Large-scale gene gains and losses molded the NLR defense arsenal during the Cucurbita evolution

Abstract Main conclusion Genome-wide annotation reveals that the gene birth–death process of the Cucurbita R family is associated with a species-specific diversification of TNL and CNL protein classes. Abstract The Cucurbitaceae family includes nearly 1000 plant species known universally as cucurbits. Cucurbita genus includes many economically important worldwide crops vulnerable to more than 200 pathogens. Therefore, the identification of pathogen-recognition genes is of utmost importance for this genus. The major class of plant-resistance (R) genes encodes nucleotide-binding site and leucine-rich repeat (NLR) proteins, and is divided into three sub-classes namely, TIR-NB-LRR (TNL), CC-NB-LRR (CNL) and RPW8-NB-LRR (RNL). Although the characterization of the NLR gene family has been carried out in important Cucurbita species, this information is still linked to the availability of sequenced genomes. In this study, we analyzed 40 de novo transcriptomes and 5 genome assemblies, which were explored to investigate the Cucurbita expressed-NLR (eNLR) and NLR repertoires using an ad hoc gene annotation approach. Over 1850 NLR-encoding genes were identified, finely characterized and compared to 96 well-characterized plant R-genes. The maximum likelihood analyses revealed an unusual diversification of CNL/TNL genes and a strong RNL conservation. Indeed, several gene gain and loss events have shaped the Cucurbita NLR family. Finally, to provide a first validation step Cucurbita, eNLRs were explored by real-time PCR analysis. The NLR repertories of the 12 Cucurbita species presented in this paper will be useful to discover novel R-genes.

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M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data

Nucleic Acids Research ◽

10.1093/nar/gkz423 ◽

2019 ◽

Vol 47 (W1) ◽

pp. W88-W92 ◽

Cited By ~ 9

Author(s):

Oren Avram ◽

Dana Rapoport ◽

Shir Portugez ◽

Tal Pupko

Keyword(s):

Large Scale ◽

Ad Hoc ◽

Evolutionary Dynamics ◽

Gene Annotation ◽

Gc Content ◽

Web Server ◽

Disease Outbreaks ◽

Open Reading Frames ◽

Microbial Genomics ◽

Bacterial Strains

Abstract Large-scale mining and analysis of bacterial datasets contribute to the comprehensive characterization of complex microbial dynamics within a microbiome and among different bacterial strains, e.g., during disease outbreaks. The study of large-scale bacterial evolutionary dynamics poses many challenges. These include data-mining steps, such as gene annotation, ortholog detection, sequence alignment and phylogeny reconstruction. These steps require the use of multiple bioinformatics tools and ad-hoc programming scripts, making the entire process cumbersome, tedious and error-prone due to manual handling. This motivated us to develop the M1CR0B1AL1Z3R web server, a ‘one-stop shop’ for conducting microbial genomics data analyses via a simple graphical user interface. Some of the features implemented in M1CR0B1AL1Z3R are: (i) extracting putative open reading frames and comparative genomics analysis of gene content; (ii) extracting orthologous sets and analyzing their size distribution; (iii) analyzing gene presence–absence patterns; (iv) reconstructing a phylogenetic tree based on the extracted orthologous set; (v) inferring GC-content variation among lineages. M1CR0B1AL1Z3R facilitates the mining and analysis of dozens of bacterial genomes using advanced techniques, with the click of a button. M1CR0B1AL1Z3R is freely available at https://microbializer.tau.ac.il/.

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Towards sex identification of Asian Palmyra palm (Borassus flabelliferL.) by DNA fingerprinting, suppression subtractive hybridization andde novotranscriptome sequencing

PeerJ ◽

10.7717/peerj.7268 ◽

2019 ◽

Vol 7 ◽

pp. e7268

Author(s):

Kwanjai Pipatchartlearnwong ◽

Piyada Juntawong ◽

Passorn Wonnapinij ◽

Somsak Apisitwanich ◽

Supachai Vuttipongchaikij

Keyword(s):

