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Chrysanthemum virus B encodes a multifunctional p12 protein that acts as a transcriptional activator in the nucleus and as a suppressor of RNA silencing in the cytoplasm. Here, we investigated the impact of p12 on accumulation of major classes of small RNAs (sRNAs). The results show dramatic changes in the sRNA profiles characterised by an overall reduction in sRNA accumulation, changes in the pattern of size distribution of canonical siRNAs and in the ratio between sense and antisense strands, lower abundance of siRNAs with a U residue at the 5′-terminus, and changes in the expression of certain miRNAs, most of which were downregulated. Electronic supplementary material The online version of this article (10.1007/s00705-020-04832-y) contains supplementary material, which is available to authorized users.

Nitrogen (N) limits crop yield, and improvement of N nutrition remains a key goal for crop research; one approach to improve N nutrition is identifying plant-interacting, N2-fixing microbes. Rhodotorula mucilaginosa JGTA-S1 is a basidiomycetous yeast endophyte of narrowleaf cattail (Typha angustifolia). JGTA-S1 could not convert nitrate or nitrite to ammonium but harbors diazotrophic (N2-fixing) endobacteria (Pseudomonas stutzeri) that allow JGTA-S1 to fix N2 and grow in a N-free environment; moreover, P. stutzeri dinitrogen reductase was transcribed in JGTA-S1 even under adequate N. Endobacteria-deficient JGTA-S1 had reduced fitness, which was restored by reintroducing P. stutzeri. JGTA-S1 colonizes rice (Oryza sativa), significantly improving its growth, N content, and relative N-use efficiency. Endofungal P. stutzeri plays a significant role in increasing the biomass and ammonium content of rice treated with JGTA-S1; also, JGTA-S1 has better N2-fixing ability than free-living P. stutzeri and provides fixed N to the plant. Genes involved in N metabolism, N transporters, and NODULE INCEPTION-like transcription factors were upregulated in rice roots within 24 h of JGTA-S1 treatment. In association with rice, JGTA-S1 has a filamentous phase and P. stutzeri only penetrated filamentous JGTA-S1. Together, these results demonstrate an interkingdom interaction that improves rice N nutrition.

Endophytic yeasts of genus Rhodotorula are gaining importance for their ability to improve plant growth. The nature of their interaction with plants, however, remains unknown. Rhodotorula mucilaginosa JGTA-S1 was isolated as an endophyte of Typha angustifolia and promoted growth in the host. To investigate the life-strategy of the yeast from a genomics perspective, we used Illumina and Oxford Nanopore reads to generate a high-quality annotated draft assembly of JGTA-S1 and compared its genome to three other Rhodotorula yeasts and the close relative Rhodosporidium toruloides. JGTA-S1 is a haploid yeast possessing several genes potentially facilitating its endophytic lifestyle such as those responsible for solubilizing phosphate and producing phytohormones. An intact mating-locus in JGTA-S1 raised the possibility of a yet unknown sexual reproductive cycle in Rhodotorula yeasts. Additionally, JGTA-S1 had functional anti-freezing genes and was also unique in lacking a functional nitrate-assimilation pathway—a feature that is associated with obligate biotrophs. Nitrogen-fixing endobacteria were found within JGTA-S1 that may circumvent this defective N-metabolism. JGTA-S1 genome data coupled with experimental evidence give us an insight into the nature of its beneficial interaction with plants.

Foliage samples from Podocarpus totara with severe needle browning and needle loss in the lower part of the crown were observed in 2011 in the Gisborne region of New Zealand. A Phytophthora genus-specific test applied directly to the needles gave a strong positive result, and subsequent isolations yielded colonies of a slow-growing oomycete. Morphological examination in vitro revealed a Phytophthora species. Preliminary comparisons of the rDNA (ITS), and ras-related protein (Ypt) gene regions with international DNA sequence revealed low sequence similarity to species from the downy mildew genus Peronospora, as well as clade 3 Phytophthora species. Other studies have also demonstrated the close relationship with Peronospora. The species was given the interim designation Phytophthora taxon tōtara pending further examination. Here, we formally describe Phytophthora podocarpi sp. Nov. and its associated disease, tōtara needle blight.

