065044) and P. aroidearum PC1 (GenBank: NC_012917) form a clade. When comparing strain YKX with L6 or PC1, the digital DNA-DNA hybridization value (83.5-83.8%) was above the species delineation threshold (70% for DDH), clearly indicating that strain YKX should be classified as P. aroidearum. Additionally, P. aroidearum was reisolated from inoculated leaves and identified based on morphological similarities and 16S rDNA sequencing, thus fulfilling Koch's postulates. It is worth noting that a previous study reported occurrences of soft rot disease on leaf mustard attributed to Rhizopus microsporus var. chinensis (Wang et al. 2020). To our knowledge, this is the first report of P. aroidearum causing soft rot on leaf mustard in China, which expands the known host range of this pathogen and benefits the control of this disease.

First report of Sphaerulina azaleae causing leaf spot on Rhododendron pulchrum Sweet in China.

Rhododendron pulchrum Sweet is a popular ornamental evergreen shrub, renowned for its exquisite flowers. In November 2020, leaf spot disease was observed at Qujing Normal University (25.527°N; 103.744°E), Qujing, Yunnan, China. Symptoms were observed on 25-35 % leaves. This led to early leaf drop, significantly reducing its ornamental value. The infected leaves exhibited irregular, dark brown to blackish spots, with random distribution. To investigate the causal agent, ten symptomatic leaves were collected for pathogen isolation. Leaf spots bearing ascomata were picked with a sterile needle, placed on water agar, and then incubated at 26 ℃ for 24 h. Individual germinated spores were transferred onto PDA for further purification and morphological study. Two pure isolates (chl01 and chl02) were obtained. The colonies on PDA were circular, raised, pink-white at the center, dark brown at the margin, and dark brown to black from reverse after four weeks at 26 °C. Moreover, colonies on PDA sporulated following a 5-hour UV light exposure in a laminar flow hood and a subsequent 14 h light: 10 h dark (14:10) cycle for 5 days at 26 °C. The conidiophores are reduced to conidiogenous cells which are 1.5-3 × 1.5-2.5 µm (n = 10), integrated, hyaline, proliferating sympodially near the apex, cylindrical, and widest at the base. Conidia are hyaline, slightly verruculose, guttulate, cylindrical, straight or irregularly curved, subobtuse at the apex, truncate at the base, and 19-28 × 3-4 µm (n= 30), with 1-3 septa. The morphological features were similar to the genus Sphaerulina (Quaedvlieg et al. 2013). To confirm the candidate pathogen, we performed PCR and gene sequencing using specific primers ACT-512F/ACT2Rd, EF1-728F/EF2, ITS4/ITS5, LSU1Fd/LR5 and fRPB2-5F/fRPB2-414R for actin (ACT), the partial translation elongation factor 1-alpha (TEF1), internal transcribed spacer region (ITS), large subunit ribosomal RNA gene (LSU), and RNA polymerase II subunit (RPB2) genes, respectively (Choi et al. 2020). Sequences were deposited in GenBank with accession numbers OR359635 (ACT), OR359637 (TEF1), OR335339 (ITS), OR335299 (LSU) and OR359636 (RPB2). BLAST searches showed 97.34% (ACT), 99.47% (TEF1), 100% (ITS), 100% (LSU) and 100% (RPB2) identity with those of Sphaerulina azaleae CBS 128605 from GenBank, respectively. A multilocus phylogenetic tree was generated using maximum likelihood (ML) based on the concatenated ACT-TEF-ITS-LSU-RPB2 sequence, placing our isolates within the S. azaleae group with high confidence. To fulfill Koch's postulates, three R. pulchrum plants in the landscape (three leaves per plant) were inoculated by pipetting 0.2 ml spore suspension (1 × 106 conidia/ml) onto the surface of each leaf (Khoo et al. 2022). Three additional plants in the landscape were inoculated with sterile water on similar aged leaves. The leaves were enclosed in plastic bags for 72 hours. At 7 days postinoculation, infected leaves exhibited the symptoms as described above, whereas the controls showed no symptoms. This experiment was repeated twice. The same fungus was reisolated from the infected leaves and identified based on morphology and Sanger sequencing. It is worth noting that S. azaleae can cause leaf spot on Rhododendron yedoense f. poukhanense (Choi et al. 2020). To our knowledge, this is the first report of S. azaleae causing leaf spot on R. pulchrum Sweet in China, indicating that appropriate management strategies are needed.

