Complete Genome Sequences and Genome-Wide Characterization of Trichoderma Biocontrol Agents Provide New Insights into their Evolution and Variation in Genome Organization, Sexual Development, and Fungal-Plant Interactions

Telomere-to-telomere and gapless reference genome assemblies are necessary to ensure that all genomic variants are studied and discovered, including centromeres, telomeres, AT-rich blocks, mating type loci, biosynthetic, and metabolic gene clusters. Here, we applied long-range sequencing technologies to determine the near-completed genome sequences of four widely used biocontrol agents or biofertilizers: Trichoderma virens Gv29-8 and FT-333, Trichoderma asperellum FT101, and Trichoderma atroviride P1.

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From raw reads to trees: Whole genome SNP phylogenetics across the tree of life

10.1101/032250 ◽

2015 ◽

Cited By ~ 10

Author(s):

Sanaa Afroz Ahmed ◽

Chien-Chi Lo ◽

Po-E Li ◽

Karen W Davenport ◽

Patrick S.G. Chain

Keyword(s):

Ad Hoc ◽

Phylogenetic Reconstruction ◽

Clinical Samples ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Complex Samples ◽

Phylogenetic Characterization ◽

Genome Wide ◽

Genome Assemblies

Next-generation sequencing is increasingly being used to examine closely related organisms. However, while genome-wide single nucleotide polymorphisms (SNPs) provide an excellent resource for phylogenetic reconstruction, to date evolutionary analyses have been performed using different ad hoc methods that are not often widely applicable across different projects. To facilitate the construction of robust phylogenies, we have developed a method for genome-wide identification/characterization of SNPs from sequencing reads and genome assemblies. Our phylogenetic and molecular evolutionary (PhaME) analysis software is unique in its ability to take reads and draft/complete genome(s) as input, derive core genome alignments, identify SNPs, construct phylogenies and perform evolutionary analyses. Several examples using genomes and read datasets for bacterial, eukaryotic and viral linages demonstrate the broad and robust functionality of PhaME. Furthermore, the ability to incorporate raw metagenomic reads from clinical samples with suspected infectious agents shows promise for the rapid phylogenetic characterization of pathogens within complex samples.

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Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides

mSphere ◽

10.1128/msphere.00213-16 ◽

2016 ◽

Vol 1 (5) ◽

Cited By ~ 54

Author(s):

José F. Muñoz ◽

Rhys A. Farrer ◽

Christopher A. Desjardins ◽

Juan E. Gallo ◽

Sean Sykes ◽

...

Keyword(s):

Positive Selection ◽

Pathogenic Fungus ◽

Geographic Range ◽

Genetic Differences ◽

Surface Proteins ◽

Ecological Niches ◽

Genome Sequences ◽

Human Pathogenic Fungus ◽

Genome Assemblies

ABSTRACT Characterization of genetic differences between lineages of the dimorphic human-pathogenic fungus Paracoccidioides can identify changes linked to important phenotypes and guide the development of new diagnostics and treatments. In this article, we compared genomes of 31 diverse isolates representing the major lineages of Paracoccidioides spp. and completed the first annotated genome sequences for the PS3 and PS4 lineages. We analyzed the population structure and characterized the genetic diversity among the lineages of Paracoccidioides, including a deep split of S1 into two lineages (S1a and S1b), and differentiated S1b, associated with most clinical cases, as the more highly recombining and diverse lineage. In addition, we found patterns of positive selection in surface proteins and secreted enzymes among the lineages, suggesting diversifying mechanisms of pathogenicity and adaptation across this species complex. These genetic differences suggest associations with the geographic range, pathogenicity, and ecological niches of Paracoccidioides lineages. The Paracoccidioides genus includes two species of thermally dimorphic fungi that cause paracoccidioidomycosis, a neglected health-threatening human systemic mycosis endemic to Latin America. To examine the genome evolution and the diversity of Paracoccidioides spp., we conducted whole-genome sequencing of 31 isolates representing the phylogenetic, geographic, and ecological breadth of the genus. These samples included clinical, environmental and laboratory reference strains of the S1, PS2, PS3, and PS4 lineages of P. brasiliensis and also isolates of Paracoccidioides lutzii species. We completed the first annotated genome assemblies for the PS3 and PS4 lineages and found that gene order was highly conserved across the major lineages, with only a few chromosomal rearrangements. Comparing whole-genome assemblies of the major lineages with single-nucleotide polymorphisms (SNPs) predicted from the remaining 26 isolates, we identified a deep split of the S1 lineage into two clades we named S1a and S1b. We found evidence for greater genetic exchange between the S1b lineage and all other lineages; this may reflect the broad geographic range of S1b, which is often sympatric with the remaining, largely geographically isolated lineages. In addition, we found evidence of positive selection for the GP43 and PGA1 antigen genes and genes coding for other secreted proteins and proteases and lineage-specific loss-of-function mutations in cell wall and protease genes; these together may contribute to virulence and host immune response variation among natural isolates of Paracoccidioides spp. These insights into the recent evolutionary events highlight important differences between the lineages that could impact the distribution, pathogenicity, and ecology of Paracoccidioides. IMPORTANCE Characterization of genetic differences between lineages of the dimorphic human-pathogenic fungus Paracoccidioides can identify changes linked to important phenotypes and guide the development of new diagnostics and treatments. In this article, we compared genomes of 31 diverse isolates representing the major lineages of Paracoccidioides spp. and completed the first annotated genome sequences for the PS3 and PS4 lineages. We analyzed the population structure and characterized the genetic diversity among the lineages of Paracoccidioides, including a deep split of S1 into two lineages (S1a and S1b), and differentiated S1b, associated with most clinical cases, as the more highly recombining and diverse lineage. In addition, we found patterns of positive selection in surface proteins and secreted enzymes among the lineages, suggesting diversifying mechanisms of pathogenicity and adaptation across this species complex. These genetic differences suggest associations with the geographic range, pathogenicity, and ecological niches of Paracoccidioides lineages.

