scholarly journals Orthology-Based Estimate of the Contribution of Horizontal Gene Transfer from Distantly Related Bacteria to the Intraspecific Diversity and Differentiation of Xylella fastidiosa

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 46
Author(s):  
Giuseppe Firrao ◽  
Marco Scortichini ◽  
Laura Pagliari
Keyword(s):  
Xylella Fastidiosa ◽  
Large Fraction ◽  
Environmental Dna ◽  
Intraspecific Diversity ◽  
Phylogenetic Position ◽  
Pan Genome ◽  
Genome Analyses ◽  
Taxonomic Groups ◽  
Xanthomonas Albilineans ◽  
Relevant Component

Xylella fastidiosa is a xylem-limited bacterium phylogenetically related to the xanthomonads, with an unusually large and diversified range of plant hosts. To ascertain the origin of its peculiarities, its pan-genome was scanned to identify the genes that are not coherent with its phylogenetic position within the order Xanthomonadales. The results of the analysis revealed that a large fraction of the genes of the Xylella pan-genome have no ortholog or close paralog in the order Xanthomonadales. For a significant part of the genes, the closest homologue was found in bacteria belonging to distantly related taxonomic groups, most frequently in the Betaproteobacteria. Other species, such as Xanthomonas vasicola and Xanthomonas albilineans which were investigated for comparison, did not show a similar genetic contribution from distant branches of the prokaryotic tree of life. This finding indicates that the process of acquisition of DNA from the environment is still a relevant component of Xylella fastidiosa evolution. Although the ability of Xylella fastidiosa strains to recombine among themselves is well known, the results of the pan-genome analyses stressed the additional relevance of environmental DNA in shaping their genomes, with potential consequences on their phytopathological features.

Biodiversity in the Andean Mountains: Two new rain frogs of the genus Pristimantis (Anura: Craugastoridae) from the northern Cordillera Central in Colombia

Zootaxa ◽  
2021 ◽  
Vol 5040 (3) ◽  
pp. 334-364
Author(s):  
MAURICIO RIVERA-CORREA ◽  
GUSTAVO A. GONZÁLEZ-DURÁN ◽  
ANA M. SALDARRIAGA-GÓMEZ ◽  
SEBASTIÁN DUARTE-MARÍN
Keyword(s):  
New Species ◽  
Species Delimitation ◽  
Intraspecific Diversity ◽  
Conservation Strategies ◽  
Phylogenetic Position ◽  
The Andes ◽  
Two New Species ◽  
Diversity Studies ◽  
First Time ◽  
Central Cordillera

Frequent biodiversity sampling and monitoring programs often lead to relevant taxonomic findings. Here, as a product of different field expeditions to two places in the northern Andes, we discover and describe two new species of rain frogs of the genus Pristimantis from the cloud forests of the Central Cordillera of Colombia. Pristimantis chocolatebari sp. nov. is diagnosed by having the following character states: dentigerous process of vomer triangular, snout large and protruding, dorsum smooth, vocal slits and vocal sac present, groin and hidden part of the thighs yellow. Pristimantis carylae sp. nov. is diagnosed by having iris copper red, dentigerous process of vomer oval, snout short and rounded, dorsum finely shagreen with scattered tubercles, double nuptial pad in males, groin and hidden part of thighs pink. We also infer, for the first time, the phylogenetic position of P. permixtus, P. platychilus, and two candidate new species. In addition, we emphasize not to use genetic distance as the only source of evidence for species delimitation, considering the high intraspecific diversity found in one of the species described here. Finally, we highlight the relevance of different habitat and ecosystem conservation strategies to promote amphibian diversity studies in the Andes.  

Past and recent biodiversity profiling in ancient Lake Chalco Mexico by a metagenomics analysis

2021 ◽  
Author(s):  
Bárbara Moguel ◽  
Liseth Pérez ◽  
Luis David Alcaraz ◽  
Socorro Lozano-García ◽  
Luis Herrera-Estrella ◽  
...  
Keyword(s):  
Volcanic Belt ◽  
Environmental Dna ◽  
Radiocarbon Dates ◽  
The Past ◽  
Mexican Volcanic Belt ◽  
History Of ◽  
High Throughput Dna Sequencing ◽  
High Altitude Lake ◽  
Taxonomic Groups ◽  
The Relationship

