scholarly journals Initial Virome Characterization of the Common Cnidarian Lab Model Nematostella vectensis

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 218
Author(s):  
Magda Lewandowska ◽  
Yael Hazan ◽  
Yehu Moran
Keyword(s):  
Developmental Stages ◽  
De Novo ◽  
Artemia Salina ◽  
Model Organisms ◽  
Nematostella Vectensis ◽  
Virus Identification ◽  
Functional Studies ◽  
Powerful Approach ◽  
Viral Communities ◽  
Viral Sequences

The role of viruses in forming a stable holobiont has been the subject of extensive research in recent years. However, many emerging model organisms still lack any data on the composition of the associated viral communities. Here, we re-analyzed seven publicly available transcriptome datasets of the starlet sea anemone Nematostella vectensis, the most commonly used anthozoan lab model, and searched for viral sequences. We applied a straightforward, yet powerful approach of de novo assembly followed by homology-based virus identification and a multi-step, thorough taxonomic validation. The comparison of different lab populations of N. vectensis revealed the existence of the core virome composed of 21 viral sequences, present in all adult datasets. Unexpectedly, we observed an almost complete lack of viruses in the samples from the early developmental stages, which together with the identification of the viruses shared with the major source of the food in the lab, the brine shrimp Artemia salina, shed new light on the course of viral species acquisition in N. vectensis. Our study provides an initial, yet comprehensive insight into N. vectensis virome and sets the first foundation for the functional studies of viruses and antiviral systems in this lab model cnidarian.

scholarly journals Initial virome characterization of the common cnidarian lab model Nematostella vectensis

2020 ◽  
Author(s):  
Magda Lewandowska ◽  
Yael Hazan ◽  
Yehu Moran
Keyword(s):  
Developmental Stages ◽  
De Novo ◽  
Artemia Salina ◽  
Model Organisms ◽  
Nematostella Vectensis ◽  
Virus Identification ◽  
Functional Studies ◽  
Powerful Approach ◽  
Viral Communities ◽  
Viral Sequences

AbstractThe role of viruses in forming a stable holobiont has been a subject of extensive research in the recent years. However, many emerging model organisms still lack any data on the composition of the associated viral communities. Here, we re-analyzed seven publicly available transcriptome datasets of the starlet sea anemone Nematostella vectensis, the most commonly used anthozoan lab model, and searched for viral sequences. We applied a straightforward, yet powerful approach of de novo assembly followed by homology-based virus identification and a multi-step, thorough taxonomic validation. The comparison of different lab populations of N. vectensis revealed the existence of the core virome composed of 21 viral sequences, present in all adult datasets. Unexpectedly, we observed almost complete lack of viruses in the samples from the early developmental stages which together with the identification of the viruses shared with the major source of the food in the lab, the brine shrimp Artemia salina, shed new light on the course of viral species acquisition in N. vectensis. Our study provides an initial, yet comprehensive insight into N. vectensis virome and sets the first foundation for functional studies of viruses and antiviral systems in this lab model cnidarian.

scholarly journals Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica)

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 979 ◽  
Author(s):  
Ping Liu ◽  
Wu Chen ◽  
Jin-Ping Chen
Keyword(s):  
De Novo ◽  
Sendai Virus ◽  
Sequence Similarity ◽  
Viral Metagenomics ◽  
Manis Javanica ◽  
Pathogenic Viruses ◽  
Viral Communities ◽  
High Level ◽  
Viral Sequences ◽  
Insight Into

Pangolins are endangered animals in urgent need of protection. Identifying and cataloguing the viruses carried by pangolins is a logical approach to evaluate the range of potential pathogens and help with conservation. This study provides insight into viral communities of Malayan Pangolins (Manis javanica) as well as the molecular epidemiology of dominant pathogenic viruses between Malayan Pangolin and other hosts. A total of 62,508 de novo assembled contigs were constructed, and a BLAST search revealed 3600 ones (≥300 nt) were related to viral sequences, of which 68 contigs had a high level of sequence similarity to known viruses, while dominant viruses were the Sendai virus and Coronavirus. This is the first report on the viral diversity of pangolins, expanding our understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals.

scholarly journals De novo characterization of the Lycium ruthenicum transcriptome and analysis of its digital gene expression profiles during fruit development and ripening