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Factorial estimating assembly base errors using k-mer abundance difference (KAD) between short reads and genome assembled sequences

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqaa075 ◽

2020 ◽

Vol 2 (3) ◽

Author(s):

Cheng He ◽

Guifang Lin ◽

Hairong Wei ◽

Haibao Tang ◽

Frank F White ◽

...

Keyword(s):

Copy Number ◽

Error Rates ◽

Genome Sequences ◽

Short Reads ◽

Sequencing Technologies ◽

Insertion And Deletion ◽

Novel Approach ◽

Long Reads ◽

Long Read ◽

Genome Assemblies

Abstract Genome sequences provide genomic maps with a single-base resolution for exploring genetic contents. Sequencing technologies, particularly long reads, have revolutionized genome assemblies for producing highly continuous genome sequences. However, current long-read sequencing technologies generate inaccurate reads that contain many errors. Some errors are retained in assembled sequences, which are typically not completely corrected by using either long reads or more accurate short reads. The issue commonly exists, but few tools are dedicated for computing error rates or determining error locations. In this study, we developed a novel approach, referred to as k-mer abundance difference (KAD), to compare the inferred copy number of each k-mer indicated by short reads and the observed copy number in the assembly. Simple KAD metrics enable to classify k-mers into categories that reflect the quality of the assembly. Specifically, the KAD method can be used to identify base errors and estimate the overall error rate. In addition, sequence insertion and deletion as well as sequence redundancy can also be detected. Collectively, KAD is valuable for quality evaluation of genome assemblies and, potentially, provides a diagnostic tool to aid in precise error correction. KAD software has been developed to facilitate public uses.

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Genome-wide characterization of RNA editing in chicken: lack of evidence for non-A-to-I events

10.1101/008912 ◽

2014 ◽

Author(s):

Laure Frésard ◽

Sophie Leroux ◽

Pierre-François Roux ◽

C Klopp ◽

Stéphane Fabre ◽

...

Keyword(s):

Rna Editing ◽

High Throughput Sequencing ◽

Nucleotide Substitutions ◽

Sequencing Technologies ◽

Genome Wide ◽

Level Increase ◽

Functional Consequences ◽

Genome Screening ◽

Editing Level

RNA editing corresponds to a post-transcriptional nucleotide change in the RNA sequence, creating an alternative nucleotide, not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is more and more described in mammals, notably since the availability of next generation sequencing technologies allowing a whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken are still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, to understand to what extent this phenomenon is conserved in vertebrates. We performed RNA and DNA sequencing from 8 embryos. Being aware of common pitfalls inherent to sequence analyses leading to false positive discovery, we stringently filtered our datasets and found less than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual editing level increase with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, and provide support of an absence of non A-to-I events from the chicken transcriptome.

