Two New Aspergillus flavus Reference Genomes Reveal a Large Insertion Potentially Contributing to Isolate Stress Tolerance and Aflatoxin Production

Efforts in genome sequencing in the Aspergillus genus have led to the development of quality reference genomes for several important species including A. nidulans, A. fumigatus, and A. oryzae. However, less progress has been made for A. flavus. As part of the effort of the USDA-ARS Annual Aflatoxin Workshop Fungal Genome Project, the isolate NRRL3357 was sequenced and resulted in a scaffold-level genome released in 2005. Our goal has been biologically driven, focusing on two areas: isolate variation in aflatoxin production and drought stress exacerbating aflatoxin production by A. flavus. Therefore, we developed two reference pseudomolecule genome assemblies derived from chromosome arms for two isolates: AF13, a MAT1-2, highly stress tolerant, and highly aflatoxigenic isolate; and NRRL3357, a MAT1-1, less stress tolerant, and moderate aflatoxin producer in comparison to AF13. Here, we report these two reference-grade assemblies for these isolates through a combination of PacBio long-read sequencing and optical mapping, and coupled them with comparative, functional, and phylogenetic analyses. This analysis resulted in the identification of 153 and 45 unique genes in AF13 and NRRL3357, respectively. We also confirmed the presence of a unique 310 Kb insertion in AF13 containing 60 genes. Analysis of this insertion revealed the presence of a bZIP transcription factor, named atfC, which may contribute to isolate pathogenicity and stress tolerance. Phylogenomic analyses comparing these and other available assemblies also suggest that the species complex of A. flavus is polyphyletic.

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Molecular analysis of the mitochondrial markers COI, 12S rDNA and 16S rDNA for six species of Iranian scorpions

BMC Research Notes ◽

10.1186/s13104-021-05449-3 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Parisa Soltan-Alinejad ◽

Javad Rafinejad ◽

Farrokh Dabiri ◽

Piero Onorati ◽

Olle Terenius ◽

...

Keyword(s):

16S Rdna ◽

Phylogenetic Analyses ◽

Coi Gene ◽

Diagnostic Tools ◽

Morphological Identification ◽

Species Determination ◽

Important Species ◽

Mitochondrial Markers ◽

12S Rdna ◽

Rdna Sequences

Abstract Objectives Annually, 1.2 million humans are stung by scorpions and severely affected by their venom. Some of the scorpion species of medical importance have a similar morphology to species with low toxicity. To establish diagnostic tools for surveying scorpions, the current study was conducted to generate three mitochondrial markers, Cytochrome Oxidase I (COI gene), 12S rDNA and 16S rDNA for six species of medically important Iranian scorpions: Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus, M. eupeus, Odontobuthus doriae, and Scorpio maurus. Results Phylogenetic analyses of the obtained sequences corroborated the morphological identification. For the first time, 12S rDNA sequences are reported from Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus and M. eupeus and also the 16S rDNA sequence from Hottentotta saulcyi. We conclude that the mitochondrial markers are useful for species determination among these medically important species of scorpions.

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Evidence of two deeply divergent co-existing mitochondrial genomes in the Tuatara reveals an extremely complex genomic organization

Communications Biology ◽

10.1038/s42003-020-01639-0 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

J. Robert Macey ◽

Stephan Pabinger ◽

Charles G. Barbieri ◽

Ella S. Buring ◽

Vanessa L. Gonzalez ◽

...

Keyword(s):

Genomic Organization ◽

Phylogenetic Analyses ◽

Genomic Polymorphism ◽

Sequencing Technologies ◽

Cold Tolerant ◽

Long Read ◽

Sphenodon Punctatus ◽

Nucleotide Divergence ◽

Mitochondrial Heteroplasmy ◽

Transmembrane Regions

AbstractAnimal mitochondrial genomic polymorphism occurs as low-level mitochondrial heteroplasmy and deeply divergent co-existing molecules. The latter is rare, known only in bivalvian mollusks. Here we show two deeply divergent co-existing mt-genomes in a vertebrate through genomic sequencing of the Tuatara (Sphenodon punctatus), the sole-representative of an ancient reptilian Order. The two molecules, revealed using a combination of short-read and long-read sequencing technologies, differ by 10.4% nucleotide divergence. A single long-read covers an entire mt-molecule for both strands. Phylogenetic analyses suggest a 7–8 million-year divergence between genomes. Contrary to earlier reports, all 37 genes typical of animal mitochondria, with drastic gene rearrangements, are confirmed for both mt-genomes. Also unique to vertebrates, concerted evolution drives three near-identical putative Control Region non-coding blocks. Evidence of positive selection at sites linked to metabolically important transmembrane regions of encoded proteins suggests these two mt-genomes may confer an adaptive advantage for an unusually cold-tolerant reptile.

