Reannotation of eight Drosophila genomes

AbstractThe sequenced genomes in the Drosophila phylogeny is a central resource for comparative work supporting the understanding of the Drosophila melanogaster non-mammalian model system. These have also facilitated studying the selected and random differences that distinguish the thousands of extant species of Drosophila. However, full utility has been hampered by uneven genome annotation. We have generated a large expression profile dataset for nine species of Drosophila and trained a transcriptome assembly approach on Drosophila melanogaster to develop a pipeline that best matched the extensively curated annotation. We then applied this to the other species to add tens of thousands of new gene models per species. We also developed new orthologs to facilitate cross-species comparisons. We validated the new annotation of the distantly related Drosophila grimshawi with an extensive collection of newly sequenced cDNAs. This reannoation will facilitate understanding both the core commonalities and the species differences in this important group of model organisms.

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Re-annotation of eight Drosophila genomes

Life Science Alliance ◽

10.26508/lsa.201800156 ◽

2018 ◽

Vol 1 (6) ◽

pp. e201800156 ◽

Cited By ~ 15

Author(s):

Haiwang Yang ◽

Maria Jaime ◽

Maxi Polihronakis ◽

Kelvin Kanegawa ◽

Therese Markow ◽

...

Keyword(s):

Species Differences ◽

Transcriptome Assembly ◽

Model Organisms ◽

The Core ◽

Extant Species ◽

Species Comparisons ◽

Central Resource ◽

Extensive Collection ◽

The Many ◽

Drosophila Grimshawi

The sequenced genomes of the Drosophila phylogeny are a central resource for comparative work supporting the understanding of the Drosophila melanogaster non-mammalian model system. These have also facilitated evolutionary studies on the selected and random differences that distinguish the thousands of extant species of Drosophila. However, full utility has been hampered by uneven genome annotation. We have generated a large expression profile dataset for nine species of Drosophila and trained a transcriptome assembly approach on D. melanogaster that best matched the extensively curated annotation. We then applied this to the other species to add more than 10000 transcript models per species. We also developed new orthologs to facilitate cross-species comparisons. We validated the new annotation of the distantly related Drosophila grimshawi with an extensive collection of newly sequenced cDNAs. This re-annotation will facilitate understanding both the core commonalities and the species differences in this important group of model organisms, and suggests a strategy for annotating the many forthcoming genomes covering the tree of life.

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Apoptosis and development

Essays in Biochemistry ◽

10.1042/bse0390011 ◽

2003 ◽

Vol 39 ◽

pp. 11-24 ◽

Cited By ~ 6

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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The brain transcriptome of the wolf spider, Schizocosa ocreata

BMC Research Notes ◽

10.1186/s13104-021-05648-y ◽

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.

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Genetic analysis of oxygen defense mechanisms in Drosophila melanogaster and identification of a novel behavioural mutant with a Shaker phenotype

Genome ◽

10.1139/g96-094 ◽

1996 ◽

Vol 39 (4) ◽

pp. 749-757 ◽

Cited By ~ 7

Author(s):

James M. Humphreys ◽

Brenda Duyf ◽

Mei-Ling A. Joiner ◽

John P. Phillips ◽

Arthur J. Hilliker

Keyword(s):

Drosophila Melanogaster ◽

Defense Mechanisms ◽

Chromosome Region ◽

Recessive Mutation ◽

Ether Anaesthesia ◽

Ros Metabolism ◽

Chromosome Mutations ◽

New Gene ◽

New Alleles

Mutants of Drosophila melanogaster that lack Cu/Zn superoxide dismutase or urate are hypersensitive to reactive oxygen species (ROS) generated in vivo by the redox-cycling agent paraquat. We have subsequently employed paraquat as a selective agent to identify adult viable mutants potentially defective in other, perhaps unknown, components of ROS metabolism. Paraquat screening of ethyl methanesulfonate-induced second- and third-chromosome mutations yielded 24 paraquat hypersensitive mutants. Two mutants were identified as being new alleles of the previously identified doublesex (dsx) and pink (p) genes. The remainder of the mutations identified previously undescribed genes, including one second chromosome paraquat hypersensitive mutant that was found to exhibit shaking legs, abdomen pulsations, and body shuddering under ether anaesthesia. This recessive mutation was mapped to the polytene chromosome region of 48A5–48B2 and defines a new gene we named quiver (qvr). This mutation is similar in phenotype to the Shaker (Sh), ether-a-gogo (eag), and Hyperkinetic (Hk) mutations, all of which affect potassium channel function in D. melanogaster. Key words : Drosophila, paraquat, EMS-mutagenesis, Shaker, oxidative-stress.