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A reference genome for the critically endangered woylie, Bettongia penicillata ogilbyi

10.1101/2021.12.07.471656 ◽

2021 ◽

Author(s):

Emma Peel ◽

Luke Silver ◽

Parice Brandies ◽

Carolyn J Hogg ◽

Katherine Belov

Keyword(s):

Wildlife Conservation ◽

Reference Genome ◽

Conservation Management ◽

Critically Endangered ◽

Rna Seq ◽

Genome Sequences ◽

Australian Species ◽

Sequencing Technologies ◽

Bettongia Penicillata ◽

Long Reads

Biodiversity is declining globally, and Australia has one of the worst extinction records for mammals. The development of sequencing technologies means that genomic approaches are now available as important tools for wildlife conservation and management. Despite this, genome sequences are available for only 5% of threatened Australian species. Here we report the first reference genome for the woylie (Bettongia penicillata ogilbyi), a critically endangered marsupial from Western Australia, and the first genome within the Potoroidae family. The woylie reference genome was generated using Pacific Biosciences HiFi long-reads, resulting in a 3.39 Gbp assembly with a scaffold N50 of 6.49 Mbp and 86.5% complete mammalian BUSCOs. Assembly of a global transcriptome from pouch skin, tongue, heart and blood RNA-seq reads was used to guide annotation with Fgenesh++, resulting in the annotation of 24,655 genes. The woylie reference genome is a valuable resource for conservation, management and investigations into disease-induced decline of this critically endangered marsupial.

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Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible FungusPleurotus ostreatus

BioMed Research International ◽

10.1155/2016/2503023 ◽

2016 ◽

Vol 2016 ◽

pp. 1-9 ◽

Cited By ~ 8

Author(s):

Jibin Qu ◽

Mengran Zhao ◽

Tom Hsiang ◽

Xiaoxing Feng ◽

Jinxia Zhang ◽

...

Keyword(s):

Genome Assembly ◽

Noncoding Rnas ◽

Genome Sequences ◽

Small Noncoding Rnas ◽

Basidiomycetous Fungus ◽

A Genome ◽

Genome Assemblies ◽

Genome Scale ◽

Identification And Characterization

Noncoding RNAs (ncRNAs) have been identified in many fungi. However, no genome-scale identification of ncRNAs has been inventoried for basidiomycetes. In this research, we detected 254 small noncoding RNAs (sncRNAs) in a genome assembly of an isolate (CCEF00389) ofPleurotus ostreatus, which is a widely cultivated edible basidiomycetous fungus worldwide. The identified sncRNAs include snRNAs, snoRNAs, tRNAs, and miRNAs. SnRNA U1 was not found in CCEF00389 genome assembly and some other basidiomycetous genomes by BLASTn. This implies that if snRNA U1 of basidiomycetes exists, it has a sequence that varies significantly from other organisms. By analyzing the distribution of sncRNA loci, we found that snRNAs and most tRNAs (88.6%) were located in pseudo-UTR regions, while miRNAs are commonly found in introns. To analyze the evolutionary conservation of the sncRNAs inP. ostreatus, we aligned all 254 sncRNAs to the genome assemblies of some other Agaricomycotina fungi. The results suggest that most sncRNAs (77.56%) were highly conserved inP. ostreatus, and 20% were conserved in Agaricomycotina fungi. These findings indicate that most sncRNAs ofP. ostreatuswere not conserved across Agaricomycotina fungi.

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Chromosome-level reference genome of the jellyfish Rhopilema esculentum

GigaScience ◽

10.1093/gigascience/giaa036 ◽

2020 ◽

Vol 9 (4) ◽

Cited By ~ 3

Author(s):

Yunfeng Li ◽

Lei Gao ◽

Yongjia Pan ◽

Meilin Tian ◽

Yulong Li ◽

...

Keyword(s):

Genome Assembly ◽

Evolutionary History ◽

Reference Genome ◽

Protein Coding ◽

Fishery Resource ◽

Rhopilema Esculentum ◽

Sequencing Technologies ◽

Genome Wide ◽

History Of ◽

Chromosome Level

Abstract Background Jellyfish belong to the phylum Cnidaria, which occupies an important phylogenetic location in the early-branching Metazoa lineages. The jellyfish Rhopilema esculentum is an important fishery resource in China. However, the genome resource of R. esculentum has not been reported to date. Findings In this study, we constructed a chromosome-level genome assembly of R. esculentum using Pacific Biosciences, Illumina, and Hi-C sequencing technologies. The final genome assembly was ∼275.42 Mb, with a contig N50 length of 1.13 Mb. Using Hi-C technology to identify the contacts among contigs, 260.17 Mb (94.46%) of the assembled genome were anchored onto 21 pseudochromosomes with a scaffold N50 of 12.97 Mb. We identified 17,219 protein-coding genes, with an average CDS length of 1,575 bp. The genome-wide phylogenetic analysis indicated that R. esculentum might have evolved more slowly than the other scyphozoan species used in this study. In addition, 127 toxin-like genes were identified, and 1 toxin-related “hub” was found by a genomic survey. Conclusions We have generated a chromosome-level genome assembly of R. esculentum that could provide a valuable genomic background for studying the biology and pharmacology of jellyfish, as well as the evolutionary history of Cnidaria.