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A New Paralog Removal Pipeline Resolves Conflict between RAD-seq and Enrichment

10.1101/2020.10.26.355248 ◽

2020 ◽

Author(s):

Wenbin Zhou ◽

John Soghigian ◽

Qiu-yun (Jenny) Xiang

Keyword(s):

High Throughput Sequencing ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Disjunct Distribution ◽

Divergence Times ◽

Target Enrichment ◽

Sequencing Technologies ◽

Duplication Events ◽

The Witch ◽

Phylogenomic Analyses

ABSTRACTTarget enrichment and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for phylogenomic studies, and the choice between methods is a practical issue for plant systematists studying the evolutionary histories of biodiversity of relatively recent origins. However, few studies have compared the congruence and conflict between results from the two methods within the same group of organisms, especially in plants, where extensive genome duplication events may complicate phylogenomic analyses. Unfortunately, currently widely used pipelines for target enrichment data analysis do not have a vigorous procedure for remove paralogs in Hyb-Seq data. In this study, we employed RAD-seq and Hyb-Seq of Angiosperm 353 genes in phylogenomic and biogeographic studies of Hamamelis (the witch-hazels) and Castanea (chestnuts), two classic examples exhibiting the well-known eastern Asian-eastern North American disjunct distribution. We compared these two methods side by side and developed a new pipeline (PPD) with a more vigorous removal of putative paralogs from Hyb-Seq data. The new pipeline considers both sequence similarity and heterozygous sites at each locus in identification of paralogous. We used our pipeline to construct robust datasets for comparison between methods and downstream analyses on the two genera. Our results demonstrated that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed significant differences between data from HybPiper and data from our new PPD pipeline, likely due to the error signals from the paralogous genes undetected by HybPiper, but trimmed by PPD. We found that phylogenies and divergence times estimated from our RAD-seq and Hyb-Seq-PPD were largely congruent. We highlight the importance of removal paralogs in enrichment data, and discuss the merits of RAD-seq and Hyb-Seq. Finally, phylogenetic analyses of RAD-seq and Hyb-Seq resulted in well-resolved species relationships, and revealed ancient introgression in both genera. Biogeographic analyses including fossil data revealed a complicated history of each genus involving multiple intercontinental dispersals and local extinctions in areas outside of the taxa’s modern ranges in both the Paleogene and Neogene. Our study demonstrates the value of additional steps for filtering paralogous gene content from Angiosperm 353 data, such as our new PPD pipeline described in this study. [RAD-seq, Hyb-Seq, paralogs, Castanea, Hamamelis, eastern Asia-eastern North America disjunction, biogeography, ancient introgression]

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Reference genome assemblies reveal the origin and evolution of allohexaploid oat

10.21203/rs.3.rs-664692/v1 ◽

2021 ◽

Author(s):

Yuanying Peng ◽

Honghai Yan ◽

Laichun Guo ◽

Cao Deng ◽

Lipeng Kang ◽

...

Keyword(s):

Large Scale ◽

Molecular Mechanisms ◽

Higher Plants ◽

Cereal Crops ◽

Origin And Evolution ◽

Avena Species ◽

Oxford Nanopore ◽

Reference Quality ◽

Phylogenomic Analyses ◽

Reference Genomes

Abstract Common oat (Avena sativa) is one of the most important cereal crops serving as a valuable source of forage and human food. While reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich, polyploid genome. By using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated the first reference-quality genome assembly of hulless common oat with a contig N50 of 93 Mb. We also assembled the genomes of diploid and tetraploid Avena ancestors, which enabled us to identify oat subgenome, large-scale structural rearrangements, and preferential gene loss in the C subgenome after hexaploidization. Phylogenomic analyses of cereal crops indicated that the oat lineage descended before wheat, offering oat as a unique window into the early evolution of polyploid plants. The origin and evolution of hexaploid oat is deduced from whole-genome sequencing, plastid genome and transcriptomes assemblies of numerous Avena species. The high-quality reference genomes of Avena species with different ploidies and the studies of their polyploidization history will facilitate the full use of crop gene resources and provide a reference for the molecular mechanisms underlying the polyploidization of higher plants, helping us to overcome food security challenges.

