scholarly journals Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces

2021 ◽  
Vol 12 ◽  
Author(s):  
Yisong Li ◽  
Meng Wang ◽  
Zhong-Zhi Sun ◽  
Bin-Bin Xie
Keyword(s):  
Secondary Metabolism ◽  
Comparative Genomic ◽  
Metabolic Potential ◽  
Genomic Features ◽  
Separate Genus ◽  
The Family ◽  
Genomic Analyses ◽  
Genome Content ◽  
Phylogenomic Analyses ◽  
Close Relatives

While the genus Streptomyces (family Streptomycetaceae) has been studied as a model for bacterial secondary metabolism and genetics, its close relatives have been less studied. The genus Kitasatospora is the second largest genus in the family Streptomycetaceae. However, its taxonomic position within the family remains under debate and the secondary metabolic potential remains largely unclear. Here, we performed systematic comparative genomic and phylogenomic analyses of Kitasatospora. Firstly, the three genera within the family Streptomycetaceae (Kitasatospora, Streptomyces, and Streptacidiphilus) showed common genomic features, including high G + C contents, high secondary metabolic potentials, and high recombination frequencies. Secondly, phylogenomic and comparative genomic analyses revealed phylogenetic distinctions and genome content differences among these three genera, supporting Kitasatospora as a separate genus within the family. Lastly, the pan-genome analysis revealed extensive genetic diversity within the genus Kitasatospora, while functional annotation and genome content comparison suggested genomic differentiation among lineages. This study provided new insights into genomic characteristics of the genus Kitasatospora, and also uncovered its previously underestimated and complex secondary metabolism.

Complete plastid genome sequences of three tropical Alseodaphne trees in the family Lauraceae

Holzforschung ◽  
2018 ◽  
Vol 72 (4) ◽  
pp. 337-345 ◽  
Author(s):  
Yu Song ◽  
Xin Yao ◽  
Bing Liu ◽  
Yunhong Tan ◽  
Richard T. Corlett
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Comparative Genomic ◽  
Inverted Repeats ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Tropical Asia ◽  
Length Difference ◽  
The Family ◽  
Genomic Analyses

AbstractAlseodaphneis a genus of timber trees (ca. 40 spp.) belonging to thePerseagroup of the Lauraceae. It is widely distributed in tropical Asia, but is often confused withDehaasiaandNothaphoebe, and the systematics of the genus is unclear. Here, the complete chloroplast genome sequences ofA. semecarpifoliawill be reported, the type species ofAlseodaphne, and two China-endemic species,A. gracilisandA. huanglianshanensis. The three plastomes were 153 051 bp, 153 099 bp and 153 070 bp, respectively. Comparative genomic analyses indicate that the threeAlseodaphneplastomes have similar genome size and those are very different with previously published plastomes of Lauraceae in length. The length difference is directly caused by inverted repeats expansion/contraction. Four highly variable loci includingpsbD-trnM,ndhF-rpl32,rpl32-trnLandycf1among the threeAlseodaphnespecies were identified as useful plastid candidate barcodes forAlseodaphneand Lauraceae species. Phylogenetic analyses based on 12 complete plastomes of Lauraceae species confirm a monophyleticPerseagroup comprising species ofAlseodaphne,Phoebe,PerseaandMachilus.

scholarly journals Comparative genomics on cultivated and uncultivated, freshwater and marine Candidatus Manganitrophaceae species implies their worldwide reach in manganese chemolithoautotrophy

2021 ◽  
Author(s):  
Hang Yu ◽  
Grayson L Chadwick ◽  
Usha F Lingappa ◽  
Jared Renton Leadbetter
Keyword(s):  
South Africa ◽  
Carbon Fixation ◽  
Comparative Genomic ◽  
Santa Barbara ◽  
Manganese Oxidation ◽  
Species Phylogeny ◽  
Core Set ◽  
The Family ◽  
Genomic Analyses ◽  
A New Species