2017 ◽  
Vol 69 (1) ◽  
pp. 181-190 ◽  
Author(s):  
Yong Peng ◽  
Huiqin Ma ◽  
Shangwu Chen
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
De Novo ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Digital Gene Expression ◽  
Orthologous Group ◽  
Functional Studies ◽  
Lycium Ruthenicum

Lycium ruthenicum Murr., which belongs to the family Solanaceae, is a resource plant for Chinese traditional medicine and nutraceutical foods. In this study, RNA sequencing was applied to obtain raw reads of L. ruthenicum fruit at different stages of ripening, and a de novo assembly of its sequence was performed. Approximately 52.45 million 100-bp paired-end raw reads were generated from the samples by deep RNA-seq analysis. These short reads were assembled to obtain 164814 contigs, and the contigs were assembled into 84968 non-redundant unigenes using the Trinity method. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group and KEGG (Kyoto Encyclopedia of Genes and Genomes)pathway terms. Digital gene expression analysis was applied to compare gene-expression patterns at different fruit developmental stages. These results contribute to existing sequence resources for Lycium spp. during the fruit-ripening stages, which is valuable for further functional studies of genes involved in L. ruthenicum fruit nutraceutical quality.

scholarly journals Evaluating a lightweight transcriptome assembly pipeline on two closely related ascidian species

2014 ◽  
Author(s):  
Elijah K Lowe ◽  
Billie J Swalla ◽  
C. Titus Brown
Keyword(s):  
Developmental Stages ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Marine Species ◽  
Model Organisms ◽  
The Past ◽  
Ascidian Species ◽  
Assembly Pipeline ◽  
Quality Filtering

De novo transcriptome sequencing and assembly for non-model organisms has become prevalent in the past decade. However, most assembly approaches are computationally expensive, and little in-depth evaluation has been done to compare de novo approaches. We sequenced several developmental stages of two free-spawning marine species—Molgula occulta and Molgula oculata—assembled their transcriptomes using four different combinations of preprocessing and assembly approaches, and evaluated the quality of the assembly. We present a straightforward and reproducible mRNAseq assembly protocol that combines quality filtering, digital normalization, and assembly, together with several metrics to evaluate our de novo assemblies. The use of digital normalization in the protocol reduces the time and memory needed to complete the assembly and makes this pipeline available to labs without large computing infrastructure. Despite varying widely in basic assembly statistics, all of the assembled transcriptomes evaluate well in metrics such as gene recovery and estimated completeness.

scholarly journals Evaluating a lightweight transcriptome assembly pipeline on two closely related ascidian species

2014 ◽  
Author(s):  
Elijah K Lowe ◽  
Billie J Swalla ◽  
C. Titus Brown
Keyword(s):  
Developmental Stages ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Marine Species ◽  
Model Organisms ◽  
The Past ◽  
Ascidian Species ◽  
Assembly Pipeline ◽  
Quality Filtering

De novo transcriptome sequencing and assembly for non-model organisms has become prevalent in the past decade. However, most assembly approaches are computationally expensive, and little in-depth evaluation has been done to compare de novo approaches. We sequenced several developmental stages of two free-spawning marine species—Molgula occulta and Molgula oculata—assembled their transcriptomes using four different combinations of preprocessing and assembly approaches, and evaluated the quality of the assembly. We present a straightforward and reproducible mRNAseq assembly protocol that combines quality filtering, digital normalization, and assembly, together with several metrics to evaluate our de novo assemblies. The use of digital normalization in the protocol reduces the time and memory needed to complete the assembly and makes this pipeline available to labs without large computing infrastructure. Despite varying widely in basic assembly statistics, all of the assembled transcriptomes evaluate well in metrics such as gene recovery and estimated completeness.

scholarly journals The Developmental Transcriptome of Bagworm, Metisa plana (Lepidoptera: Psychidae) and Insights into Chitin Biosynthesis Genes

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 7
Author(s):  
Nur Lina Rahmat ◽  
Anis Nadyra Zifruddin ◽  
Cik Mohd Rizuan Zainal Abidin ◽  
Nor-Azlan Nor Muhammad ◽  
Maizom Hassan
Keyword(s):  
Oil Palm ◽  
Developmental Stages ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Insect Pest ◽  
Instar Larva ◽  
Orthologous Group ◽  
Kegg Pathways ◽  
Developmental Gene Expression ◽  
Functional Studies