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LEA Proteins and the Evolution of the WHy Domain

Applied and Environmental Microbiology ◽

10.1128/aem.00539-18 ◽

2018 ◽

Vol 84 (15) ◽

Cited By ~ 12

Author(s):

Jasmin Mertens ◽

Habibu Aliyu ◽

Don A. Cowan

Keyword(s):

Stress Tolerance ◽

Protein Denaturation ◽

Phylogenetic Analyses ◽

Late Embryogenesis Abundant ◽

Abiotic Stress Response ◽

Lea Proteins ◽

Protective Function ◽

Content Type ◽

Reading Frame

ABSTRACT The late embryogenesis abundant (LEA) family is composed of a diverse collection of multidomain and multifunctional proteins found in all three domains of the tree of life, but they are particularly common in plants. Most members of the family are known to play an important role in abiotic stress response and stress tolerance in plants but are also part of the plant hypersensitive response to pathogen infection. The mechanistic basis for LEA protein functionality is still poorly understood. The group of LEA 2 proteins harbor one or more copies of a unique domain, the water stress and hypersensitive response (WHy) domain. This domain sequence has recently been identified as a unique open reading frame (ORF) in some bacterial genomes (mostly in the phylum Firmicutes), and the recombinant bacterial WHy protein has been shown to exhibit a stress tolerance phenotype in Escherichia coli and an in vitro protein denaturation protective function. Multidomain phylogenetic analyses suggest that the WHy protein gene sequence may have ancestral origins in the domain Archaea, with subsequent acquisition in Bacteria and eukaryotes via endosymbiont or horizontal gene transfer mechanisms. Here, we review the structure, function, and nomenclature of LEA proteins, with a focus on the WHy domain as an integral component of the LEA constructs and as an independent protein.

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Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae)

Plants ◽

10.3390/plants9091143 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1143 ◽

Cited By ~ 1

Author(s):

Hang Ran ◽

Yanyan Liu ◽

Cui Wu ◽

Yanan Cao

Keyword(s):

Genomic Structure ◽

Phylogenetic Analyses ◽

Sister Relationship ◽

Plastome Evolution ◽

Chloroplast Genomes ◽

Flora Of China ◽

Phylogenetic Resolution ◽

Sister Relationships ◽

Phylogenomic Analyses ◽

Cp Genome

Phylogenetic analyses of complete chloroplast genome sequences have yielded significant improvements in our understanding of relationships in the woody flowering genus Viburnum (Adoxaceae, Dipsacales); however, these relationships were evaluated focusing only on Viburnum species within Central and South America and Southeast Asia. By contrast, despite being a hotspot of Viburnum diversity, phylogenetic relationships of Viburnum species in China are less well known. Here, we characterized the complete chloroplast (cp) genomes of 21 Viburnum species endemic to China, as well as three Sambucus species. These 24 plastomes were highly conserved in genomic structure, gene order and content, also when compared with other Adoxaceae. The identified repeat sequences, simple sequence repeats (SSRs) and highly variable plastid regions will provide potentially valuable genetic resources for further population genetics and phylogeographic studies on Viburnum and Sambucus. Consistent with previous combined phylogenetic analyses of 113 Viburnum species, our phylogenomic analyses based on the complete cp genome sequence dataset confirmed the sister relationship between Viburnum and the Sambucus-Adoxa-Tetradoxa-Sinadoxa group, the monophyly of four recognized sections in Flora of China (i.e., Viburnum sect. Tinus, Viburnum sect. Solenotinus, Viburnum sect. Viburnum and Viburnum sect. Pseudotinus) and the nonmonophyly of Viburnum sect. Odontotinus and Viburnum sect. Megalotinus. Additionally, our study confirmed the sister relationships between the clade Valvatotinus and Viburnum sect. Pseudotinus, as well as between Viburnum sect. Opulus and the Odontotinus-Megalotinus group. Overall, our results clearly document the power of the complete cp genomes in improving phylogenetic resolution, and will contribute to a better understanding of plastome evolution in Chinese Adoxaceae.

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Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process

DNA Research ◽

10.1093/dnares/dsaa014 ◽

2020 ◽

Vol 27 (3) ◽

Cited By ~ 1

Author(s):

Rei Kajitani ◽

Dai Yoshimura ◽

Yoshitoshi Ogura ◽

Yasuhiro Gotoh ◽

Tetsuya Hayashi ◽

...

Keyword(s):

High Resolution ◽

Large Scale ◽

De Novo ◽

Bacterial Genomes ◽

Long Reads ◽

Wide Range ◽

Long Read ◽

Phylogenomic Analyses ◽

Error Removal ◽

Iterative Error

Abstract De novo assembly of short DNA reads remains an essential technology, especially for large-scale projects and high-resolution variant analyses in epidemiology. However, the existing tools often lack sufficient accuracy required to compare closely related strains. To facilitate such studies on bacterial genomes, we developed Platanus_B, a de novo assembler that employs iterations of multiple error-removal algorithms. The benchmarks demonstrated the superior accuracy and high contiguity of Platanus_B, in addition to its ability to enhance the hybrid assembly of both short and nanopore long reads. Although the hybrid strategies for short and long reads were effective in achieving near full-length genomes, we found that short-read-only assemblies generated with Platanus_B were sufficient to obtain ≥90% of exact coding sequences in most cases. In addition, while nanopore long-read-only assemblies lacked fine-scale accuracies, inclusion of short reads was effective in improving the accuracies. Platanus_B can, therefore, be used for comprehensive genomic surveillances of bacterial pathogens and high-resolution phylogenomic analyses of a wide range of bacteria.