Genome and transcriptome sequencing data are extremely useful resources for researchers in carrying out biological experiments that involves cloning and characterizing genes. We are presenting here genome sequence data from different clades of life including photosynthetic prokaryotes; oomycetes pathogens; probiotic bacteria; endophytic yeasts and filamentous fungus and pathogenic protozoa Leishmania donovani. In addition, we are also presenting paired control and treated stress response transcriptomes of Cyanobacteria growing in extreme conditions. The Cyanobacterial species that are included in this dataset were isolated from extreme conditions including desiccated monuments, hot springs and saline archipelagos. The probiotic Lactobacillus paracasei was isolated from Indian sub-continent. The Kala azar causing protozoan Leishmania donovani, whose early infectious stage is also included in this dataset. The endophyte Arthrinium malaysianum was isolated as a contaminant has significant bio-remediation property. Our collaborators have isolated endophyte Rhodotorula mucilaginosa JGTA1 from Jaduguda mines, West Bengal, India infested with Uranium. Our collaborators have isolated a heterozygous diploid oomycetes pathogen, Phytophthora ramorum causing sudden oak death in CA, USA coast is also part of the data. These dataset presents a unique heterogeneous collection from various sources that are analyzed using “Genome Annotator Light (GAL): A Docker-based package for genome analysis and visualization” (Panda et al., 2019) and are presented in a web site automatically created by GAL at http://www.eumicrobedb.org/cglab. Keywords: Annotation, Genome, Transcriptome

We have developed EuMicrobedbLite – A light weight comprehensive genome resource and sequence analysis platform for oomycete organisms. EuMicrobedbLite is a successor of the VBI Microbial Database (VMD) that was built using the Genome Unified Schema (GUS). In this version, the GUS schema has been greatly simplified with removal of many obsolete modules and redesign of others to incorporate contemporary data. Several dependencies such as perl object layers used for data loading in VMD have been replaced with independent light weight scripts. EumicrobedbLite now runs on a powerful annotation engine developed at our lab called “Genome Annotator Lite”. Currently this database has 26 publicly available genomes and 10 EST datasets of oomycete organisms. The browser page has dynamic tracks presenting comparative genomics analyses, coding and non-coding data, tRNA genes, repeats and EST alignments. In addition, we have defined 44,777 core conserved proteins from twelve oomycete organisms that form 2974 clusters. Synteny viewing is enabled by incorporation of the Genome Synteny Viewer (GSV) tool. The user interface has undergone major changes for ease of browsing. Queryable comparative genomics information, conserved orthologous genes and pathways are among the new key features updated in this database. The browser has been upgraded to enable user upload of GFF files for quick view of genome annotation comparisons. The toolkit page integrates the EMBOSS package and has a gene prediction tool. Annotations for the organisms are updated once every six months to ensure quality. The database resource is available at www.eumicrobedb.org. This article is protected by copyright. All rights reserved.

Free-living marine nematodes are ubiquitous in marine benthic ecosystems and play a key role in ecosystem processes. However limited information exists to date on free-living marine nematode community structure and diversity from biodiversity-rich tropical coastal environments. In this study, molecular tools based on the amplification, clone library generation and sequencing of the nematode 18S rRNA marker were employed to study free-living marine nematode community structure from two sites located in the Central West coast of India. Results based on the sequencing of 110 clones showed dominance of Enoplid and Chromadorid-like nematode 18S rRNA sequences, in addition to Monhysterid and Desmodorid-like sequences across study sites. Ptycholaimellus and Tripyloides-like nematode 18S rRNA sequences were abundant in clone libraries from the study sites. Based on morpho-taxonomic analysis, nineteen free-living marine nematode taxa were identified from both the study sites. Many of the identified taxa such as Ptycholaimellus sp., Tripyloides sp., and Terschellingia longicaudata were also detected in clone library sequences indicating that there was congruency between molecular and morphological approaches. At the same time, a sizeable number of sequences showed identity scores of only 87–96 % with published marine nematode 18S rRNA sequences available in databases indicating that the study sites harbour unreported species of marine nematodes. This finding was also supported by the presence of novel sub-clades based on phylogeny and OTU analysis where a sizeable number of singletons were detected. This study highlights the importance of including 18S rRNA marine nematode sequences in published nucleotide databases targeted specifically from biodiversity-rich tropical coastal regions so that it can ultimately improve our understanding of marine nematode community structure and diversity patterns, population genetics and nematode systematics.