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The Neurotransmitters Involved in Drosophila Alcohol-Induced Behaviors

Frontiers in Behavioral Neuroscience ◽

10.3389/fnbeh.2020.607700 ◽

2020 ◽

Vol 14 ◽

Author(s):

Maggie M. Chvilicek ◽

Iris Titos ◽

Adrian Rothenfluh

Keyword(s):

Drosophila Melanogaster ◽

Behavioral Response ◽

Recent Progress ◽

Mammalian Species ◽

Health And Safety ◽

Model Organisms ◽

Negative Consequences ◽

Behavioral Repertoire ◽

Significant Research ◽

Alcohol Response

Alcohol is a widely used and abused substance with numerous negative consequences for human health and safety. Historically, alcohol's widespread, non-specific neurobiological effects have made it a challenge to study in humans. Therefore, model organisms are a critical tool for unraveling the mechanisms of alcohol action and subsequent effects on behavior. Drosophila melanogaster is genetically tractable and displays a vast behavioral repertoire, making it a particularly good candidate for examining the neurobiology of alcohol responses. In addition to being experimentally amenable, Drosophila have high face and mechanistic validity: their alcohol-related behaviors are remarkably consistent with humans and other mammalian species, and they share numerous conserved neurotransmitters and signaling pathways. Flies have a long history in alcohol research, which has been enhanced in recent years by the development of tools that allow for manipulating individual Drosophila neurotransmitters. Through advancements such as the GAL4/UAS system and CRISPR/Cas9 mutagenesis, investigation of specific neurotransmitters in small subsets of neurons has become ever more achievable. In this review, we describe recent progress in understanding the contribution of seven neurotransmitters to fly behavior, focusing on their roles in alcohol response: dopamine, octopamine, tyramine, serotonin, glutamate, GABA, and acetylcholine. We chose these small-molecule neurotransmitters due to their conservation in mammals and their importance for behavior. While neurotransmitters like dopamine and octopamine have received significant research emphasis regarding their contributions to behavior, others, like glutamate, GABA, and acetylcholine, remain relatively unexplored. Here, we summarize recent genetic and behavioral findings concerning these seven neurotransmitters and their roles in the behavioral response to alcohol, highlighting the fitness of the fly as a model for human alcohol use.

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A practical guide to buildde-novoassemblies for single tissues of non-model organisms: the example of a Neotropical frog

PeerJ ◽

10.7717/peerj.3702 ◽

2017 ◽

Vol 5 ◽

pp. e3702 ◽

Cited By ~ 5

Author(s):

Santiago Montero-Mendieta ◽

Manfred Grabherr ◽

Henrik Lantz ◽

Ignacio De la Riva ◽

Jennifer A. Leonard ◽

...

Keyword(s):

Defense Mechanisms ◽

De Novo ◽

Transcriptome Assembly ◽

Cost Effective ◽

Model Organisms ◽

Rna Seq ◽

Assembly Pipeline ◽

Wide Variability ◽

History Of ◽

Inexperienced User

Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembledde-novo. We used RNA-seq to obtain the transcriptomic profile forOreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome ofO. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating ade-novotranscriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to buildde-novotranscriptome assemblies using readily available software and is freely available at:https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.

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Biogeography and Host Usage of Coral-Associated Crustaceans: Barnacles, Copepods, and Gall Crabs as Model Organisms

Evolution and Biogeography ◽

10.1093/oso/9780190637842.003.0008 ◽

2020 ◽

pp. 183-215

Author(s):

Benny K. K. Chan ◽

Kingsley J. H. Wong ◽

Yu-Rong Cheng

Keyword(s):

Deep Sea ◽

Model Organisms ◽

Coral Host ◽

West Pacific ◽

Pacific Waters ◽

Extant Species ◽

The Family ◽

The Caribbean ◽

Diverse Groups ◽

Gall Crabs

Most of the diverse groups of crustaceans associated with scleractinian and fire corals form symbiotic relationship with their coral hosts. Coral-associated barnacles include species from the orders Acrothoracica and Thoracica. Most of the coral-associated barnacles belong to the family Pyrgomatidae in Thoracica. Within Pyrgomatidae, the subfamily Ceratoconchinae contains mostly extant species and is present from Florida through the Caribbean to Brazilian waters. The subfamily Megatrematinae has lower species diversity and has a cosmopolitan distribution (except the Eastern Pacific). The Pyrgomatinae are the most species-rich subfamily and distributed only in Indo-West Pacific waters. Host usage of pyrgomatinid barnacles varies spatially, probably related to coral host diversity. Copepods are the most common and most abundant coral-associated crustaceans, often associated with scleractinian, gorgonian, and alcyonacean corals. More than 90% of coral-associated copepods are endemic to the Indo-West Pacific. In contrast, only a few species (<10%) have been discovered from the Atlantic due to several historical perturbations reducing the diversity of their coral hosts. The communities of coral-associated copepods thus show dramatic differences between geographic regions, notably between the Indian, Pacific, and Atlantic Oceans. Brachyurans of the family Cryptochiridae (gall crabs) are obligate associates or parasites, of scleractinian coral hosts in tropical and subtropical seas, being a monophyletic group of only 52 species, from the intertidal to the deep sea (to 512 m) habitats with most (46) recorded in the seas of the tropical Indo-West Pacific and none being cosmopolitan. Atlantic species of Cryptochiridae, apparently not phylogenetically related, display less strict host specificity than their Indo-West Pacific counterparts. Current phylogenetic understandings of the group remain preliminary, while one consistent Indo-West Pacific clade reflects rapid species diversification during the last ~15 million years.