Dna Fingerprinting ◽

Suppression Subtractive Hybridization ◽

Transcriptome Sequencing ◽

Large Scale ◽

De Novo ◽

Subtractive Hybridization ◽

Pcr Analysis ◽

Dna Fingerprints ◽

Juvenile Period ◽

Male And Female

BackgroundAsian Palmyra palm, the source of palm-sugar, is dioecious with a long juvenile period requiring at least 12 years to reach its maturity. To date, there is no reliable molecular marker for identifying sexes before the first bloom, limiting crop designs and utilization. We aimed to identify sex-linked markers for this palm using PCR-based DNA fingerprinting, suppression subtractive hybridization (SSH) and transcriptome sequencing.MethodsDNA fingerprints were generated between males and females based on RAPD, AFLP, SCoT, modified SCoT, ILP, and SSR techniques. Large-scale cloning and screening of SSH libraries andde novotranscriptome sequencing of male and female cDNA from inflorescences were performed to identify sex-specific genes for developing sex-linked markers.ResultsThrough extensive screening and re-testing of the DNA fingerprints (up to 1,204 primer pairs) and transcripts from SSH (>10,000 clones) and transcriptome data, however, no sex-linked marker was identified. Althoughde novotranscriptome sequencing of male and female inflorescences provided ∼32 million reads and 187,083 assembled transcripts, PCR analysis of selected sex-highly represented transcripts did not yield any sex-linked marker. This result may suggest the complexity and small sex-determining region of the Asian Palmyra palm. To this end, we provide the first global transcripts of male and female inflorescences of Asian Palmyra palm. Interestingly, sequence annotation revealed a large proportion of transcripts related to sucrose metabolism, which corresponds to the sucrose-rich sap produced in the inflorescences, and these transcripts will be useful for further understanding of sucrose production in sugar crop plants. Provided lists of sex-specific and differential-expressed transcripts would be beneficial to the further study of sexual development and sex-linked markers in palms and related species.

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A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

10.1101/2020.09.15.298315 ◽

2020 ◽

Author(s):

J. Mitchell (Mitch) McGrath ◽

Andrew Funk ◽

Paul Galewski ◽

Shujun Ou ◽

Belinda Townsend ◽

...

Keyword(s):

Sugar Beet ◽

Beta Vulgaris ◽

Genome Assembly ◽

Copy Number ◽

Large Scale ◽

De Novo ◽

Gene Annotation ◽

Gene Copy ◽

De Novo Genome Assembly ◽

Short Read

AbstractA contiguous assembly of the inbred ‘EL10’ sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short read error correction. The EL10.1 assembly was 540 Mb, of which 96.7% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNAseq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals drawn from EL10 progeny and three unrelated germplasm accessions, producing estimates from 633 to 875 Mb/1C. Read depth mapping with short-read whole genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation.

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M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data

Access Microbiology ◽

10.1099/acmi.ac2020.po1014 ◽

2020 ◽

Vol 2 (7A) ◽

Author(s):

Oren Avram ◽

Dana Rapoport ◽

Shir Portugez ◽

Tal Pupko

Keyword(s):

Large Scale ◽

Ad Hoc ◽

Evolutionary Dynamics ◽

Gene Annotation ◽

Gc Content ◽

Web Server ◽

Disease Outbreaks ◽

Open Reading Frames ◽

Microbial Genomics ◽

Bacterial Strains

Large-scale mining and analysis of bacterial datasets contribute to the comprehensive characterization of complex microbial dynamics within a microbiome and among different bacterial strains, e.g., during disease outbreaks. The study of large-scale bacterial evolutionary dynamics poses many challenges. These include data-mining steps, such as gene annotation, ortholog detection, sequence alignment, and phylogeny reconstruction. These steps require the use of multiple bioinformatics tools and ad-hoc programming scripts, making the entire process cumbersome, tedious and error-prone due to manual handling. This motivated us to develop the M1CR0B1AL1Z3R web server, a ‘one-stop shop’ for conducting microbial genomics data analyses via a simple graphical user interface (Avram, et al., Nucleic Acids Res., 2019). Some of the features implemented in M1CR0B1AL1Z3R are: (i) extracting putative open reading frames and comparative genomics analysis of gene content; (ii) extracting orthologous sets and analyzing their size distribution; (iii) analyzing gene presence-absence patterns; (iv) reconstructing a phylogenetic tree based on the extracted orthologous set; (v) inferring GC-content variation among lineages. M1CR0B1AL1Z3R facilitates the mining and analysis of dozens of bacterial genomes using advanced techniques, with the click of a button. M1CR0B1AL1Z3R is freely available at https://microbializer.tau.ac.il/ [https://microbializer.tau.ac.il/].