Elevational changes in soil properties shaping fungal community assemblages in terrestrial forest.

Environmental variables shifted by climate change act as driving factors in determining plant-associated microbial communities in terrestrial ecosystems. However, how elevation-induced changes in soil properties shape the microbial community in forest ecosystems remains less understood. Thus, the Pinus tabuliformis forests at elevations of 1500 m, 1900 m, and 2300 m above sea level were investigated to explore the effect of environmental factors on microbial assemblage. Significant changes in the soil physicochemical properties were found across the investigated elevations, such as soil moisture, temperature, pH, nitrogen (N), and phosphorus (P). Soil enzymatic activities, including soil sucrase, phosphatase, and dehydrogenase, were significantly affected by elevation, and sucrase showed a linear correlation with soil organic matter. Furthermore, the richness of fungal communities in the rhizosphere was decreased as elevation increased, while a humpback pattern was found for roots. Certain core microbiota members, such as Agaricomycetes, Leotiomycetes, and Pezizomycetes, were crucial in maintaining a stable ecological niche in both the root and rhizosphere. We also found that shifting of fungal communities in the rhizosphere were more related to physical properties (e.g., pH, soil moisture, and soil temperature), while changes in root fungal communities along elevation gradient were related mostly to soil nutrients (e.g., soil N and P). Overall, this study demonstrates that the assemblage of the root and rhizosphere fungal communities in P. tabuliformis forest primarily depends on elevation-induced changes in environmental variables and highlights the importance of predicting fungal responses to future climate change.

Complete Genome Sequence Data of Pseudomonas bijieensis SP1 Associated with Root Soft Rot of Yam Bean.

Pseudomonas bijieensis is a newly established species with antifungal activity. Here, we report the high-quality and complete genome sequence for P. bijieensis strain SP1, created by hybrid assembly using both short reads and long reads. The length of the circular chromosome is about 6.67 Mb, with a GC content of 60.89%. Bioinformatic analyses revealed gene clusters for the biosynthesis of antimicrobial metabolites 2,4-diacetylphloroglucinol as well as bacterial secretion systems (type I to III and type V to VI). Interestingly, this strain can cause soft rot symptoms in the roots of yam bean, showing the potential to be a plant pathogen. The genomic data will be a valuable resource for exploring the virulence mechanism and antifungal activity of this strain.

Arbuscular mycorrhizal fungi contribute to reactive oxygen species homeostasis of Bombax ceiba L. under drought stress.

Drought stress is one of the major abiotic factors limiting plant growth and causing ecological degradation. The regulation of reactive oxygen species (ROS) generation and ROS scavenging is essential to plant growth under drought stress. To investigate the role of arbuscular mycorrhizal fungi (AMF) on ROS generation and ROS scavenging ability under drought stress in Bombax ceiba, the ROS content, the expression levels of respiratory burst oxidase homologue (Rbohs), and the antioxidant response were evaluated in AMF and NMF (non-inoculated AMF) plants under drought stress. 14 BcRboh genes were identified in the B. ceiba genome and divided into five subgroups based on phylogenetic analysis. The effect of AMF on the expression profiles of BcRbohs were different under our conditions. AMF mainly downregulated the expression of Rbohs (BcRbohA, BcRbohD, BcRbohDX2, BcRbohE, BcRbohFX1, and BcRbohI) in drought-stressed seedlings. For well-water (WW) treatment, AMF slightly upregulated Rbohs in seedlings. AMF inoculation decreased the malondialdehyde (MDA) content by 19.11 and 20.85%, decreased the O2⋅- production rate by 39.69 and 65.20% and decreased H2O2 content by 20.06 and 43.21% compared with non-mycorrhizal (NMF) plants under drought stress in root and shoot, respectively. In addition, AMF inoculation increased the non-enzymatic antioxidants glutathione (GSH) and ascorbic acid (AsA) content in roots by 153.52 and 28.18% under drought stress, respectively. The activities of antioxidant enzymes (SOD, PX, CAT, APX, GPX, GR, MDAR, and DHAR) all increased ranging from 19.47 - 131.54% due to AMF inoculation under drought stress. In conclusion, these results reveal that AMF inoculation can maintain ROS homeostasis by mitigating drought-induced ROS burst, via decreasing ROS generation and enhancing ROS scavenging ability of B. ceiba seedlings.

Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics.

