scholarly journals Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 1972 ◽  
Author(s):  
Amy L. Longmuir ◽  
Peter L. Beech ◽  
Mark F. Richardson
Keyword(s):  
Plant Pathogen ◽  
Reference Genome ◽  
Phytophthora Cinnamomi ◽  
Gene Prediction ◽  
Single Copy ◽  
Draft Assembly ◽  
Protein Encoding ◽  
Pathogen Control ◽  
Genome Assemblies ◽  
Encoding Genes

Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The current reference genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, robust genome assemblies of more typical strains are required. Here we report the genome sequencing, draft assembly, and preliminary annotation of two geographically separated Australian strains of P. cinnamomi. Findings:  Some 308 million raw reads were generated for the two strains, DU054 and WA94.26. Independent genome assembly produced final genome sequences of 62.8 Mb (in 14,268 scaffolds) and 68.1 Mb (in 10,084 scaffolds), which are comparable in size and contiguity to other Phytophthora genomes. Gene prediction yielded > 22,000 predicted protein-encoding genes within each genome, while BUSCO assessment showed 94.4% and 91.5% of the stramenopile single-copy orthologs to be present in the assembled genomes, respectively. Conclusions: The assembled genomes of two geographically distant isolates of Phytophthora cinnamomi will provide a valuable resource for further comparative analyses and evolutionary studies of this destructive pathogen, and further annotation of the presented genomes may yield possible targets for novel pathogen control methods.

scholarly journals Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1972 ◽  
Author(s):  
Amy L. Longmuir ◽  
Peter L. Beech ◽  
Mark F. Richardson
Keyword(s):  
Plant Pathogen ◽  
Phytophthora Cinnamomi ◽  
Gene Prediction ◽  
Single Copy ◽  
Control Methods ◽  
Draft Assembly ◽  
Protein Encoding ◽  
Evolutionary Studies ◽  
Pathogen Control ◽  
Encoding Genes

Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The currently available genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, more robust assemblies of the genomes of more typical strains are required. Here we report the genome sequencing, draft assembly, and preliminary annotation of two geographically separated Australian strains of P. cinnamomi. Findings:  Some 308 million raw reads were generated for the two strains. Independent genome assembly produced final genomes of 62.8 Mb (in 14,268 scaffolds) and 68.1 Mb (in 10,084 scaffolds), which are comparable in size and contiguity to other Phytophthora genomes. Gene prediction yielded > 22,000 predicted protein-encoding genes within each genome, while BUSCO assessment showed 82.5% and 81.8% of the eukaryote universal single-copy orthologs to be present in the assembled genomes, respectively. Conclusions: The assembled genomes of two geographically distant isolates of Phytophthora cinnamomi will provide a valuable resource for further comparative analysis and evolutionary studies of this destructive pathogen, and further annotation of the presented genomes may yield possible targets for novel pathogen control methods.

scholarly journals Genome Assembly of the Canadian Two-row Malting Barley Cultivar AAC Synergy

2021 ◽  
Author(s):  
Wayne Xu ◽  
James R Tucker ◽  
Wubishet A Bekele ◽  
Frank M You ◽  
Yong-Bi Fu ◽  
...  
Keyword(s):  
Reference Genome ◽  
Single Copy ◽  
Barley Cultivar ◽  
Malting Barley ◽  
Orthologous Genes ◽  
Hordeum Vulgare L ◽  
Chromosome Conformation ◽  
Mate Pair ◽  
Genome Assemblies ◽  
First Time

Abstract Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cultivar Morex reference genome has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic diversity analysis studies, gene discovery, and marker development when working in two-row germplasm that is more common to Canadian barley. Here we assembled, for the first time, the genome sequence of a Canadian two-row malting barley, cultivar AAC Synergy. We applied deep Illumina paired-end reads, long mate-pair reads, PacBio sequences, 10X chromium linked read libraries, and chromosome conformation capture sequencing (Hi-C) to generate a contiguous assembly. The genome assembled from super-scaffolds had a size of 4.85 Gb, N50 of 2.32 Mb and an estimated 93.9% of complete genes from a plant database (BUSCO, benchmarking universal single-copy orthologous genes). After removal of small scaffolds (< 300 Kb), the assembly was arranged into pseudomolecules of 4.14 Gb in size with seven chromosomes plus unanchored scaffolds. The completeness and annotation of the assembly were assessed by comparing it with the updated version of six-row Morex and recently released two-row Golden Promise genome assemblies.

scholarly journals A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jiorgos Kourelis ◽  
Farnusch Kaschani ◽  
Friederike M. Grosse-Holz ◽  
Felix Homma ◽  
Markus Kaiser ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Draft Genome ◽  
Model Organism ◽  
Functional Annotations ◽  
Draft Genome Assembly ◽  
Extracellular Proteome ◽  
Protein Encoding ◽  
Gene Models ◽  
Genome Assemblies ◽  
Encoding Genes

