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 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.

scholarly journals Integrative analysis of histomorphology, transcriptome and whole genome resequencing identified DIO2 gene as a crucial gene for the protuberant knob located on forehead in geese

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yan Deng ◽  
Shenqiang Hu ◽  
Chenglong Luo ◽  
Qingyuan Ouyang ◽  
Li Li ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Protein Secondary Structure ◽  
Genomic Analysis ◽  
Production Performance ◽  
Genetic Mechanism ◽  
Farm Animals ◽  
Practical Significance ◽  
Genome Resequencing ◽  
Genomic Analyses ◽  
Whole Genome Resequencing

Abstract Background During domestication, remarkable changes in behavior, morphology, physiology and production performance have taken place in farm animals. As one of the most economically important poultry, goose owns a unique appearance characteristic called knob, which is located at the base of the upper bill. However, neither the histomorphology nor the genetic mechanism of the knob phenotype has been revealed in geese. Results In the present study, integrated radiographic, histological, transcriptomic and genomic analyses revealed the histomorphological characteristics and genetic mechanism of goose knob. The knob skin was developed, and radiographic results demonstrated that the knob bone was obviously protuberant and pneumatized. Histologically, there were major differences in structures in both the knob skin and bone between geese owing knob (namely knob-geese) and those devoid of knob (namely non-knob geese). Through transcriptome analysis, 592 and 952 genes differentially expressed in knob skin and bone, and significantly enriched in PPAR and Calcium pathways in knob skin and bone, respectively, which revealed the molecular mechanisms of histomorphological differences of the knob between knob- and non-knob geese. Furthermore, integrated transcriptomic and genomic analysis contributed to the identification of 17 and 21 candidate genes associated with the knob formation in the skin and bone, respectively. Of them, DIO2 gene could play a pivotal role in determining the knob phenotype in geese. Because a non-synonymous mutation (c.642,923 G > A, P265L) changed DIO2 protein secondary structure in knob geese, and Sanger sequencing further showed that the AA genotype was identified in the population of knob geese, and was prevalent in a crossing population which was artificially selected for 10 generations. Conclusions This study was the first to uncover the knob histomorphological characteristics and genetic mechanism in geese, and DIO2 was identified as the crucial gene associated with the knob phenotype. These data not only expand and enrich our knowledge on the molecular mechanisms underlying the formation of head appendages in both mammalian and avian species, but also have important theoretical and practical significance for goose breeding.

scholarly journals An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
João PL Castro ◽  
Michelle N Yancoskie ◽  
Marta Marchini ◽  
Stefanie Belohlavy ◽  
Layla Hiramatsu ◽  
...  
Keyword(s):  
Bone Growth ◽  
Rapid Evolution ◽  
Genomic Analysis ◽  
Selection Response ◽  
Major Effect ◽  
Selection Experiment ◽  
Genomic Analyses ◽  
Selection Experiments ◽  
Polygenic Adaptation ◽  
History Of

Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.

scholarly journals Chronology of terraces in the Rio Grande rift, Socorro basin, New Mexico: Implications for terrace formation

Geosphere ◽  
2020 ◽  
Vol 16 (6) ◽  
pp. 1457-1478
Author(s):  
Brad D. Sion ◽  
Fred M. Phillips ◽  
Gary J. Axen ◽  
J. Bruce J. Harrison ◽  
David W. Love ◽  
...  
Keyword(s):  
New Mexico ◽  
Late Quaternary ◽  
Rio Grande ◽  
New Age ◽  
Alluvial Fan ◽  
Rio Grande Rift ◽  
Arid Environments ◽  
Alluvial Deposits ◽  
Continental Scale ◽  
Geomorphic Surfaces