Bacterial soft rot is a devastating disease for a wide range of crops, vegetables, and ornamental plants including konjac (Amorphophallus konjac). However, the pangenome and genomic plasticity of the konjac soft rot pathogens is little explored. In this study, we reported the complete genome sequences of 11 bacterial isolates that can cause typical soft rot symptoms in konjac by in vitro and in vivo pathogenicity tests. Based on in silico DNA-DNA hybridization, average nucleotide identity and phylogenomic analysis, all 11 isolates were determined to be Pectobacterium aroidearum. In addition, synteny analysis of these genomes revealed considerable chromosomal inversions, one of which is triggered by homologous recombination of ribose operon. Pangenome analysis and COG enrichment analysis showed that the pangenome of P. aroidearum is open and that accessory genes are enriched in replication, recombination, and repair. Variations in type IV secretion system and type VI secretion system were found, while plant cell wall degrading enzymes were conserved. Furthermore, sequence analyses also provided evidence for the presence of a type V secretion system in Pectobacterium. These findings advance our understanding of the pathogenicity determinants, genomic plasticity, and evolution of P. aroidearum.

First report of Pseudomonas palleroniana causing potato soft rot in China.

Slimy potato (Solanum tuberosum) tubers with a foul-smelling odor were obtained from a potato field during harvest in Huize county (25.94°N; 103.40°E), Yunnan province, China in August 2021. The incidence of symptomatic potato tubers was approximately 5% while no symptoms were observed on potato stems. To isolate the causal agent, potato tubers were surface-disinfected and infected tissues were mashed in a 15 ml sterile centrifuge tube with 2 ml sterile distilled water. After a series of dilutions, a volume of 200 µl bacterial suspension from each dilution was spread on nutrient agar (NA) medium and incubated at 28 °C for 48 h. Single colonies randomly selected from NA plates were then picked and separately subcultured in nutrient broth (NB) medium. Pure cultures were acquired by successive streaking on NA medium. The colonies with irregular shapes were white and opaque (Fig. S1A). Among all the isolates, strain Q1 exhibited pectinolytic activity on inoculated potato tubers using a pin prick method with an inoculum concentration of 108 CFU/ml while no symptoms appeared for the control group using sterile water (Fig. S1B). However, no obvious pits were observed for strain Q1 when tested on crystal violet pectin (CVP) medium. To further identify the strain Q1, total DNA was extracted using the TaKaRa MiniBEST Bacteria Genomic DNA Extraction Kit. PCR amplification of 16S rDNA of strain Q1 was performed using the universal PCR primer pair 27F/1492R and followed by Sanger sequencing. The BLASTn analysis of the sequence (NCBI accession number ON631256) based on NCBI rRNA/ITS databases revealed 100% query coverage and 99.78% identity to the 16S rDNA sequences of type strain Pseudomonas tolaasii ATCC 33618 and Pseudomonas palleroniana CFBP 4389, respectively. Whole-genome sequencing of strain Q1 was then performed using the Illumina and Nanopore sequencing platform. A single contig (NCBI accession number CP092411) with a length of approx. 6.2 MB was obtained by de novo assembly using Raven (v1.5.1) (Vaser and Sikic 2021) and Pilon (v1.24) (Walker et al. 2014). The completeness and redundancy of this assembly was evaluated by BUSCO (v5.2.2) (Manni et al. 2021), and a score of 100% completeness indicated a high quality of the assembly. The genome sequence of strain Q1 was uploaded to the Type Strain Genome Server (TYGS) for a whole genome-based taxonomic analysis (Meier-Kolthoff and Göker 2019). The distance-based phylogeny revealed that strain Q1 is well clustered together with Pseudomonas palleroniana (Fig. S1C). Furthermore, a digital DNA-DNA hybridization (dDDH) value (86.9%) between strain Q1 and P. palleroniana was above the species boundary (≥70%), indicating that strain Q1 should be classified as P. palleroniana. In addition, P. palleroniana was re-isolated from potato tubers inoculated using a pin prick method with an inoculum concentration of 108 CFU/ml and was identified by morphological similarities and 16s rDNA sequencing described above, thus fulfilling Koch's postulates. Furthermore, aerial stem rot symptoms were observed after 3-5 days post inoculation of strain Q1 with a concentration of 108 CFU/ml on stems of young potato plants using a pin prick method (Fig. S1D). Notably, a couple of Pseudomonas spp. have been reported to cause soft rot in carrot (Godfrey and Marshall 2002) and melon (Zhang et al. 2016). To our knowledge, this is the first report of P. palleroniana causing soft rot on potato tuber in China.