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Splicing and editing of ionotropic glutamate receptors: a comprehensive analysis based on human RNA-Seq data

Cellular and Molecular Life Sciences ◽

10.1007/s00018-021-03865-z ◽

2021 ◽

Author(s):

Robin Herbrechter ◽

Nadine Hube ◽

Raoul Buchholz ◽

Andreas Reiner

Keyword(s):

Alternative Splicing ◽

Human Brain ◽

Glutamate Receptors ◽

Large Scale ◽

De Novo ◽

Ionotropic Glutamate Receptors ◽

Variable Degree ◽

Rna Seq ◽

Amino Terminal ◽

Species Specific

AbstractIonotropic glutamate receptors (iGluRs) play key roles for signaling in the central nervous system. Alternative splicing and RNA editing are well-known mechanisms to increase iGluR diversity and to provide context-dependent regulation. Earlier work on isoform identification has focused on the analysis of cloned transcripts, mostly from rodents. We here set out to obtain a systematic overview of iGluR splicing and editing in human brain based on RNA-Seq data. Using data from two large-scale transcriptome studies, we established a workflow for the de novo identification and quantification of alternative splice and editing events. We detected all canonical iGluR splice junctions, assessed the abundance of alternative events described in the literature, and identified new splice events in AMPA, kainate, delta, and NMDA receptor subunits. Notable events include an abundant transcript encoding the GluA4 amino-terminal domain, GluA4-ATD, a novel C-terminal GluD1 (delta receptor 1) isoform, GluD1-b, and potentially new GluK4 and GluN2C isoforms. C-terminal GluN1 splicing may be controlled by inclusion of a cassette exon, which shows preference for one of the two acceptor sites in the last exon. Moreover, we identified alternative untranslated regions (UTRs) and species-specific differences in splicing. In contrast, editing in exonic iGluR regions appears to be mostly limited to ten previously described sites, two of which result in silent amino acid changes. Coupling of proximal editing/editing and editing/splice events occurs to variable degree. Overall, this analysis provides the first inventory of alternative splicing and editing in human brain iGluRs and provides the impetus for further transcriptome-based and functional investigations.

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MetaPlatanus: a metagenome assembler that combines long-range sequence links and species-specific features

Nucleic Acids Research ◽

10.1093/nar/gkab831 ◽

2021 ◽

Author(s):

Rei Kajitani ◽

Hideki Noguchi ◽

Yasuhiro Gotoh ◽

Yoshitoshi Ogura ◽

Dai Yoshimura ◽

...

Keyword(s):

Long Range ◽

Large Scale ◽

De Novo ◽

Gene Clusters ◽

Human Saliva ◽

Bacterial Genomes ◽

Specific Sequence ◽

Metagenome Assembly ◽

Downstream Analysis ◽

Species Specific

Abstract De novo metagenome assembly is effective in assembling multiple draft genomes, including those of uncultured organisms. However, heterogeneity in the metagenome hinders assembly and introduces interspecies misassembly deleterious for downstream analysis. For this purpose, we developed a hybrid metagenome assembler, MetaPlatanus. First, as a characteristic function, it assembles the basic contigs from accurate short reads and then iteratively utilizes long-range sequence links, species-specific sequence compositions, and coverage depth. The binning information was also used to improve contiguity. Benchmarking using mock datasets consisting of known bacteria with long reads or mate pairs revealed the high contiguity MetaPlatanus with a few interspecies misassemblies. For published human gut data with nanopore reads from potable sequencers, MetaPlatanus assembled many biologically important elements, such as coding genes, gene clusters, viral sequences, and over-half bacterial genomes. In the benchmark with published human saliva data with high-throughput nanopore reads, the superiority of MetaPlatanus was considerably more evident. We found that some high-abundance bacterial genomes were assembled only by MetaPlatanus as near-complete. Furthermore, MetaPlatanus can circumvent the limitations of highly fragmented assemblies and frequent interspecies misassembles obtained by the other tools. Overall, the study demonstrates that MetaPlatanus could be an effective approach for exploring large-scale structures in metagenomes.

