scholarly journals AN APPROACH TO TRANSCRIPTOME ANALYSIS OF NON-MODEL ORGANISMS USING SHORT-READ SEQUENCES

2008 ◽  
Author(s):  
LESLEY J COLLINS ◽  
PATRICK J BIGGS ◽  
CLAUDIA VOELCKEL ◽  
SIMON JOLY
Keyword(s):  
Transcriptome Analysis ◽  
Model Organisms ◽  
Short Read

scholarly journals Realizing the potential of full-length transcriptome sequencing

2019 ◽  
Vol 374 (1786) ◽  
pp. 20190097 ◽  
Author(s):  
Ashley Byrne ◽  
Charles Cole ◽  
Roger Volden ◽  
Christopher Vollmers
Keyword(s):  
Single Cell ◽  
Transcriptome Analysis ◽  
Transcriptome Sequencing ◽  
Model Organisms ◽  
Sequencing Technology ◽  
Short Read ◽  
Short Read Sequencing ◽  
Unicellular Eukaryotes ◽  
Long Read ◽  
Future Work

Long-read sequencing holds great potential for transcriptome analysis because it offers researchers an affordable method to annotate the transcriptomes of non-model organisms. This, in turn, will greatly benefit future work on less-researched organisms like unicellular eukaryotes that cannot rely on large consortia to generate these transcriptome annotations. However, to realize this potential, several remaining molecular and computational challenges will have to be overcome. In this review, we have outlined the limitations of short-read sequencing technology and how long-read sequencing technology overcomes these limitations. We have also highlighted the unique challenges still present for long-read sequencing technology and provided some suggestions on how to overcome these challenges going forward. This article is part of a discussion meeting issue ‘Single cell ecology’.

scholarly journals Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus)

2019 ◽  
Author(s):  
Ashley Byrne ◽  
Megan A. Supple ◽  
Roger Volden ◽  
Kristin L. Laidre ◽  
Beth Shapiro ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Whole Blood ◽  
Polar Bear ◽  
Ursus Maritimus ◽  
Full Length ◽  
The Arctic ◽  
Model Organisms ◽  
Short Read ◽  
Full Length Cdna ◽  
Long Read

AbstractTranscriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic as they compete with and prevent the detection of rare RNA transcripts, obscuring their biological importance. This issue is more pronounced when using long-read sequencing technologies for isoform-level transcriptome analysis, as they have relatively lower throughput compared to short-read sequencers. As a result long-read based transcriptome analysis is prohibitively expensive for non-model organisms. While there are off-the-shelf kits available for select model organisms capable of depleting highly abundant transcripts for alpha (HBA) and beta (HBB) hemoglobin, they are unsuitable for non-model organisms. To address this, we have adapted the recent CRISPR/Cas9 based depletion method (Depletion of Abundant Sequences by Hybridization) for long-read full-length cDNA sequencing approaches that we call Long-DASH. Using a recombinant Cas9 protein with appropriate guide RNAs, full-length hemoglobin transcripts can be depleted in-vitro prior to performing any short- and long-read sequencing library preparations. Using this method, we sequenced depleted full-length cDNA in parallel using both our Oxford Nanopore Technology (ONT) based R2C2 long-read approach, as well as the Illumina short-read based Smart-seq2 approach. To showcase this, we have applied our methods to create an isoform-level transcriptome from whole blood samples derived from three polar bears (Ursus maritimus). Using Long-DASH, we succeeded in depleting hemoglobin transcripts and generated deep Smart-seq2 Illumina datasets and 3.8 million R2C2 full-length cDNA consensus reads. Applying Long-DASH with our isoform identification pipeline, Mandalorion we discovered ~6,000 high-confidence isoforms and a number of novel genes. This indicates there is a high diversity of gene isoforms within Ursus maritimus not yet reported. This reproducible and straightforward approach has not only improved the polar bear transcriptome annotations but will serve as the foundation for future efforts to investigate transcriptional dynamics within the 19 polar bear subpopulations around the Arctic.

scholarly journals A de novo approach to disentangle partner identity and function in holobiont systems