Abstract Background Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. Results Here we present an improved proteome based on the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. Due to the fragmented nature of the Niben1.0.1 draft genome, many protein-encoding genes are missing or partial. We complement these missing proteins by similarly annotating other draft genome assemblies. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better in assigning spectra than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously predicted to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal inactivation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. Finally, we use this new proteome annotation to characterize the extracellular proteome as compared to a total leaf proteome, which highlights the enrichment of hydrolases in the apoplast. Conclusions This proteome annotation provides the community working with Nicotiana benthamiana with an important new resource for functional proteomics.

scholarly journals What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes

2021 ◽  
Vol 9 (2) ◽  
pp. 299
Author(s):  
Angela Conti ◽  
Laura Corte ◽  
Debora Casagrande Pierantoni ◽  
Vincent Robert ◽  
Gianluigi Cardinali
Keyword(s):  
Single Copy ◽  
Sensu Stricto ◽  
Fungal Species ◽  
Rrna Genes ◽  
Taxonomic Resolution ◽  
Protein Encoding ◽  
The Many ◽  
Next Generation Sequencing Ngs ◽  
Encoding Genes

Fungal species delimitation was traditionally carried out with multicopy ribosomal RNA (rRNA) genes, principally for their ease of amplification. Since the efficacy of these markers has been questioned, single-copy protein-encoding genes have been proposed alone or in combination for Multi-Locus Sequence Typing (MLST). In this context, the role of the many sequences obtained with Next-Generation Sequencing (NGS) techniques, in both genomics and metagenomics, further pushes toward an analysis of the efficacy of NGS-derived markers and of the metrics to evaluate the marker efficacy in discriminating fungal species. This paper aims at proposing MeTRe (Mean Taxonomic Resolution), a novel index that could be used both for measuring marker efficacy and for assessing the actual resolution (i.e., the level of separation) between species obtained with different markers or their combinations. In this paper, we described and then employed this index to compare the efficacy of two rRNAs and four single-copy markers obtained from public databases as both an amplicon-based approach and genome-derived sequences. Two different groups of species were used, one with a pathogenic species of Candida that was characterized by relatively well-separated taxa, whereas the other, comprising some relevant species of the sensu stricto group of the genus Saccharomyces, included close species and interspecific hybrids. The results showed the ability of MeTRe to evaluate marker efficacy in general and genome-derived markers specifically.

scholarly journals Long-read sequencing improves assembly of Trichinella genomes 10-fold, revealing substantial synteny between lineages diverged over 7 million years

Parasitology ◽  
2017 ◽  
Vol 144 (10) ◽  
pp. 1302-1315 ◽  
Author(s):  
PETER C. THOMPSON ◽  
DANTE S. ZARLENGA ◽  
MING-YUAN LIU ◽  
BENJAMIN M. ROSENTHAL
Keyword(s):  
Reference Genome ◽  
Trichinella Spiralis ◽  
Evolutionary Genetics ◽  
Invasion Biology ◽  
Phenotypic Traits ◽  
Draft Assembly ◽  
Long Read ◽  
Genome Assemblies ◽  
First Time ◽  
Insight Into

SUMMARYGenome assemblies can form the basis of comparative analyses fostering insight into the evolutionary genetics of a parasite's pathogenicity, host–pathogen interactions, environmental constraints and invasion biology; however, the length and complexity of many parasite genomes has hampered the development of well-resolved assemblies. In order to improve Trichinella genome assemblies, the genome of the sylvatic encapsulated species Trichinella murrelli was sequenced using third-generation, long-read technology and, using syntenic comparisons, scaffolded to a reference genome assembly of Trichinella spiralis, markedly improving both. A high-quality draft assembly for T. murrelli was achieved that totalled 63·2 Mbp, half of which was condensed into 26 contigs each longer than 571 000 bp. When compared with previous assemblies for parasites in the genus, ours required 10-fold fewer contigs, which were five times longer, on average. Better assembly across repetitive regions also enabled resolution of 8 Mbp of previously indeterminate sequence. Furthermore, syntenic comparisons identified widespread scaffold misassemblies in the T. spiralis reference genome. The two new assemblies, organized for the first time into three chromosomal scaffolds, will be valuable resources for future studies linking phenotypic traits within each species to their underlying genetic bases.

scholarly journals Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola

2017 ◽  
Author(s):  
Kirill Grigorev ◽  
Sergey Kliver ◽  
Pavel Dobrynin ◽  
Aleksey Komissarov ◽  
Walter Wolfsberger ◽  
...  
Keyword(s):  
Reference Genome ◽  
Single Copy ◽  
Selection Signatures ◽  
Caribbean Islands ◽  
Assembly Strategy ◽  
Genome Data ◽  
String Graph ◽  
Additional Sequence ◽  
The Caribbean ◽  
Genome Assemblies