A chromosome-level genome assembly of Amorphophallus konjac provides insights into konjac glucomannan biosynthesis.

Amorphophallus konjac, a perennial herb in the Araceae family, is a cash crop that can produce a large amount of konjac glucomannan. To explore mechanisms underlying such large genomes in the genus Amorphophallus as well as the gene regulation of glucomannan biosynthesis, we present a chromosome-level genome assembly of A. konjac with a total genome size of 5.60 Gb and a contig N50 of 1.20 Mb. Comparative genomic analysis reveals that A. konjac has undergone two whole-genome duplication (WGD) events in quick succession. Two recent bursts of transposable elements are identified in the A. konjac genome, which contribute greatly to the large genome size. Our transcriptomic analysis of the developmental corms characterizes key genes involved in the biosynthesis of glucomannan and related starches. High expression of cellulose synthase-like A, Cellulose synthase-like D, mannan-synthesis related 1, GDP-mannose pyrophosphorylase and phosphomannomutase fructokinase contributes to glucomannan synthesis during the corm expansion period while high expression of starch synthase, starch branching enzyme and phosphoglucomutase is responsible for starch synthesis in the late corm development stage. In conclusion, we generate a high-quality genome of A. konjac with different sequencing technologies. The expansion of transposable elements has caused the large genome of this species. And the identified key genes in the glucomannan biosynthesis provide valuable candidates for molecular breeding of this crop in the future.

Genome-Wide SNPs Provide Insights on the Cryptic Genetic Structure and Signatures of Climate Adaption in Amorphophallus albus Germplasms.

Domesticated species represent unique systems in which the evolutionary genomic consequences of intensive selective breeding and adaptation can be thoroughly investigated. Amorphophallus albus occurs naturally and is in cultivation throughout the downstream region of the Jinshajiang River in Southwest China. This species is characterised by high konjac glucomannan content, and has been cultivated in China for nearly 2,000 years. To study genetic differentiation and local adaption of A. albus, we sampled 13 distinct local cultivated populations of this species. Restriction site-associated DNA sequencing was conducted with 87 samples, resulting in 24,225 SNPs. The population structure analyses suggest two main genetic groups: one in the relatively upstream region, and one downstream. We found evidence of additional sub-structure within the upstream group, demonstrating the statistical power of genomic SNPs in discovering subtle genetic structure. The environmental and geographic factors were all identified as significant in shaping the genetic differentiation of this species. Notably, the proportion of environmental factors was larger than geographic factors in influencing the population genetic patterns of A. albus. We also discovered loci that were associated with local adaptation. These findings will help us understand the genetic differentiation of this newly domesticated species, thereby informing future breeding programs of A. albus.

Inoculation With Ectomycorrhizal Fungi and Dark Septate Endophytes Contributes to the Resistance of Pinus spp. to Pine Wilt Disease.

Pine wilt disease (PWD) is a deadly disease to pines (Pinus spp.) worldwide. The occurrence of PWD can reduce the relative abundance of root ectomycorrhizal fungi (ECMF) and dark septate endophytes (DSE). However, the effects of exogenous ECMF/DSE inoculation on the rhizosphere microbial community structure of Pinus tabulaeformis infected by pine wood nematode (PWN) is little known. Here, we tested how ECMF/DSE may improve resistance to PWD by quantifying microbial carbon biomass and soil enzymatic activity among different treatments at 6 and 9 months after PWN infection. Denaturing gradient gel electrophoresis (DGGE) was used to study the microbial community structure at 3, 6, and 9 months after PWN infection in the rhizosphere of P. tabulaeformis seedlings inoculated with ECMF/DSE. The results showed that exogenous ECMF/DSE inoculation reduced the disease severity caused by PWN infection. After PWN infection, the rhizosphere microbial carbon of seedlings inoculated with Amanita vaginata, Suillus bovinus, Gaeumannomyces cylindrosporus, and Paraphoma chrysanthemicola was 38.16, 49.67, 42.11, and 96.05% higher than that of the control group, respectively. Inoculation of ECMF/DSE inhibited the decrease of rhizosphere microbial biomass caused by PWN infection. The richness and diversity of P. tabulaeformis rhizosphere fungi at 9 months were reduced by PWN infection but partially recovered by the exogenous fungi (ECMF/DSE) inoculation except for P. chrysanthemicola, which indicates a role of ECMF/DSE in maintaining stability of the microbial community. Inoculation with ECMF/DSE increased the beneficial bacterial (Thauera sp., Mesorhizobium sp., etc.) and fungal groups (Tomentella ellisii, Wilcoxina mikolae, etc.) of in the rhizosphere. In summary, exogenous ECMF/DSE inoculation could increase P. tabulaeformis resistance to PWD probably by improving the rhizosphere microenvironment.