2017 ◽  
Author(s):  
Arnaud Meng ◽  
Camille Marchet ◽  
Erwan Corre ◽  
Pierre Peterlongo ◽  
Adriana Alberti ◽  
...  
Keyword(s):  
Functional Diversity ◽  
De Novo ◽  
Model Organisms ◽  
Symbiotic Association ◽  
Proof Of Concept ◽  
Short Read ◽  
Symbiotic Associations ◽  
Functional Annotations ◽  
And Function ◽  
Similarity Method

AbstractBackgroundStudy of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. The study of holobiont transcriptomes shares similarities with meta-transcriptomic, and hence, is also affected by challenges invoked above. Here we propose an innovative approach to tackle such difficulties which was applied to the study of marine holobiont models as a proof of concept.ResultsWe considered three holobionts models, of which two transcriptomes were previously assembled and published, and a yet unpublished transcriptome, to analyze their raw reads and assign them to the host and/or to the symbiont(s) using Short Read Connector, a k-mer based similarity method. We were able to define four distinct categories of reads for each holobiont transcriptome: host reads, symbiont reads, shared reads and unassigned reads. The result of the independent assemblies for each category within a transcriptome led to a significant diminution of de novo assembled chimeras compared to classical assembly methods. Combining independent functional and taxonomic annotations of each partner’s transcriptome is particularly convenient to explore the functional diversity of an holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts and a first transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is limited. ConclusionsIn contrast to classical assembly approaches, our bioinformatic strategy not only allows biologists to studying separately host and symbiont data from a holobiont mixture, but also generates improved transcriptome assemblies. The use of Short Read Connector has proven to be an effective way to tackle meta-transcriptomic challenges to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages such as the newly sequenced marine plankton Radiolaria-Dinophyta symbiosis and ultimately expand our knowledge about these marine symbiotic associations.

A Comprehensive Ultrastructure and Transcriptome Analyses of Early Regeneration in Ophryotrocha Xiamen Sp. Nov. (Annelida: Dorvilleidae)

2020 ◽  
Author(s):  
Ruanni Chen ◽  
Irum Mukhtar ◽  
Shurong Wei ◽  
Siyi Wu ◽  
Jianming Chen
Keyword(s):  
Transcriptome Analysis ◽  
Expression Patterns ◽  
Model Organisms ◽  
Suitable Model ◽  
Potential Candidate ◽  
Comparative Transcriptome ◽  
Coastal Zones ◽  
Model Species ◽  
Comparative Transcriptome Analysis ◽  
Early Regeneration

Abstract BackgroundIn recent years, significant progress has been made using powerful genetic approaches with newly developed models for understanding on regeneration, however, the molecular and cellular basis of early regeneration remains unclear. Annelids of the genus Ophryotrocha have long been subjects of research use as model species in ecological, toxicological, reproductive, and regenerative investigations. Although, Ophryotrocha spp., are amenable to molecular, cellular, and functional analyses, still in need to explore new model organisms in this genus to understand regeneration mechanisms. Here, we focus on a newly identified Ophryotrocha species for its early regeneration developmental mode.ResultsBased on detailed morphological (K-maxillae, rosette gland, and chromosome number) and molecular analyses, we present, O. xiamen as a new suitable model species to investigate the early regeneration mechanism. The comparative transcriptome analysis showed the gene expression patterns were related to transcriptional regulation, energy metabolism profiles and structure and signal transduction during early stages of regeneration. Data also exhibited that genes such as neurotrypsin, Nos2, DMBT1, SCO spondin, and endotubin associated to regulate inflammation, enterocyte differentiation, apoptosis, and neuroepithelial, were up-regulated during early regeneration stages (wound healing and blastema formation). Additionally, most of the known regeneration-related genes of annelids were also identified in O. xiamen which enabled to explore the precise functions of genes involved in regeneration process.ConclusionsThis study enriches the identification of genus Ophryotrocha in Chinese coastal zones, an area with high abundances of annelids. The comparative transcriptome analysis provided the whole expression changes during early regeneration process. Morphology and molecular shred of evidences in O. xiamen revealed similar features of early regeneration with other invertebrates. Information on potential candidate genes associated with early regeneration in O. xiamen, will be useful for further studies.