Chemolithoautotrophic manganese oxidation has long been theorized, but only recently demonstrated in a bacterial co-culture. The majority member of the co-culture, Candidatus Manganitrophus noduliformans, is a distinct but not yet isolated lineage in the phylum Nitrospirota (Nitrospirae). Here, we established two additional MnCO3-oxidizing cultures using inocula from Santa Barbara (USA) and Boetsap (South Africa). Both cultures were dominated by strains of a new species, designated Candidatus Manganitrophus morganii. The next abundant members differed in the available cultures, suggesting that while Ca. Manganitrophus species have not been isolated in pure culture, they may not require a specific syntrophic relationship with another species. Phylogeny of cultivated Ca. Manganitrophus and related metagenome-assembled genomes revealed a coherent taxonomic family, Candidatus Manganitrophaceae, from both freshwater and marine environments and distributed globally. Comparative genomic analyses support this family being Mn(II)-oxidizing chemolithoautotrophs. Among the 895 shared genes were a subset of those hypothesized for Mn(II) oxidation (Cyc2 and PCC_1) and oxygen reduction (TO_1 and TO_2) that could facilitate Mn(II) lithotrophy. An unusual, plausibly reverse Complex 1 containing 2 additional pumping subunits was also shared by the family, as were genes for the reverse TCA carbon fixation cycle, which could enable Mn(II) autotrophy. All members of the family lacked genes for nitrification found in Nitrospira species. The results suggest that Ca. Manganitrophaceae share a core set of candidate genes for the newly discovered manganese dependent chemolithoautotrophic lifestyle, and likely have a broad, global distribution.

scholarly journals Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov.

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3203-3215 ◽  
Author(s):  
Chantal Campbell ◽  
Mobolaji Adeolu ◽  
Radhey S. Gupta
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Core Protein ◽  
Phylogenetic Analyses ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Conserved Signature Indels ◽  
The Family ◽  
Genomic Analyses

The class Negativicutes is currently divided into one order and two families on the basis of 16S rRNA gene sequence phylogenies. We report here comprehensive comparative genomic analyses of the sequenced members of the class Negativicutes to demarcate its different evolutionary groups in molecular terms, independently of phylogenetic trees. Our comparative genomic analyses have identified 14 conserved signature indels (CSIs) and 48 conserved signature proteins (CSPs) that either are specific for the entire class or differentiate four main groups within the class. Two CSIs and nine CSPs are shared uniquely by all or most members of the class Negativicutes, distinguishing this class from all other sequenced members of the phylum Firmicutes. Four other CSIs and six CSPs were specific characteristics of the family Acidaminococcaceae, two CSIs and four CSPs were uniquely present in the family Veillonellaceae, six CSIs and eight CSPs were found only in Selenomonas and related genera, and 17 CSPs were identified uniquely in Sporomusa and related genera. Four additional CSPs support a pairing of the groups containing the genera Selenomonas and Sporomusa. We also report detailed phylogenetic analyses for the Negativicutes based on core protein sequences and 16S rRNA gene sequences, which strongly support the four main groups identified by CSIs and by CSPs. Based on the results from different lines of investigation, we propose a division of the class Negativicutes into an emended order Selenomonadales containing the new families Selenomonadaceae fam. nov. and Sporomusaceae fam. nov. and two new orders, Acidaminococcales ord. nov. and Veillonellales ord. nov., respectively containing the families Acidaminococcaceae and Veillonellaceae.

scholarly journals Comparison and Phylogenetic Analyses of Nine Complete Chloroplast Genomes of Zingibereae

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 710
Author(s):  
Heng Liang ◽  
Juan Chen
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Plastome Evolution ◽  
Chloroplast Genomes ◽  
The Family ◽  
Phylogenomic Analyses ◽  
Close Relatives ◽  
Rna Genes ◽  
Insight Into ◽  
Simple Sequence