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Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs

Applied and Environmental Microbiology ◽

10.1128/aem.02852-15 ◽

2015 ◽

Vol 82 (4) ◽

pp. 1215-1226 ◽

Cited By ~ 14

Author(s):

Francy Jimenez-Infante ◽

David Kamanda Ngugi ◽

Manikandan Vinu ◽

Intikhab Alam ◽

Allan Anthony Kamau ◽

...

Keyword(s):

Red Sea ◽

Novel Species ◽

Phylogenetic Analyses ◽

Niche Differentiation ◽

Content Type ◽

Nadh:Quinone Oxidoreductase ◽

Distinct Cluster ◽

The Family ◽

Phylogenomic Analyses ◽

Cultivation Techniques

ABSTRACTThe OM43 clade within the familyMethylophilaceaeofBetaproteobacteriarepresents a group of methylotrophs that play important roles in the metabolism of C1compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields.

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Analyses of separate and concatenated cox1 and 18S rRNA gene sequences indicate that the bat piroplasm Babesia vesperuginis is phylogenetically close to Cytauxzoon felis and the ‘prototheilerid’ Babesia conradae

Acta Veterinaria Hungarica ◽

10.1556/004.2018.010 ◽

2018 ◽

Vol 66 (1) ◽

pp. 107-115 ◽

Cited By ~ 4

Author(s):

Sándor Hornok ◽

Alexandra Corduneanu ◽

Jenő Kontschán ◽

Katinka Bekő ◽

Krisztina Szőke ◽

...

Keyword(s):

Phylogenetic Trees ◽

18S Rrna ◽

Phylogenetic Analyses ◽

18S Rrna Gene ◽

Sensu Stricto ◽

Rrna Gene ◽

Sequence Comparisons ◽

Important Species ◽

Cytauxzoon Felis ◽

Phylogenetic Status

Babesia vesperuginis is the only piroplasm known to infect bats. Unlike most members of the genus Babesia, it is probably transmitted by a soft tick species (i.e. Argas vespertilionis). Recently, two studies have been conducted to clarify the phylogenetic status of this species, and both agreed on placing it into a basal position among Babesia sensu stricto (s.s.). However, several important groups of piroplasms were not included in the already reported phylogenetic trees of B. vesperuginis isolates. Therefore, the aim of the present study was to amplify an approx. 950-bp fragment of the cytochrome c oxidase subunit 1 (cox1) gene of B. vesperuginis from A. vespertilionis specimens, and to compare its sequences with those from other piroplasmid groups in a broader phylogenetic context. Sequence comparisons focusing on either 18S rRNA or cox1 genes, as well as phylogenetic analyses involving separate and concatenated 18S rRNA and cox1 sequences indicate that B. vesperuginis is more closely related to the phylogenetic group of Theileriidae than to Babesia s.s. In particular, B. vesperuginis clustered closest to Cytauxzoon felis and the ‘prototheilerid’ B. conradae. The results of this study highlight that B. vesperuginis is a unique and taxonomically important species, which should be included in future studies aimed at resolving the comprehensive phylogeny of Piroplasmida.

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Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

10.1101/2020.03.15.992941 ◽

2020 ◽

Cited By ~ 15

Author(s):

Arang Rhie ◽

Brian P. Walenz ◽

Sergey Koren ◽

Adam M. Phillippy

Keyword(s):

De Novo ◽

High Accuracy ◽

Link Type ◽

Base Level ◽

Project Home Page ◽

Set Operations ◽

Assembly Evaluation ◽

Long Read ◽

Genome Assemblies ◽

Reference Genomes

AbstractRecent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present Merqury, a novel tool for reference-free assembly evaluation based on efficient k-mer set operations. By comparing k-mers in a de novo assembly to those found in unassembled high-accuracy reads, Merqury estimates base-level accuracy and completeness. For trios, Merqury can also evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors. Multiple visualizations, such as k-mer spectrum plots, can be generated for evaluation. We demonstrate on both human and plant genomes that Merqury is a fast and robust method for assembly validation.Availability of data and materialProject name: MerquryProject home page: https://github.com/marbl/merqury, https://github.com/marbl/merylArchived version: https://github.com/marbl/merqury/releases/tag/v1.0Operating system(s): Platform independentProgramming language: C++, Java, PerlOther requirements: gcc 4.8 or higher, java 1.6 or higherLicense: Public domain (see https://github.com/marbl/merqury/blob/master/README.license) Any restrictions to use by non-academics: No restrictions applied

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