We have developed EumicrobeDBLite-a lightweight comprehensive genome resource and sequence analysis platform for oomycete organisms. EumicrobeDBLite is a successor of the VBI Microbial Database (VMD) that was built using the Genome Unified Schema (GUS). In this version, GUS has been greatly simplified with the removal of many obsolete modules and the redesign of others to incorporate contemporary data. Several dependences, such as perl object layers used for data loading in VMD, have been replaced with independent lightweight scripts. EumicrobeDBLite now runs on a powerful annotation engine developed at our laboratory, called 'Genome Annotator Lite'. Currently, this database has 26 publicly available genomes and 10 expressed sequence tag (EST) datasets of oomycete organisms. The browser page has dynamic tracks presenting comparative genomics analyses, coding and non-coding data, tRNA genes, repeats and EST alignments. In addition, we have defined 44 777 core conserved proteins from 12 oomycete organisms which form 2974 clusters. Synteny viewing is enabled by the incorporation of the Genome Synteny Viewer (GSV) tool. The user interface has undergone major changes for ease of browsing. Queryable comparative genomics information, conserved orthologous genes and pathways are among the new key features updated in this database. The browser has been upgraded to enable user upload of GFF files for quick view of genome annotation comparisons. The toolkit page integrates the EMBOSS package and has a gene prediction tool. Annotations for the organisms are updated once every 6 months to ensure quality. The database resource is available at www.eumicrobedb.org.

Plasmids of the incompatibility group IncP-1 can transfer and replicate in many genera of the Proteobacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental remediation. Although it is well understood that the accessory genes are transferred horizontally between plasmids, recent studies have also provided examples of recombination in the backbone genes of IncP-1 plasmids. As a consequence, phylogeny estimation based on backbone genes is expected to produce conflicting gene tree topologies. The main goal of this study was therefore to infer the evolutionary history of IncP-1 plasmids in the presence of both vertical and horizontal gene transfer. This was achieved by quantifying the incongruence among gene trees and attributing it to known causes such as 1) phylogenetic uncertainty, 2) coalescent stochasticity, and 3) horizontal inheritance. Topologies of gene trees exhibited more incongruence than could be attributed to phylogenetic uncertainty alone. Species-tree estimation using a Bayesian framework that takes coalescent stochasticity into account was well supported, but it differed slightly from the maximum-likelihood tree estimated by concatenation of backbone genes. After removal of the gene that demonstrated a signal of intergroup recombination, the concatenated tree was congruent with the species-tree estimate, which itself was robust to inclusion/exclusion of the recombinant gene. Thus, in spite of horizontal gene exchange both within and among IncP-1 subgroups, the backbone genome of these IncP-1 plasmids retains a detectable vertical evolutionary history.

Lyngbya confervoides strain BDU141951 is a fast-growing, unicellular, marine, nonheterocystous cyanobacterium forming long unbranched filaments inside sheaths. Here, we report the draft genome assembly of Lyngbya confervoides BDU141951 for the first time. The genome size is 8,799,693 bp and has 6,093 putative protein-coding genes assembled into 298 scaffolds.

We report here the draft genome sequence of Scytonema millei VB511283, a cyanobacterium isolated from biofilms on the exterior of stone monuments in Santiniketan, eastern India. The draft genome is 11,627,246 bp long (11.63 Mb), with 118 scaffolds. About 9,011 protein-coding genes, 117 tRNAs, and 12 rRNAs are predicted from this assembly.

The draft genome assembly of Hassallia byssoidea strain VB512170 with a genome size of ~13 Mb and 10,183 protein-coding genes in 62 scaffolds is reported here for the first time. This is a terrestrial hydrophobic cyanobacterium isolated from monuments in India. We report several copies of luciferase and antibiotic genes in this organism.

We report here the draft genome sequence of the filamentous nitrogen-fixing cyanobacterium Tolypothrix boutellei strain VB521301. The organism is lipid rich and hydrophobic and produces polyunsaturated fatty acids which can be harnessed for industrial purpose. The draft genome sequence assembled into 11,572,263 bp with 70 scaffolds and 7,777 protein coding genes.