Zingibereae is a large tribe in the family Zingiberaceae, which contains plants with important medicinal, edible, and ornamental values. Although tribes of Zingiberaceae are well circumscribed, the circumscription of many genera within Zingibereae and the relationships among them remain elusive, especially for the genera of Boesenbergia, Curcuma, Kaempferia and Pyrgophyllum. In this study, we investigated the plastome variation in nine species representing five genera of Zingibereae. All plastomes showed a typical quadripartite structure with lengths ranging from 162,042 bp to 163,539 bp and contained 132–134 genes, consisting of 86–88 coding genes, 38 transfer RNA genes and eight ribosomal RNA genes. Moreover, the characteristics of the long repeats sequences and simple sequence repeats (SSRs) were detected. In addition, we conducted phylogenomic analyses of the Zingibereae and related taxa with plastomes data from additional 32 species from Genbank. Our results confirmed that Stahlianthus is closely related to Curcuma, supporting the idea of merging it into Curcuma. Kaempferia, Boesenbergia and Zingiber were confirmed as close relatives and grouped together as the Kaempferia group. Pyrgophyllum is not allied with the Curcuma clade but instead is embedded within the Hedychium clade. Our results demonstrate the power of plastid phylogenomics in improving the phylogenetic relationships within Zingibereae and provide a new insight into plastome evolution in Zingibereceae.

scholarly journals Marseilleviruses: An Update in 2021

2021 ◽  
Vol 12 ◽  
Author(s):  
Dehia Sahmi-Bounsiar ◽  
Clara Rolland ◽  
Sarah Aherfi ◽  
Hadjer Boudjemaa ◽  
Anthony Levasseur ◽  
...  
Keyword(s):  
Deep Sea ◽  
Environmental Water ◽  
Comparative Genomic ◽  
Acanthamoeba Polyphaga ◽  
Deep Sea Sediment ◽  
Worldwide Distribution ◽  
The Family ◽  
Genomic Analyses ◽  
Giant Viruses ◽  
Rats And Mice

The family Marseilleviridae was the second family of giant viruses that was described in 2013, after the family Mimiviridae. Marseillevirus marseillevirus, isolated in 2007 by coculture on Acanthamoeba polyphaga, is the prototype member of this family. Afterward, the worldwide distribution of marseilleviruses was revealed through their isolation from samples of various types and sources. Thus, 62 were isolated from environmental water, one from soil, one from a dipteran, one from mussels, and two from asymptomatic humans, which led to the description of 67 marseillevirus isolates, including 21 by the IHU Méditerranée Infection in France. Recently, five marseillevirus genomes were assembled from deep sea sediment in Norway. Isolated marseilleviruses have ≈250 nm long icosahedral capsids and 348–404 kilobase long mosaic genomes that encode 386–545 predicted proteins. Comparative genomic analyses indicate that the family Marseilleviridae includes five lineages and possesses a pangenome composed of 3,082 clusters of genes. The detection of marseilleviruses in both symptomatic and asymptomatic humans in stool, blood, and lymph nodes, and an up-to-30-day persistence of marseillevirus in rats and mice, raise questions concerning their possible clinical significance that are still under investigation.

scholarly journals Genomic Analysis of Diverse Members of the Fungal Genus Monosporascus Reveals Novel Lineages, Unique Genome Content and a Potential Bacterial Associate

2020 ◽  
Vol 10 (8) ◽  
pp. 2573-2583 ◽  
Author(s):  
Aaron J. Robinson ◽  
Donald O. Natvig ◽  
Patrick S. G. Chain
Keyword(s):  
New Mexico ◽  
Genomic Analysis ◽  
Arid Ecosystems ◽  
Arid Environments ◽  
Culture Studies ◽  
Disease Symptoms ◽  
Class Differences ◽  
Genomic Analyses ◽  
Genome Content ◽  
Close Relatives