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Estimating Assembly Base Errors Using K-mer Abundance Difference (KAD) Between Short Reads and Genome Assembled Sequences

10.1101/2020.03.17.994566 ◽

2020 ◽

Cited By ~ 1

Author(s):

Cheng He ◽

Guifang Lin ◽

Hairong Wei ◽

Haibao Tang ◽

Frank F White ◽

...

Keyword(s):

Copy Number ◽

Error Rates ◽

Genome Sequences ◽

Short Reads ◽

Sequencing Technologies ◽

Insertion And Deletion ◽

Novel Approach ◽

Long Reads ◽

Long Read ◽

Genome Assemblies

ABSTRACTGenome sequences provide genomic maps with a single-base resolution for exploring genetic contents. Sequencing technologies, particularly long reads, have revolutionized genome assemblies for producing highly continuous genome sequences. However, current long-read sequencing technologies generate inaccurate reads that contain many errors. Some errors are retained in assembled sequences, which are typically not completely corrected by using either long reads or more accurate short reads. The issue commonly exists but few tools are dedicated for computing error rates or determining error locations. In this study, we developed a novel approach, referred to as K-mer Abundance Difference (KAD), to compare the inferred copy number of each k-mer indicated by short reads and the observed copy number in the assembly. Simple KAD metrics enable to classify k-mers into categories that reflect the quality of the assembly. Specifically, the KAD method can be used to identify base errors and estimate the overall error rate. In addition, sequence insertion and deletion as well as sequence redundancy can also be detected. Therefore, KAD is valuable for quality evaluation of genome assemblies and, potentially, provides a diagnostic tool to aid in precise error correction. KAD software has been developed to facilitate public uses.

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Barley Long Non-Coding RNAs and Their Tissue-Specific Co-expression Pattern with Coding-Transcripts

10.1101/229559 ◽

2017 ◽

Cited By ~ 2

Author(s):

Gökhan Karakülah ◽

Turgay Unver

Keyword(s):

Expression Pattern ◽

Functional Characterization ◽

Cooperative Interaction ◽

Environmental Response ◽

Sequencing Technologies ◽

Transcriptional Suppression ◽

Genome Wide ◽

A Genome ◽

Non Coding Rnas

AbstractLong non-coding RNAs (lncRNA) with non-protein or small peptide-coding potential transcripts are emerging regulatory molecules. With the advent of next-generation sequencing technologies and novel bioinformatics tools, a tremendous number of lncRNAs has been identified in several plant species. Recent reports demonstrated roles of plant lncRNAs such as development and environmental response. Here, we reported a genome-wide discovery of ~8,000 barley lncRNAs and measured their expression pattern upon excessive boron (B) treatment. According to the tissue-based comparison, leaves have a greater number of B-responsive differentially expressed lncRNAs than the root. Functional annotation of the coding transcripts, which were co-expressed with lncRNAs, revealed that molecular function of the ion transport, establishment of localization, and response to stimulus significantly enriched only in the leaf. On the other hand, 32 barley endogenous target mimics (eTM) as lncRNAs, which potentially decoy the transcriptional suppression activity of 18 miRNAs, were obtained. Presented data including identification, expression measurement, and functional characterization of barley lncRNAs suggest that B-stress response might also be regulated by lncRNA expression via cooperative interaction of miRNA-eTM-coding target transcript modules.

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Rapid characterization of complex genomic regions using Cas9 enrichment and Nanopore sequencing

10.1101/2021.03.11.434935 ◽

2021 ◽

Author(s):

Jesse Bruijnesteijn ◽

Marit van der Wiel ◽

Natasja G. de Groot ◽

Ronald E. Bontrop

Keyword(s):

Sequence Similarity ◽

Gene Clusters ◽

Oxford Nanopore ◽

Long Read ◽

Number Variation ◽

Rapid Characterization ◽

Multiple Species ◽

Genomic Regions ◽

Genome Assemblies

AbstractLong-read sequencing approaches have considerably improved the quality and contiguity of genome assemblies. Such platforms bear the potential to resolve even extremely complex regions, such as multigenic families and repetitive stretches of DNA. Deep sequencing coverage, however, is required to overcome low nucleotide accuracy, especially in regions with high homopolymer density, copy number variation, and sequence similarity, such as the MHC and KIR gene clusters of the immune system. Therefore, we have adapted a targeted enrichment protocol in combination with long-read sequencing to efficiently annotate complex genomic regions. Using Cas9 endonuclease activity, segments of the complex KIR gene cluster were enriched and sequenced on an Oxford Nanopore Technologies platform. This provided sufficient coverage to accurately resolve and phase highly complex KIR haplotypes. Our strategy facilitates rapid characterization of large and complex multigenic regions, including its epigenetic footprint, in multiple species, even in the absence of a reference genome.

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