Broad-host-range self-transferable plasmids are known to facilitate bacterial adaptation by spreading genes between phylogenetically distinct hosts. These plasmids typically have a conserved backbone region and a variable accessory region that encodes host-beneficial traits. We do not know, however, how well plasmids that do not encode accessory functions can survive in nature. The goal of this study was to characterize the backbone and accessory gene content of plasmids that were captured from freshwater sources without selecting for a particular phenotype or cultivating their host. To do this, triparental matings were used such that the only required phenotype was the plasmid's ability to mobilize a nonconjugative plasmid. Based on complete genome sequences of 10 plasmids, only 5 carried identifiable accessory gene regions, and none carried antibiotic resistance genes. The plasmids belong to four known incompatibility groups (IncN, IncP-1, IncU, and IncW) and two potentially new groups. Eight of the plasmids were shown to have a broad host range, being able to transfer into alpha-, beta-, and gammaproteobacteria. Because of the absence of antibiotic resistance genes, we resampled one of the sites and compared the proportion of captured plasmids that conferred antibiotic resistance to their hosts with the proportion of such plasmids captured from the effluent of a local wastewater treatment plant. Few of the captured plasmids from either site encoded antibiotic resistance. A high diversity of plasmids that encode no or unknown accessory functions is thus readily found in freshwater habitats. The question remains how the plasmids persist in these microbial communities.

Broad-host-range plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to antibiotics and heavy metals or degradation of pollutants. Although some broad-host-range plasmids have been extensively studied, their evolutionary history and genetic diversity remain largely unknown. The goal of this study was to analyze and compare the genomes of 12 broad-host-range plasmids that were previously isolated from Norwegian soils by exogenous plasmid isolation and that encode mercury resistance. Complete nucleotide sequencing followed by phylogenetic analyses based on the relaxase gene traI showed that all the plasmids belong to one of two subgroups (β and ε) of the well-studied incompatibility group IncP-1. A diverse array of accessory genes was found to be involved in resistance to antimicrobials (streptomycin, spectinomycin, and sulfonamides), degradation of herbicides (2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenoxypropionic acid), and a putative new catabolic pathway. Intramolecular transposition of insertion sequences followed by deletion was found to contribute to the diversity of some of these plasmids. The previous observation that the insertion sites of a Tn 501 -related element are identical in four IncP-1β plasmids (pJP4, pB10, R906, and R772) was further extended to three more IncP-1β plasmids (pAKD15, pAKD18, and pAKD29). We proposed a hypothesis for the evolution of these Tn 501 -bearing IncP-1β plasmids that predicts recent diversification followed by worldwide spread. Our study increases the available collection of complete IncP-1 plasmid genome sequences by 50% and will aid future studies to enhance our understanding of the evolution and function of this important plasmid family.

Plasmids of the incompatibility group IncP-1 are important agents of horizontal gene transfer and contribute to the spread of antibiotic resistance and xenobiotic degradation within bacterial communities. Even though some prototype plasmids have been studied in much detail, the diversity of this plasmid group was still greatly underestimated until recently, as only two of the five currently known divergent sub-groups had been described. To further improve our insight into the diversity and evolutionary history of this family of broad-host-range plasmids, we compared the complete nucleotide sequence of a new IncP-1delta plasmid pAKD4 to the genomes of other IncP-1 plasmids. Plasmid pAKD4 was previously isolated by exogenous plasmid isolation from an agricultural soil in Norway. Its 56,803bp nucleotide sequence shows high similarity in gene sequence and gene order to both plasmids pEST4011 and pIJB1, the only other IncP-1delta plasmids sequenced so far. While all three plasmids have a typical IncP-1 backbone comprising replication, transfer, and stable inheritance/control genes, the low sequence similarity in some regions and presence/absence of some backbone genes compared to other IncP-1 plasmids cluster them in a divergent sub-group. Therefore this study validates the presence of a real IncP-1delta clade with multiple plasmids. Moreover, since both pEST4011 and pIJB1 are missing a portion of their transfer genes, pAKD4 represents the first completely sequenced self-transferable plasmid with a complete IncP-1delta backbone. We therefore propose it to be the prototype IncP-1delta plasmid.