The genus Monosporascus represents an enigmatic group of fungi important in agriculture and widely distributed in natural arid ecosystems. Of the nine described species, two (M. cannonballus and M. eutypoides) are important pathogens on the roots of members of Cucurbitaceae in agricultural settings. The remaining seven species are capable of colonizing roots from a diverse host range without causing obvious disease symptoms. Recent molecular and culture studies have shown that members of the genus are nearly ubiquitous as root endophytes in arid environments of the Southwestern United States. Isolates have been obtained from apparently healthy roots of grasses, shrubs and herbaceous plants located in central New Mexico and other regions of the Southwest. Phylogenetic and genomic analyses reveal substantial diversity in these isolates. The New Mexico isolates include close relatives of M. cannonballus and M. ibericus, as well as isolates that represent previously unrecognized lineages. To explore evolutionary relationships within the genus and gain insights into potential ecological functions, we sequenced and assembled the genomes of three M. cannonballus isolates, one M. ibericus isolate, and six diverse New Mexico isolates. The assembled genomes were significantly larger than what is typical for the Sordariomycetes despite having predicted gene numbers similar to other members of the class. Differences in predicted genome content and organization were observed between endophytic and pathogenic lineages of Monosporascus. Several Monosporascus isolates appear to form associations with members of the bacterial genus Ralstonia (Burkholdariaceae).

scholarly journals Complete Nucleotide Sequence, Genome Organization, and Comparative Genomic Analyses of Citrus Yellow-Vein Associated Virus (CYVaV)

2021 ◽  
Vol 12 ◽  
Author(s):  
Sun-Jung Kwon ◽  
Sohrab Bodaghi ◽  
Tyler Dang ◽  
Kiran R. Gadhave ◽  
Thien Ho ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Open Reading Frames ◽  
Yellow Vein ◽  
Comparative Genomic ◽  
Rna Seq ◽  
Ribosomal Frameshifting ◽  
The Family ◽  
Genomic Analyses ◽  
Vein Disease ◽  
Reading Frames

Citrus yellow-vein disease (CYVD) was first reported in California in 1957. We now report that CYVD is associated with a virus-like agent, provisionally named citrus yellow-vein associated virus (CYVaV). The CYVaV RNA genome has 2,692 nucleotides and codes for two discernable open reading frames (ORFs). ORF1 encodes a protein of 190 amino acid (aa) whereas ORF2 is presumably generated by a −1 ribosomal frameshifting event just upstream of the ORF1 termination signal. The frameshift product (717 aa) encodes the RNA-dependent RNA polymerase (RdRp). Phylogenetic analyses suggest that CYVaV is closely related to unclassified virus-like RNAs in the family Tombusviridae. Bio-indexing and RNA-seq experiments indicate that CYVaV can induce yellow vein symptoms independently of known citrus viruses or viroids.

scholarly journals Assessing the Genomic Variability of Gardnerella vaginalis through Comparative Genomic Analyses: Evolutionary and Ecological Implications

2020 ◽  
Vol 87 (1) ◽  
Author(s):  
Chiara Tarracchini ◽  
Gabriele Andrea Lugli ◽  
Leonardo Mancabelli ◽  
Christian Milani ◽  
Francesca Turroni ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Human Population ◽  
Gardnerella Vaginalis ◽  
Comparative Genomic ◽  
Genetic Traits ◽  
Content Type ◽  
Microbial Taxon ◽  
Virulence Potential ◽  
Genomic Analyses ◽  
Phylogenomic Analyses