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LtrDetector: A modern tool-suite for detecting long terminal repeat retrotransposons de-novo on the genomic scale

10.1101/448969 ◽

2018 ◽

Author(s):

Joseph D Valencia ◽

Hani Z Girgis

Keyword(s):

Long Terminal Repeat ◽

Large Scale ◽

De Novo ◽

False Positive Rate ◽

Long Terminal Repeat Retrotransposons ◽

Terminal Repeat ◽

Plant Genomes ◽

Positive Rate ◽

Genomic Scale ◽

Species Specific

AbstractLong terminal repeat retrotransposons are the most abundant transposons in plants. They play important roles in alternative splicing, recombination, gene regulation, and genomic evolution. Large-scale sequencing projects for plant genomes are currently underway. Software tools are important for annotating long terminal repeat retrotransposons in these newly available genomes. However, the available tools are not very sensitive to known elements and perform inconsistently on different genomes. Some are hard to install or obsolete. They may struggle to process large plant genomes. None are concurrent or have features to support manual review of new elements. To overcome these limitations, we developed LtrDetector, which uses signal-processing techniques. LtrDetector is easy to install and use. It is not species specific. It utilizes multi-core processors available in personal computers. It is more sensitive than other tools by 14.4%–50.8% while maintaining a low false positive rate on six plant genomes.

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The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae)

Genome Biology and Evolution ◽

10.1093/gbe/evz245 ◽

2019 ◽

Vol 11 (12) ◽

pp. 3353-3371 ◽

Cited By ~ 6

Author(s):

Valerie L Soza ◽

Dale Lindsley ◽

Adam Waalkes ◽

Elizabeth Ramage ◽

Rupali P Patwardhan ◽

...

Keyword(s):

Genome Annotation ◽

Large Scale ◽

De Novo ◽

Gene Annotation ◽

Whole Genome ◽

Genomic Libraries ◽

Gene Pairs ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Large Genus

Abstract The genus Rhododendron (Ericaceae), which includes horticulturally important plants such as azaleas, is a highly diverse and widely distributed genus of >1,000 species. Here, we report the chromosome-scale de novo assembly and genome annotation of Rhododendron williamsianum as a basis for continued study of this large genus. We created multiple short fragment genomic libraries, which were assembled using ALLPATHS-LG. This was followed by contiguity preserving transposase sequencing (CPT-seq) and fragScaff scaffolding of a large fragment library, which improved the assembly by decreasing the number of scaffolds and increasing scaffold length. Chromosome-scale scaffolding was performed by proximity-guided assembly (LACHESIS) using chromatin conformation capture (Hi-C) data. Chromosome-scale scaffolding was further refined and linkage groups defined by restriction-site associated DNA (RAD) sequencing of the parents and progeny of a genetic cross. The resulting linkage map confirmed the LACHESIS clustering and ordering of scaffolds onto chromosomes and rectified large-scale inversions. Assessments of the R. williamsianum genome assembly and gene annotation estimate them to be 89% and 79% complete, respectively. Predicted coding sequences from genome annotation were used in syntenic analyses and for generating age distributions of synonymous substitutions/site between paralgous gene pairs, which identified whole-genome duplications (WGDs) in R. williamsianum. We then analyzed other publicly available Ericaceae genomes for shared WGDs. Based on our spatial and temporal analyses of paralogous gene pairs, we find evidence for two shared, ancient WGDs in Rhododendron and Vaccinium (cranberry/blueberry) members that predate the Ericaceae family and, in one case, the Ericales order.

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Target-Templated de novo Design of Macrocyclic D-/L-Peptides: Inhibitors of the PD-1/PD-L1 Interaction

10.26434/chemrxiv.11663337.v3 ◽

2020 ◽

Author(s):

Salvador Guardiola ◽

Monica Varese ◽

Xavier Roig ◽

Jesús Garcia ◽

Ernest Giralt

Keyword(s):

Protein Interactions ◽

Cyclic Peptides ◽

General Framework ◽

Large Scale ◽

De Novo ◽

Inhibitory Effect ◽

Original Text ◽

Protein Protein Interactions ◽

Retraction Notice ◽

Pharmaceutical Properties

NOTE: This preprint has been retracted by consensus from all authors. See the retraction notice in place above; the original text can be found under "Version 1", accessible from the version selector above. ------------------------------------------------------------------------ Peptides, together with antibodies, are among the most potent biochemical tools to modulate challenging protein-protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing target-specific binders with improved pharmaceutical properties, such as macrocyclic peptides. Here we report a general framework that leverages the computational power of Rosetta for large-scale backbone sampling and energy scoring, followed by side-chain composition, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we identified two peptides (PD-i3 and PD-i6) that target PD-1, a key immune checkpoint, and work as protein ligand decoys. A comprehensive biophysical evaluation confirmed their binding mechanism to PD-1 and their inhibitory effect on the PD-1/PD-L1 interaction. Finally, elucidation of their solution structures by NMR served as validation of our de novo design approach. We anticipate that our results will provide a general framework for designing target-specific drug-like peptides.

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