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rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

10.1101/420208 ◽

2018 ◽

Cited By ~ 13

Author(s):

Elena Bushmanova ◽

Dmitry Antipov ◽

Alla Lapidus ◽

Andrey D. Prjibelski

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Model Organisms ◽

Challenging Problem ◽

Rna Seq ◽

De Novo Transcriptome ◽

Weak Points ◽

Transcriptome Reconstruction ◽

Evaluation Approaches ◽

Genome Assembler

AbstractSummaryPossibility to generate large RNA-seq datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the model organisms with finished and annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing and paralogous genes. In this paper we describe a novel transcriptome assembler called rnaSPAdes, which is developed on top of SPAdes genome assembler and explores surprising computational parallels between assembly of transcriptomes and single-cell genomes. We also present quality assessment reports for rnaSPAdes assemblies, compare it with modern transcriptome assembly tools using several evaluation approaches on various RNA-Seq datasets, and briefly highlight strong and weak points of different assemblers.Availability and implementationrnaSPAdes is implemented in C++ and Python and is freely available at cab.spbu.ru/software/rnaspades/.

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K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity

10.1101/149948 ◽

2017 ◽

Author(s):

Chang Sik Kim ◽

Martyn D. Winn ◽

Vipin Sachdeva ◽

Kirk E. Jordan

Keyword(s):

Clustering Algorithm ◽

De Novo ◽

Transcriptome Assembly ◽

Initial Step ◽

Computer Hardware ◽

Model Organisms ◽

De Bruijn Graph ◽

Memory Representation ◽

Novel Approach ◽

Sequencing Problems

AbstractBackgroundDe novo transcriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo assemblers using the de Bruijn graph of a set of the RNA sequences rely on in-memory representation of this graph. However, current methods analyse the complete set of read-derived k-mer sequence at once, resulting in the need for computer hardware with large shared memory.ResultsWe introduce a novel approach that clusters k-mers as the first step. The clusters correspond to small sets of gene products, which can be processed quickly to give candidate transcripts. We implement the clustering step using the MapReduce approach for parallelising the analysis of large datasets, which enables the use of compute clusters. The computational task is distributed across the compute system, and no specialised hardware is required. Using this approach, we have re-implemented the Inchworm module from the widely used Trinity pipeline, and tested the method in the context of the full Trinity pipeline. Validation tests on a range of real datasets show large reductions in the runtime and per-node memory requirements, when making use of a compute cluster.ConclusionsOur study shows that MapReduce-based clustering has great potential for distributing challenging sequencing problems, without loss of accuracy. Although we have focussed on the Trinity package, we propose that such clustering is a useful initial step for other assembly pipelines.

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Spectrum of protein localization in proteomes captures evolutionary relation between species

10.1101/845362 ◽

2019 ◽

Author(s):

Valérie Marot-Lassauzaie ◽

Tatyana Goldberg ◽

Burkhard Rost

Keyword(s):

Protein Function ◽

Homo Sapiens ◽

Protein Localization ◽

Model Organisms ◽

Prediction Methods ◽

Systematic Bias ◽

Human Protein Atlas ◽

Species Comparisons ◽

The One ◽

Evolutionary Comparisons

AbstractThe native subcellular localization or cellular compartment of a protein is the one in which it acts most often; it is one aspect of protein function. Do ten eukaryotic model organisms differ in their location spectrum, i.e. the fraction of its proteome in each of its seven major compartments? As experimental annotations of locations remain biased and incomplete, we need prediction methods to answer this question. To gauge the bias of prediction methods, we merged all available experimental annotations for the human proteome. In doing so, we found important values in both Swiss-Prot and the Human Protein Atlas (HPA). After systematic bias corrections, the complete but faulty prediction methods appeared to be more appropriate to compare location spectra between species than the incomplete more accurate experimental data. This work compared the location spectra for ten eukaryotes: Homo sapiens, Gorilla gorilla, Pan troglodytes, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Anopheles gambiae, Caenorhabitis elegans, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Overall, the predicted location spectra were similar. However, the detailed differences were significant enough to plot trees and 2D (PCA) maps relating the ten organisms using a simple Euclidean distance in seven states, corresponding to the seven studied localization classes. The relations based on the simple predicted location spectra captured aspects of cross-species comparisons usually revealed only by much more detailed evolutionary comparisons.

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