Bagworm, Metisa plana (Lepidoptera: Psychidae) is a ubiquitous insect pest in the oil palm plantations. M. plana infestation could reduce the oil palm productivity by 40% if it remains untreated over two consecutive years. Despite the urgency to tackle this issue, the genome and transcriptome of M. plana have not yet been fully elucidated. Here, we report a comprehensive transcriptome dataset from four different developmental stages of M. plana, comprising of egg, third instar larva, pupa and female adult. The de novo transcriptome assembly of the raw data had produced a total of 193,686 transcripts, which were then annotated against UniProt, NCBI non-redundant (NR) database, Gene Ontology, Cluster of Orthologous Group, and Kyoto Encyclopedia of Genes and Genomes databases. From this, 46,534 transcripts were annotated and mapped to 146 known metabolic or signalling KEGG pathways. The paper further identified 41 differentially expressed transcripts encoding seven genes in the chitin biosynthesis pathways, and their expressions across each developmental stage were further analysed. The genetic diversity of M. plana was profiled whereby there were 21,516 microsatellite sequences and 379,895 SNPs loci found in the transcriptome of M. plana. These datasets add valuable transcriptomic resources for further study of developmental gene expression, transcriptional regulations and functional gene activities involved in the development of M. plana. Identification of regulatory genes in the chitin biosynthesis pathway may also help in developing an RNAi-mediated pest control management by targeting certain pathways, and functional studies of the genes in M. plana.

scholarly journals Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms

2021 ◽  
Author(s):  
José Cerca ◽  
Marius F. Maurstad ◽  
Nicolas C. Rochette ◽  
Angel G. Rivera‐Colón ◽  
Niraj Rayamajhi ◽  
...  
Keyword(s):  
De Novo ◽  
Model Organisms

scholarly journals In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2226
Author(s):  
Sazia Kunvar ◽  
Sylwia Czarnomska ◽  
Cino Pertoldi ◽  
Małgorzata Tokarska
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Model Organism ◽  
Genotyping By Sequencing ◽  
Model Organisms ◽  
European Bison ◽  
Model Animal ◽  
Pcr Duplicates ◽  
Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

scholarly journals The brain transcriptome of the wolf spider, Schizocosa ocreata

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Daniel Stribling ◽  
Peter L. Chang ◽  
Justin E. Dalton ◽  
Christopher A. Conow ◽  
Malcolm Rosenthal ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Model Organisms ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Wolf Spiders ◽  
Schizocosa Ocreata ◽  
Genomic Studies ◽  
The Brain

Abstract Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

scholarly journals Genome-wide characterization of 2-oxoglutarate and Fe(II)-dependent dioxygenase family genes in tomato during growth cycle and their roles in metabolism

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shuo Wei ◽  
Wen Zhang ◽  
Rao Fu ◽  
Yang Zhang
Keyword(s):  
Metabolic Pathways ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Growth Cycle ◽  
Model Organisms ◽  
Gibberellin Biosynthesis ◽  
Type I ◽  
Multiple Model ◽  
Genome Wide ◽  
Tomato Growth

Abstract Background 2-Oxoglutarate and Fe(II)-dependent dioxygenases (2ODDs) belong to the 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily and are involved in various vital metabolic pathways of plants at different developmental stages. These proteins have been extensively investigated in multiple model organisms. However, these enzymes have not been systematically analyzed in tomato. In addition, type I flavone synthase (FNSI) belongs to the 2ODD family and contributes to the biosynthesis of flavones, but this protein has not been characterized in tomato. Results A total of 131 2ODDs from tomato were identified and divided into seven clades by phylogenetic classification. The Sl2ODDs in the same clade showed similar intron/exon distributions and conserved motifs. The Sl2ODDs were unevenly distributed across the 12 chromosomes, with different expression patterns among major tissues and at different developmental stages of the tomato growth cycle. We characterized several Sl2ODDs and their expression patterns involved in various metabolic pathways, such as gibberellin biosynthesis and catabolism, ethylene biosynthesis, steroidal glycoalkaloid biosynthesis, and flavonoid metabolism. We found that the Sl2ODD expression patterns were consistent with their functions during the tomato growth cycle. These results indicated the significance of Sl2ODDs in tomato growth and metabolism. Based on this genome-wide analysis of Sl2ODDs, we screened six potential FNSI genes using a phylogenetic tree and coexpression analysis. However, none of them exhibited FNSI activity. Conclusions Our study provided a comprehensive understanding of the tomato 2ODD family and demonstrated the significant roles of these family members in plant metabolism. We also suggest that no FNSI genes in tomato contribute to the biosynthesis of flavones.

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