Seasonal Changes in Pinus tabuliformis Root-Associated Fungal Microbiota Drive N and P Cycling in Terrestrial Ecosystem.

In terrestrial ecosystems, mycorrhizal roots play a key role in the cycling of soil carbon (C) and other nutrients. The impact of environmental factors on the mycorrhizal fungal community has been well studied; however, the seasonal variations in the root-associated fungal microbiota affected by environmental changes are less clear. To improve the understanding of how environmental factors shape the fungal microbiota in mycorrhizal roots, seasonal changes in Pinus tabuliformis root-associated fungi were investigated. In the present study, the seasonal dynamics of edaphic properties, soil enzymatic activities, root fungal colonization rates, and root-associated fungal microbiota in P. tabuliformis forests were studied across four seasons during a whole year to reveal their correlations with environmental changes. The results indicate that the soil functions, such as the enzymatic activities related to nitrogen (N) and phosphorus (P) degradation, were varied with the seasonal changes in microclimate factors, resulting in a significant fluctuation of edaphic properties. In addition, the ectomycorrhizal fungal colonization rate in the host pine tree roots increased during warm seasons (summer and autumn), while the fungal colonization rate of dark septate endophyte was declined. Moreover, the present study indicates that the fungal biomass increased in both the pine roots and rhizospheric soils during warm seasons, while the fungal species richness and diversity decreased. While the Basidiomycota and Ascomycota were the two dominant phyla in both root and soil fungal communities, the higher relative abundance of Basidiomycota taxa presented in warm seasons. In addition, the fungal microbial network complexity declined under the higher temperature and humidity conditions. The present study illustrates that the varieties in connectivity between the microbial networks and in functional taxa of root-associated fungal microbiota significantly influence the soil ecosystem functions, especially the N and P cycling.

Rubroshiraia gen. nov., a second hypocrellin-producing genus in Shiraiaceae (Pleosporales).

Shiraiaceae is an important family in Pleosporales (Dothideomycetes), which includes medical fungi and plant pathogens. Two hypocrellin-producing taxa, Shiraia bambusicola and a novel genus Rubroshiraia gen. nov., typified by Rubroshiraia bambusae are treated in this article. Maximum likelihood analysis, generated via RAxML (GTR+G model), using a combined SSU, LSU, TEF1 and RPB2 sequence dataset, shows that Rubroshiraia is close to Shiraia and belongs to the family Shiraiaceae. Descriptions, illustrations and a taxonomic key are provided for the genera in Shiraiaceae. Rubroshiraia morphologically differs from Shiraia in having small and dark ascostromata and filiform ascospores. Production of the ascostromatal metabolites, hypocrellin A and B, were examined by HPLC and spectrophotometer. The content of hypocrellin A and B of specimen HKAS 102255 (R. bambusae) is twice that produced by HKAS 102253 (S. bambusicola). To clarify the relationship between R. bambusae and Hypocrella bambusae, type material of the latter was examined and provided the illustration.

Fungal Systematics and Evolution: FUSE 5.