ABSTRACT Gardnerella vaginalis is described as a common anaerobic vaginal bacterium whose presence may correlate with vaginal dysbiotic conditions. In the current study, we performed phylogenomic analyses of 72 G. vaginalis genome sequences, revealing noteworthy genome differences underlying a polyphyletic organization of this taxon. Particularly, the genomic survey revealed that this species may actually include nine distinct genotypes (GGtype1 to GGtype9). Furthermore, the observed link between sialidase and phylogenomic grouping provided clues of a connection between virulence potential and the evolutionary history of this microbial taxon. Specifically, based on the outcomes of these in silico analyses, GGtype3, GGtype7, GGtype8, and GGtype9 appear to have virulence potential since they exhibited the sialidase gene in their genomes. Notably, the analysis of 34 publicly available vaginal metagenomic samples allowed us to trace the distribution of the nine G. vaginalis genotypes identified in this study among the human population, highlighting how differences in genetic makeup could be related to specific ecological properties. Furthermore, comparative genomic analyses provided details about the G. vaginalis pan- and core genome contents, including putative genetic elements involved in the adaptation to the ecological niche as well as many putative virulence factors. Among these putative virulence factors, particularly noteworthy genes identified were the gene encoding cholesterol-dependent cytolysin (CDC) toxin vaginolysin and genes related to microbial biofilm formation, iron uptake, adhesion to the vaginal epithelium, as well as macrolide antibiotic resistance. IMPORTANCE The identification of nine different genotypes among members of G. vaginalis allowed us to distinguish an uneven distribution of virulence-associated genetic traits within this taxon and thus suggest the potential occurrence of putative pathogen and commensal G. vaginalis strains. These findings, coupled with metagenomics microbial profiling of human vaginal microbiota, permitted us to get insights into the distribution of the genotypes among the human population, highlighting the presence of different structural communities in terms of G. vaginalis genotypes.

scholarly journals The saccharibacterium TM7x elicits differential responses across its host range

2020 ◽  
Vol 14 (12) ◽  
pp. 3054-3067 ◽  
Author(s):  
Daniel R. Utter ◽  
Xuesong He ◽  
Colleen M. Cavanaugh ◽  
Jeffrey S. McLean ◽  
Batbileg Bor
Keyword(s):  
Host Range ◽  
Growth Dynamics ◽  
Comparative Genomic ◽  
Bacterial Host ◽  
Genomic Features ◽  
Initial Infection ◽  
Symbiotic Interactions ◽  
Ideal System ◽  
Genomic Analyses ◽  
Crash Recovery

Abstract Host range is a fundamental component of symbiotic interactions, yet it remains poorly characterized for the prevalent yet enigmatic subcategory of bacteria/bacteria symbioses. The recently characterized obligate bacterial epibiont Candidatus Nanosynbacter lyticus TM7x with its bacterial host Actinomyces odontolyticus XH001 offers an ideal system to study such a novel relationship. In this study, the host range of TM7x was investigated by coculturing TM7x with various related Actinomyces strains and characterizing their growth dynamics from initial infection through subsequent co-passages. Of the twenty-seven tested Actinomyces, thirteen strains, including XH001, could host TM7x, and further classified into “permissive” and “nonpermissive” based on their varying initial responses to TM7x. Ten permissive strains exhibited growth/crash/recovery phases following TM7x infection, with crash timing and extent dependent on initial TM7x dosage. Meanwhile, three nonpermissive strains hosted TM7x without a growth-crash phase despite high TM7x dosage. The physical association of TM7x with all hosts, including nonpermissive strains, was confirmed by microscopy. Comparative genomic analyses revealed distinguishing genomic features between permissive and nonpermissive hosts. Our results expand the concept of host range beyond a binary to a wider spectrum, and the varying susceptibility of Actinomyces strains to TM7x underscores how small genetic differences between hosts can underly divergent selective trajectories.

scholarly journals The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Josué Barrera-Redondo ◽  
Guillermo Sánchez-de la Vega ◽  
Jonás A. Aguirre-Liguori ◽  
Gabriela Castellanos-Morales ◽  
Yocelyn T. Gutiérrez-Guerrero ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Population Level ◽  
Growth Hormones ◽  
Comparative Genomic ◽  
Structural Variants ◽  
Closely Related Species ◽  
Level Data ◽  
Genomic Analyses ◽  
Genotype By Sequencing ◽  
Regulation Of Growth

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

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