Abstract The Rio Grande rift hosts a remarkable record of Quaternary river incision preserved in an alluvial terrace sequence that has been studied for more than a century. However, our understanding of Rio Grande incision history in central New Mexico since the end of basin filling ca. 0.78 Ma remains hampered by poor age control. Robust correlations among Rio Grande terrace sequences in central and southern New Mexico are lacking, making it difficult to address important process-related questions about terrace formation in continental-scale river systems. We present new age controls using a combination of 40Ar/39Ar, 36Cl surface-exposure, and 14C dating techniques from alluvial deposits in the central New Mexico Socorro area to document the late Quaternary incision history of the Rio Grande. These new age controls (1) provide constraints to establish a firm foundation for Socorro basin terrace stratigraphy, (2) allow terrace correlations within the rift basin, and (3) enable testing of alternative models of terrace formation. We identified and mapped a high geomorphic surface interpreted to represent the end of basin filling in the Socorro area and five distinct, post–Santa Fe Group (ca. 0.78 Ma) alloformations and associated geomorphic surfaces using photogrammetric methods, soil characterization, and stratigraphic descriptions. Terrace deposits exhibit tread heights up to 70 m above the valley floor and are 5 to >30 m thick. Their fills generally have pebble-to-cobble bases overlain by fine-to-pebbly sand and local thin silt and clay tops. Alluvial-fan terraces and associated geomorphic surfaces grade to former valley levels defined by axial terrace treads. Carbon-14 ages from detrital charcoal above and below a buried tributary terrace tread show that the most recent aggradation event persisted until ca. 3 ka during the transition from glacial to modern climate conditions. Drill-log data show widespread valley fill ∼30 m thick that began aggrading after glacial retreat in northern New Mexico and southern Colorado (ca. 14 ka). Aggradation during this transition was likely due to hillslope destabilization, increased sediment yield, decreased runoff, and reduced stream competence. Chlorine-36 ages imply similar controls on earlier terraces that have surface ages of ca. 27–29, 64–70, and 135 ka, and suggest net incision during glacial expansions when increased runoff favored down-cutting and bedload mobilization. Our terrace chronology supports existing climate-response models of arid environments and links tributary responses to the axial Rio Grande system throughout the central Rio Grande rift. The terrace chronology also reflects a transition from modest (60 m/m.y.) to rapid (300 m/m.y.) incision between 610 and 135 ka, similar to patterns observed throughout the Rio Grande rift and the western United States in general.

scholarly journals Sequencing and Comparative Genomic Analysis of pK29, a 269-Kilobase Conjugative Plasmid Encoding CMY-8 and CTX-M-3 β-Lactamases in Klebsiella pneumoniae

2007 ◽  
Vol 51 (8) ◽  
pp. 3004-3007 ◽  
Author(s):  
Ying-Tsong Chen ◽  
Tsai-Ling Lauderdale ◽  
Tsai-Lien Liao ◽  
Yih-Ru Shiau ◽  
Hung-Yu Shu ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Conjugative Plasmid ◽  
Comparative Genomic ◽  
Antimicrobial Resistance Genes ◽  
Genomic Analyses ◽  
The Common

ABSTRACT A 269-kilobase conjugative plasmid, pK29, from a Klebsiella pneumoniae strain was sequenced. The plasmid harbors multiple antimicrobial resistance genes, including those encoding CMY-8 AmpC-type and CTX-M-3 extended-spectrum β-lactamases in the common backbone of IncHI2 plasmids. Mechanisms for dissemination of the resistance genes are highlighted in comparative genomic analyses.

scholarly journals Sterol and genomic analyses validate the sponge biomarker hypothesis

2016 ◽  
Vol 113 (10) ◽  
pp. 2684-2689 ◽  
Author(s):  
David A. Gold ◽  
Jonathan Grabenstatter ◽  
Alex de Mendoza ◽  
Ana Riesgo ◽  
Iñaki Ruiz-Trillo ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Duplication Event ◽  
Cambrian Explosion ◽  
Living Animal ◽  
Molecular Fossil ◽  
Molecular Fossils ◽  
Genomic Analyses ◽  
History Of ◽  
Salpingoeca Rosetta ◽  
Close Relatives