Thirteen new species are formally described: Cortinarius brunneocarpus from Pakistan, C. lilacinoarmillatus from India, Curvularia khuzestanica on Atriplex lentiformis from Iran, Gloeocantharellus neoechinosporus from China, Laboulbenia bernaliana on species of Apenes, Apristus, and Philophuga (Coleoptera, Carabidae) from Nicaragua and Panama, L. oioveliicola on Oiovelia machadoi (Hemiptera, Veliidae) from Brazil, L. termiticola on Macrotermes subhyalinus (Blattodea, Termitidae) from the DR Congo, Pluteus cutefractus from Slovenia, Rhizoglomus variabile from Peru, Russula phloginea from China, Stagonosporopsis flacciduvarum on Vitis vinifera from Italy, Strobilomyces huangshanensis from China, Uromyces klotzschianus on Rumex dentatus subsp. klotzschianus from Pakistan. The following new records are reported: Alternaria calendulae on Calendula officinalis from India; A. tenuissima on apple and quince fruits from Iran; Candelariella oleaginescens from Turkey; Didymella americana and D. calidophila on Vitis vinifera from Italy; Lasiodiplodia theobromae causing tip blight of Dianella tasmanica 'variegata' from India; Marasmiellus subpruinosus from Madeira, Portugal, new for Macaronesia and Africa; Mycena albidolilacea, M. tenuispinosa, and M. xantholeuca from Russia; Neonectria neomacrospora on Madhuca longifolia from India; Nothophoma quercina on Vitis vinifera from Italy; Plagiosphaera immersa on Urtica dioica from Austria; Rinodina sicula from Turkey; Sphaerosporium lignatile from Wisconsin, USA; and Verrucaria murina from Turkey. Multi-locus analysis of ITS, LSU, rpb1, tef1 sequences revealed that P. immersa, commonly classified within Gnomoniaceae (Diaporthales) or as Sordariomycetes incertae sedis, belongs to Magnaporthaceae (Magnaporthales). Analysis of a six-locus Ascomycota-wide dataset including SSU and LSU sequences of S. lignatile revealed that this species, currently in Ascomycota incertae sedis, belongs to Pyronemataceae (Pezizomycetes, Pezizales).

De novo genome assembly of the red silk cotton tree (Bombax ceiba).

Background: Bombax ceiba L. (the red silk cotton tree) is a large deciduous tree that is distributed in tropical and sub-tropical Asia as well as northern Australia. It has great economic and ecological importance, with several applications in industry and traditional medicine in many Asian countries. To facilitate further utilization of this plant resource, we present here the draft genome sequence for B. ceiba. Findings: We assembled a relatively intact genome of B. ceiba by using PacBio single-molecule sequencing and BioNano optical mapping technologies. The final draft genome is approximately 895 Mb long, with contig and scaffold N50 sizes of 1.0 Mb and 2.06 Mb, respectively. Conclusions: The high-quality draft genome assembly of B. ceiba will be a valuable resource enabling further genetic improvement and more effective use of this tree species.

Identification, Expression Patterns, and Functional Characterization of Chemosensory Proteins in Dendroctonus armandi (Coleoptera: Curculionidae: Scolytinae).

The Chinese white pine beetle, Dendroctonus armandi Tsai and Li (Coleoptera: Curculionidae: Scolytinae), is a serious pest of coniferous forests in China. Thus, there is considerable interest in developing eco-friendly pest-control methods, with the use of semiochemicals as a distinct possibility. Olfaction is extremely important for fitness of D. armandi because it is the primary mechanism through which the insect locates hosts and mates. Thus, here we characterized nine full-length genes encoding chemosensory proteins (CSPs) from D. armandi. The genes were ubiquitously and multiply expressed across different developmental stages and adult tissues, indicating various roles in developmental metamorphosis, olfaction, and gustation. Ligand-binding assays implied that DarmCSP2 may be the carrier of D. armandi pheromones and various plant host volatiles. These volatiles were identified through RNA interference of DarmCSP2 as: (+)-α-pinene, (+)-ß-pinene, (-)-ß-pinene, (+)-camphene, (+)-3-carene, and myrcene. The systematic chemosensory functional analysis of DarmCSP2 in this study clarified the molecular mechanisms underlying D. armandi olfaction and provided a theoretical foundation for eco-friendly pest control.

The complete mitochondrial genome of Bombax ceiba.

Bombax ceiba is a beautiful and deciduous tree with important economic and ecological values. Here, we sequenced the intact mitochondrial genome (mitogenome) of B. ceiba on the PacBio sequencing platform (Pacific Biosciences, Menlo Park, CA). The mitogenome is 594,390 bp and is comprised of 35 protein-coding genes, two rRNA genes, and 25 tRNA genes. The phylogeny analysis suggested that B. ceiba was closely clustered with the genus Gossypium.

Complete chloroplast genome sequence of the red silk cotton tree (Bombax ceiba).

Bombax ceiba L. is a beautiful and deciduous tree with great ecological and economic importance. The third generation sequencing of chloroplast genome of B. ceiba was conducted on the PacBio sequencing platform (Pacific Biosciences). The complete chloroplast genome was 158,997 bp, which contains a large single-copy (LSC) region (89,021 bp), a small single-copy (SSC) region (21,110 bp), and two inverted repeats (IRs) (24,433 bp). In total, 116 genes were annotated, including 81 protein-coding genes, eight rRNA genes, and 27 tRNA genes. The phylogenetic tree showed that B. ceiba was closely clustered with one clade of Malvaceae.