AbstractSolenodons are insectivores living on the Caribbean islands, with few surviving related taxa. The genus occupies one of the most ancient branches among the placental mammals. The history, unique biology and adaptations of these enigmatic venomous species, can be greatly advanced given the availability of genome data, but the whole genome assembly for solenodons has never been previously performed, partially due to the difficulty in obtaining samples from the field. Island isolation has likely resulted in extreme homozygosity within the Hispaniolan solenodon (Solenodon paradoxus), thus we tested the performance of several assembly strategies for performance with genetically impoverished species’ genomes. The string-graph based assembly strategy seems a better choice compared to the conventional de Brujn graph approach, due to the high levels of homozygosity, which is often a hallmark of endemic or endangered species. A consensus reference genome was assembled from sequences of five individuals from the southern subspecies (S. p. woodi). In addition, we obtained one additional sequence of the northern subspecies (S. p. paradoxus). The resulting genome assemblies were compared to each other, and annotated for genes, with a specific emphasis on the venomous genes, repeats, variable microsatellite loci and other genomic variants. Phylogenetic positioning and selection signatures were inferred based on 4,416 single copy orthologs from 10 other mammals. Patterns of SNP variation allowed us to infer population demography, which indicated a subspecies split within the Hispaniolan solenodon at least 300 Kya.

scholarly journals What’s all the phos about? Insights into the phosphorylation state of the RNA polymerase II C-terminal domain via mass spectrometry

2021 ◽  
Author(s):  
Blase Matthew LeBlanc ◽  
Rosamaria Yvette Moreno ◽  
Edwin Escobar ◽  
Mukesh Kumar Venkat Ramani ◽  
Jennifer S Brodbelt ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Phosphorylation State ◽  
Terminal Domain ◽  
Carboxy Terminal Domain ◽  
Protein Encoding ◽  
Small Nuclear Rnas ◽  
Rnap Ii ◽  
Carboxy Terminal ◽  
Encoding Genes

RNA polymerase II (RNAP II) is one of the primary enzymes responsible for expressing protein-encoding genes and some small nuclear RNAs. The enigmatic carboxy-terminal domain (CTD) of RNAP II and...

scholarly journals Autotransporter Protein-Encoding Genes of Diarrheagenic Escherichia coli Are Found in both Typical and Atypical Enteropathogenic E. coli Strains

2012 ◽  
Vol 79 (1) ◽  
pp. 411-414 ◽  
Author(s):  
Afonso G. Abreu ◽  
Vanessa Bueris ◽  
Tatiane M. Porangaba ◽  
Marcelo P. Sircili ◽  
Fernando Navarro-Garcia ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Content Type ◽  
E Coli ◽  
Diarrheagenic Escherichia Coli ◽  
Virulence Markers ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Specific Virulence

ABSTRACTAutotransporter (AT) protein-encoding genes of diarrheagenicEscherichia coli(DEC) pathotypes (cah,eatA,ehaABCDJ,espC,espI,espP,pet,pic,sat, andtibA) were detected in typical and atypical enteropathogenicE. coli(EPEC) in frequencies between 0.8% and 39.3%. Although these ATs have been described in particular DEC pathotypes, their presence in EPEC indicates that they should not be considered specific virulence markers.

scholarly journals Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christopher Alan Smith
Keyword(s):  
Evolutionary History ◽  
Lentinula Edodes ◽  
Reference Genome ◽  
Genomic Change ◽  
Diverse Species ◽  
The World ◽  
Cultivated Mushroom ◽  
Genome Assemblies ◽  
High Degree ◽  
Chromosome Level

AbstractThe basidiomycete fungus Lentinula novae-zelandiae is endemic to New Zealand and is a sister taxon to Lentinula edodes, the second most cultivated mushroom in the world. To explore the biology of this organism, a high-quality chromosome level reference genome of L. novae-zelandiae was produced. Macrosyntenic comparisons between the genome assembly of L. novae-zelandiae, L. edodes and a set of three genome assemblies of diverse species from the Agaricomycota reveal a high degree of macrosyntenic restructuring within L. edodes consistent with signal of domestication. These results show L. edodes has undergone significant genomic change during the course of its evolutionary history, likely a result of its cultivation and domestication over the last 1000 years.

Enhanced surface display efficiency of β-glucosidase in Saccharomyces cerevisiae by disruption of cell wall protein-encoding genes YGP1 and CWP2

2021 ◽  
pp. 108305
Author(s):  
Jantima Arnthong ◽  
Jatupong Ponjarat ◽  
Piyada Bussadee ◽  
Pacharawan Deenarn ◽  
Parichat Prommana ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Wall ◽  
Surface Display ◽  
Cell Wall Protein ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Enhanced Surface
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