Molecular fossils (or biomarkers) are key to unraveling the deep history of eukaryotes, especially in the absence of traditional fossils. In this regard, the sterane 24-isopropylcholestane has been proposed as a molecular fossil for sponges, and could represent the oldest evidence for animal life. The sterane is found in rocks ∼650–540 million y old, and its sterol precursor (24-isopropylcholesterol, or 24-ipc) is synthesized today by certain sea sponges. However, 24-ipc is also produced in trace amounts by distantly related pelagophyte algae, whereas only a few close relatives of sponges have been assayed for sterols. In this study, we analyzed the sterol and gene repertoires of four taxa (Salpingoeca rosetta,Capsaspora owczarzaki,Sphaeroforma arctica, andCreolimax fragrantissima), which collectively represent the major living animal outgroups. We discovered that all four taxa lack C30sterols, including 24-ipc. By building phylogenetic trees for key enzymes in 24-ipc biosynthesis, we identified a candidate gene (carbon-24/28 sterol methyltransferase, orSMT) responsible for 24-ipc production. Our results suggest that pelagophytes and sponges independently evolved C30sterol biosynthesis through clade-specificSMTduplications. Using a molecular clock approach, we demonstrate that the relevant spongeSMTduplication event overlapped with the appearance of 24-isopropylcholestanes in the Neoproterozoic, but that the algalSMTduplication event occurred later in the Phanerozoic. Subsequently, pelagophyte algae and their relatives are an unlikely alternative to sponges as a source of Neoproterozoic 24-isopropylcholestanes, consistent with growing evidence that sponges evolved long before the Cambrian explosion ∼542 million y ago.

SUPPLEMENTAL POLLINATION – INCREASING OLIVE (OLEA EUROPAEA) YIELDS IN HOT, ARID ENVIRONMENTS

2004 ◽  
Vol 40 (4) ◽  
pp. 481-491 ◽  
Author(s):  
RICARDO AYERZA ◽  
WAYNE COATES
Keyword(s):  
Sonoran Desert ◽  
Olea Europaea ◽  
Fruit Set ◽  
Climatic Conditions ◽  
Arid Ecosystems ◽  
Arid Environments ◽  
Olive Trees ◽  
La Rioja ◽  
Supplemental Pollination ◽  
Arid Chaco

In general, olive trees are self-compatible, but under some climatic conditions a number of cultivars have demonstrated problems with pollination and fruit set. The Manzanillo cultivar is usually self-pollinating, but under hot conditions its pollen develops slowly, resulting in little or no fertilization. Trials were carried out in two hot, arid ecosystems (Arid Chaco in La Rioja, Argentina and Sonoran Desert in Arizona, USA) to determine if supplemental pollination of a Manzanillo cultivar has the potential to increase yields, and to assess the effectiveness of three different cultivars as sources of pollen. Branches that received supplemental pollination produced 21% more total olives than the control. In Arizona, total olive and shotberry (unpollinated olive) production were significantly different between treatments. Branches that received supplemental pollination produced 98% more olives, and had 58% fewer shotberries than did branches in the control rows. Significantly more olives were produced on branches pollinated with Sevillano and Arbequina pollen, compared with those pollinated with Ascolano pollen and with the control.

scholarly journals Searching for a “Hidden” Prophage in a Marine Bacterium

2009 ◽  
Vol 76 (2) ◽  
pp. 589-595 ◽  
Author(s):  
Yanlin Zhao ◽  
Kui Wang ◽  
Hans-Wolfgang Ackermann ◽  
Rolf U. Halden ◽  
Nianzhi Jiao ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Genomic Analysis ◽  
Bioinformatic Analysis ◽  
Open Reading Frames ◽  
Careful Examination ◽  
Comparative Genomic ◽  
Bacterial Genomes ◽  
Genomic Analyses ◽  
Experimental Laboratory ◽  
Bacterial Genes