<p>For decades, paleoecological studies in lake sediments have focused on reconstructing the environments of the past and explaining phenomena linked to climatic variations. Recent advances in high-throughput DNA sequencing have allowed access to environmental DNA (eDNA) and ancient sedimentary DNA (sedaDNA) as a new and efficient proxy for past and present biodiversity. The basin of Mexico (BM) is located in the central part of the Trans-Mexican Volcanic Belt at 2,200 m a.s.l.; with the southern portion harboring the Chalco sub-basin. Lake Chalco is one of the last remaining natural aquatic ecosystems within the ever-expanding urban area surrounding Mexico City. The paleoenvironmental history of this lake has been previously characterized using sedimentological and geochemical proxies, as well as preserved microfossils (diatoms, pollen) with a temporal framework based on multiple radiocarbon dates. However, information for the remaining taxonomic groups and metabolic pathways remained unexplored. Here, we present the first metagenomics-based study for the Holocene in a high-altitude lake in Central Mexico –Lake Chalco. We explored the relationship between the lake’s paleoenvironmental condition and estimations of taxonomic and metabolic profiles across the sedimentary sequence (2.5 meters long). Multiple biological and abiotic variables revealed three main environmental phases: 1) a cool freshwater lake (FW1: 11,500-11,000 cal years BP), 2) a warm hyposaline lake (HS2: 11,000-6,000 cal years BP), and 3) a temperate, subsaline lake (SS3, <6,000 cal years BP). We describe the structure of the microbiota community and taxonomy richness turnover in the three Holocene paleoenvironmental phases. During the past 12 000 years BP the most abundant domains in Lake Chalco sediments were Bacteria, followed by Archaea, and Eukarya (36,722 genera). The analysis of functional proteins showed high biodiversity with a total of 27,636,243 proteins identified, but it was only possible to annotate 3,227,398 of them. Also, we identified several genes associated with some relevant pathways, such as methanogenesis. Altogether, this study allowed us to reconstruct the natural history of lake Chalco and its surroundings.</p>

scholarly journals Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

NeoBiota ◽  
2021 ◽  
Vol 70 ◽  
pp. 151-165
Author(s):  
Francesco Zangaro ◽  
Benedetta Saccomanno ◽  
Eftychia Tzafesta ◽  
Fabio Bozzeda ◽  
Valeria Specchia ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Special Focus ◽  
Indigenous Species ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
The Mediterranean ◽  
Taxonomic Groups ◽  
Non Indigenous Species

The biodiversity of the Mediterranean Sea is currently threatened by the introduction of Non-Indigenous Species (NIS). Therefore, monitoring the distribution of NIS is of utmost importance to preserve the ecosystems. A promising approach for the identification of species and the assessment of biodiversity is the use of DNA barcoding, as well as DNA and eDNA metabarcoding. Currently, the main limitation in the use of genomic data for species identification is the incompleteness of the DNA barcode databases. In this research, we assessed the availability of DNA barcodes in the main reference libraries for the most updated inventory of 665 confirmed NIS in the Mediterranean Sea, with a special focus on the cytochrome oxidase I (COI) barcode and primers. The results of this study show that there are no barcodes for 33.18% of the species in question, and that 45.30% of the 382 species with COI barcode, have no primers publicly available. This highlights the importance of directing scientific efforts to fill the barcode gap of specific taxonomic groups in order to help in the effective application of the eDNA technique for investigating the occurrence and the distribution of NIS in the Mediterranean Sea.

scholarly journals Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits

mSystems ◽  
2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Daniel Castillo ◽  
Paul D. Alvise ◽  
Ruiqi Xu ◽  
Faxing Zhang ◽  
Mathias Middelboe ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Bacterial Species ◽  
Vibrio Anguillarum ◽  
Genomic Diversity ◽  
Comparative Genome ◽  
Accessory Genome ◽  
Pan Genome ◽  
Virulent Strains ◽  
Genome Analyses ◽  
Unique Core

ABSTRACT Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes. Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whole-genome sequences of a collection of V. anguillarum strains and compared them to virulence of the strains as determined in larval challenge assays. Previously identified virulence factors were globally distributed among the strains, with some genetic diversity. However, the pan-genome revealed that six out of nine high-virulence strains possessed a unique accessory genome that was attributed to pathogenic genomic islands, prophage-like elements, virulence factors, and a new set of gene clusters involved in biosynthesis, modification, and transport of polysaccharides. In contrast, V. anguillarum strains that were medium to nonvirulent had a high degree of genomic homogeneity. Finally, we found that a phylogeny based on the core genomes clustered the strains with moderate to no virulence, while six out of nine high-virulence strains represented phylogenetically separate clusters. Hence, we suggest a link between genotype and virulence characteristics of Vibrio anguillarum, which can be used to unravel the molecular evolution of V. anguillarum and can also be important from survey and diagnostic perspectives. IMPORTANCE Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes.