scholarly journals The Transcriptome Analysis and Comparison Explorer—T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms

2012 ◽  
Vol 28 (6) ◽  
pp. 777-783 ◽  
Author(s):  
E. E. R. Philipp ◽  
L. Kraemer ◽  
D. Mountfort ◽  
M. Schilhabel ◽  
S. Schreiber ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Model Organisms ◽  
Graphical Tool

scholarly journals Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tatiana Maroilley ◽  
Xiao Li ◽  
Matthew Oldach ◽  
Francesca Jean ◽  
Susan J. Stasiuk ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Chromosomal Rearrangements ◽  
Large Deletion ◽  
Genomic Rearrangements ◽  
Model Organisms ◽  
Whole Genome ◽  
Short Read ◽  
C Elegans ◽  
Long Read

AbstractGenomic rearrangements cause congenital disorders, cancer, and complex diseases in human. Yet, they are still understudied in rare diseases because their detection is challenging, despite the advent of whole genome sequencing (WGS) technologies. Short-read (srWGS) and long-read WGS approaches are regularly compared, and the latter is commonly recommended in studies focusing on genomic rearrangements. However, srWGS is currently the most economical, accurate, and widely supported technology. In Caenorhabditis elegans (C. elegans), such variants, induced by various mutagenesis processes, have been used for decades to balance large genomic regions by preventing chromosomal crossover events and allowing the maintenance of lethal mutations. Interestingly, those chromosomal rearrangements have rarely been characterized on a molecular level. To evaluate the ability of srWGS to detect various types of complex genomic rearrangements, we sequenced three balancer strains using short-read Illumina technology. As we experimentally validated the breakpoints uncovered by srWGS, we showed that, by combining several types of analyses, srWGS enables the detection of a reciprocal translocation (eT1), a free duplication (sDp3), a large deletion (sC4), and chromoanagenesis events. Thus, applying srWGS to decipher real complex genomic rearrangements in model organisms may help designing efficient bioinformatics pipelines with systematic detection of complex rearrangements in human genomes.

Reductionist thinking and animal models in neuropsychiatric research

2019 ◽  
Vol 42 ◽  
Author(s):  
Nicole M. Baran
Keyword(s):  
Animal Models ◽  
Mental Disorders ◽  
Environmental Factors ◽  
Neuropsychiatric Disorders ◽  
Model Organisms ◽  
Developmental Genetic ◽  
Term Study ◽  
Genetic And Environmental Factors ◽  
Mechanisms Of Plasticity

AbstractReductionist thinking in neuroscience is manifest in the widespread use of animal models of neuropsychiatric disorders. Broader investigations of diverse behaviors in non-model organisms and longer-term study of the mechanisms of plasticity will yield fundamental insights into the neurobiological, developmental, genetic, and environmental factors contributing to the “massively multifactorial system networks” which go awry in mental disorders.

Apoptosis and development

2003 ◽  
Vol 39 ◽  
pp. 11-24 ◽  
Author(s):  
Justin V McCarthy
Keyword(s):  
Drosophila Melanogaster ◽  
Mammalian Cells ◽  
Cell Number ◽  
Model Organisms ◽  
Biological Processes ◽  
Nematode Caenorhabditis Elegans ◽  
Apoptotic Pathway ◽  
Genetic Pathways ◽  
Evolutionarily Conserved ◽  
Multicellular Organisms

Apoptosis is an evolutionarily conserved process used by multicellular organisms to developmentally regulate cell number or to eliminate cells that are potentially detrimental to the organism. The large diversity of regulators of apoptosis in mammalian cells and their numerous interactions complicate the analysis of their individual functions, particularly in development. The remarkable conservation of apoptotic mechanisms across species has allowed the genetic pathways of apoptosis determined in lower species, such as the nematode Caenorhabditis elegans and the fruitfly Drosophila melanogaster, to act as models for understanding the biology of apoptosis in mammalian cells. Though many components of the apoptotic pathway are conserved between species, the use of additional model organisms has revealed several important differences and supports the use of model organisms in deciphering complex biological processes such as apoptosis.

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