ABSTRACT Prophages are common in many bacterial genomes. Distinguishing putatively viable prophages from nonviable sequences can be a challenge, since some prophages are remnants of once-functional prophages that have been rendered inactive by mutational changes. In some cases, a putative prophage may be missed due to the lack of recognizable prophage loci. The genome of a marine roseobacter, Roseovarius nubinhibens ISM (hereinafter referred to as ISM), was recently sequenced and was reported to contain no intact prophage based on customary bioinformatic analysis. However, prophage induction experiments performed with this organism led to a different conclusion. In the laboratory, virus-like particles in the ISM culture increased more than 3 orders of magnitude following induction with mitomycin C. After careful examination of the ISM genome sequence, a putative prophage (ISM-pro1) was identified. Although this prophage contains only minimal phage-like genes, we demonstrated that this “hidden” prophage is inducible. Genomic analysis and reannotation showed that most of the ISM-pro1 open reading frames (ORFs) display the highest sequence similarity with Rhodobacterales bacterial genes and some ORFs are only distantly related to genes of other known phages or prophages. Comparative genomic analyses indicated that ISM-pro1-like prophages or prophage remnants are also present in other Rhodobacterales genomes. In addition, the lysis of ISM by this previously unrecognized prophage appeared to increase the production of gene transfer agents (GTAs). Our study suggests that a combination of in silico genomic analyses and experimental laboratory work is needed to fully understand the lysogenic features of a given bacterium.

scholarly journals “Sifarchaeota” a novel Asgard phylum from Costa Rica sediment capable of polysaccharide degradation and anaerobic methylotrophy

2021 ◽  
Author(s):  
Ibrahim F. Farag ◽  
Rui Zhao ◽  
Jennifer F. Biddle
Keyword(s):  
Costa Rica ◽  
Marine Sediments ◽  
Genomic Analysis ◽  
Close Relation ◽  
Comparative Genomic ◽  
Niche Adaptation ◽  
Genomic Analyses ◽  
Ecological Roles ◽  
Costa Rica Margin ◽  
Metagenome Sequencing

The Asgard superphylum is a deeply branching monophyletic group of Archaea, recently described as some of the closest relatives of the eukaryotic ancestor. The wide application of genomic analyses from metagenome sequencing has established six distinct phyla, whose genomes encode for diverse metabolic capacities and play important biogeochemical and ecological roles in marine sediments. Here, we describe two metagenome-assembled genomes (MAGs) recovered from deep marine sediments off Costa Rica margin, defining a novel lineage phylogenetically married to Thorarchaeota, as such we propose the name “Sifarchaeota” for this phylum. The two “Sifarchaeota” MAGs encode for an anaerobic pathway for methylotrophy enabling the utilization of C1-C3 compounds (methanol and methylamines) to synthesize acetyl CoA. The MAGs showed a remarkable saccharolytic capabilities compared to other Asgard lineages and encoded for diverse classes of carbohydrate active enzymes (CAZymes) targeting different mono-, di- and oligosaccharides. Comparative genomic analysis based on the full metabolic profiles of different Asgard lineages revealed the close relation between “Sifarchaeota” and Odinarchaeota MAGs, which suggested similar metabolic potentials and ecological roles. Furthermore, we identified multiple HGT events from different bacterial donors within “Sifarchaetoa” MAGs, which hypothetically expanded “Sifarchaeota” capacities for substrate utilization, energy production and niche adaptation. Importance The exploration of deep marine sediments has unearthed many new lineages of microbes. The finding of this novel phylum of Asgard archaea is important since understanding the diversity and evolution of Asgard archaea may inform also about the evolution of eukaryotic cells. The comparison of metabolic potentials of the Asgard archaea can help inform about selective pressures the lineages have faced during evolution.

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