scholarly journals Pan-genome Analyses of 3 Strains of Inonotus obliquus and Prediction of Polysaccharide and Terpenoid Genes

2021 ◽  
Vol 16 (11) ◽  
pp. 1934578X2110609
Author(s):  
Xiaofan Guo ◽  
Shouming Wang
Keyword(s):  
Genome Sequencing ◽  
Molecular Level ◽  
Gene Families ◽  
Core Gene ◽  
Accessory Gene ◽  
Bioactive Substances ◽  
Inonotus Obliquus ◽  
Pan Genome ◽  
Medicinal Fungus ◽  
Genome Analyses

Inonotus obliquus is a rare, edible and medicinal fungus that is widely used as a remedy for various diseases. Its main bioactive substances are polysaccharides and terpenoids. In this study, we characterized and investigated the pan-genome of three strains of I. obliquus. The genome sizes of JL01, HE, and NBRC8681 were 32.04, 29.04, and 31.78 Mb, respectively. There were 6 543 core gene families and 6 197 accessory gene families among the three strains, with 14 polysaccharide-related core gene families and seven accessory gene families. For terpenoids, there were 13 core gene families and 17 accessory gene families. Pan-genome sequencing of I. obliquus has improved our understanding of biological characteristics related to the biosynthesis of polysaccharides and terpenoids at the molecular level, which in turn will enable us to increase the production of polysaccharides and terpenoids by this mushroom.

scholarly journals Species detections in environmental DNA using metabarcoding: a useful tool in estuaries monitoring

2015 ◽  
Author(s):  
Adrián Mártinez-Marqués ◽  
Carlos Enrique Carleos ◽  
Eva García-Vazquez ◽  
Yaisel J. Borrell Pichs
Keyword(s):  
Dna Analysis ◽  
Anthropogenic Activities ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Coi Gene ◽  
Universal Primers ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Cantabrian Coast ◽  
Taxonomic Groups

Estuaries are amongst the most productive habitats in Earth, producing more organic materia than forests, meadows or agricultural lands. In addition, estuaries exhibit high, and precious, biodiversity levels. In this study an environmental DNA analysis of the two most important estuaries in Asturias (Cantabrian Coast, north Iberia) in terms of food production (Ría del Eo and Ría de Villaviciosa) was carried out. The objective was to monitor aquatic biodiversity and also to detect alien species that can be associated with anthropogenic activities (e.g.: aquaculture). To achieve these objectives, a metabarcoding methodology based in NGS (next generation sequencing) and the mitochondrial COI gene as a DNA Barcode was used. Results showed that this methodology was useful to detect the presence of three different non-native genera (Crepidula, Lymnaea, Macrobrachium) that are probably parasitating species cultured in these estuaries. It is true that Metabarcoding has still unsolved problems such as the lack of 100% universal primers and paucity of referenced sequences for some taxonomic groups in the databases. However, it represents already a powerful tool to manage the resources of these important ecosystems and to guarantee their long-term sustainailibity.

scholarly journals Spatio-temporal patterns of multi-trophic biodiversity and food-web characteristics across a river catchment

2021 ◽  
Author(s):  
Rosetta C Blackman ◽  
Hsi-Cheng Ho ◽  
Jean-Claude Walser ◽  
Florian Altermatt
Keyword(s):  
Food Web ◽  
Environmental Dna ◽  
Ecological Communities ◽  
Food Web Structure ◽  
Spatial And Temporal Scales ◽  
Natural Systems ◽  
Α Diversity ◽  
Link Density ◽  
Spatio Temporal ◽  
Taxonomic Groups

Accurate characterisation of ecological communities with respect to their biodiversity and food-web structure is essential for conservation. However, combined empirical study of biodiversity and multi-trophic food webs at a large spatial and temporal resolution has been prohibited by the lack of appropriate access to such data from natural systems. Here, we assessed biodiversity and food-web characteristics across a 700 km2 riverine network through time using environmental DNA. We find contrasting biodiversity patterns, with richness (α-diversity) of fish increasing towards downstream positions within the catchment, while freshwater bacteria and invertebrates having an invariant and minimal decrease in richness, respectively, with downstream position. Food-web characteristics, such as link density and nestedness, however, were relatively conserved across space, but varied over season. Patterns of biodiversity across major taxonomic groups are thus not directly scalable to food-web structures at the same spatial and temporal scales, indicating that effective conservation measures must consider them jointly.

scholarly journals Secondary metabolite biosynthetic diversity in Arctic Ocean metagenomes

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Adriana Rego ◽  
Antonio Fernandez-Guerra ◽  
Pedro Duarte ◽  
Philipp Assmy ◽  
Pedro N. Leão ◽  
...  
Keyword(s):  
Heterologous Expression ◽  
Arctic Ocean ◽  
High Throughput Sequencing ◽  
Large Fraction ◽  
Environmental Dna ◽  
Gene Clusters ◽  
Biosynthetic Gene Clusters ◽  
Bacterial Isolation ◽  
Biosynthetic Genes ◽  
Peptide Synthetases

Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are mega enzymes responsible for the biosynthesis of a large fraction of natural products (NPs). Molecular markers for biosynthetic genes, such as the ketosynthase (KS) domain of PKSs, have been used to assess the diversity and distribution of biosynthetic genes in complex microbial communities. More recently, metagenomic studies have complemented and enhanced this approach by allowing the recovery of complete biosynthetic gene clusters (BGCs) from environmental DNA. In this study, the distribution and diversity of biosynthetic genes and clusters from Arctic Ocean samples (NICE-2015 expedition), was assessed using PCR-based strategies coupled with high-throughput sequencing and metagenomic analysis. In total, 149 KS domain OTU sequences were recovered, 36 % of which could not be assigned to any known BGC. In addition, 74 bacterial metagenome-assembled genomes were recovered, from which 179 BGCs were extracted. A network analysis identified potential new NP families, including non-ribosomal peptides and polyketides. Complete or near-complete BGCs were recovered, which will enable future heterologous expression efforts to uncover the respective NPs. Our study represents the first report of biosynthetic diversity assessed for Arctic Ocean metagenomes and highlights the potential of Arctic Ocean planktonic microbiomes for the discovery of novel secondary metabolites. The strategy employed in this study will enable future bioprospection, by identifying promising samples for bacterial isolation efforts, while providing also full-length BGCs for heterologous expression.

scholarly journals Molecular and Chromosomal Markers for Evolutionary Considerations in Torpediniformes (Chondrichthyes, Batoidea)

ISRN Genetics ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Lucia Rocco
Keyword(s):  
Genomic Organization ◽  
Cartilaginous Fish ◽  
Phylogenetic Position ◽  
Repeated Dna ◽  
Characteristic Distribution ◽  
Molecular Approaches ◽  
Chromosomal Markers ◽  
Taxonomic Groups ◽  
Basal Position ◽  
Specific Nucleotide

Due to their basal position in the vertebrate phylogenetic tree, the study on elasmobranch genetics and cytogenetics can provide remarkable information on the mechanisms underlying the evolution of all vertebrates. In recent years, different molecular approaches have been used to study the relationships between the different taxonomic groups of cartilaginous fish, among them are the physical mapping of specific nucleotide sequences on chromosomes. However, these are controversial, particularly in Torpediniformes in which the species have different karyological parameters. The purpose of this paper is to gather the molecular markers so far present in literature that were used to reconstruct the phylogenetic position of Torpediniformes with respect to the other Batoidea and to discriminate between the various chromosome pairs in the endemic species in the Mediterranean Sea, Torpedo torpedo, T. marmorata and T. nobiliana. The 5S and 18S ribosomal DNA, the HpaI and Alu SINE, the telomeric (TTAGGG)n and the spermatogenesis-related SPATA 16, SPATA 18, and UTY sequences were particularly useful. These last genomic segments were also able to differentiate between the male and the female karyotypes. Moreover, the torpedoes showed a particular genomic organization, especially Torpedo torpedo, in which large quantities of highly repeated DNA and a characteristic distribution of heterochromatin, which is never centromeric, were observed.

scholarly journals Prediction of Host-Specific Genes by Pan-Genome Analyses of the Korean Ralstonia solanacearum Species Complex

2019 ◽  
Vol 10 ◽  
Author(s):  
Heejung Cho ◽  
Eun-Sung Song ◽  
Sunggi Heu ◽  
JeongHo Baek ◽  
Young Kee Lee ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
Species Complex ◽  
Pan Genome ◽  
Genome Analyses
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