Comparative transcriptomics of early dipteran development

BMC Genomics
Eva Jiménez-GuriJohannes Jaeger

Abstract

Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo). We have sequenced early embryonic transcriptomes of two non-drosophilid dipteran species: the moth midge Clogmia albipunctata, and the scuttle fly Megaselia abdita. Our analysis includes a third, published, transcriptome for the hoverfly Episyrphus balteatus. These emerging models for comparative developmental studies close an important phylogenetic gap between Drosophila melanogaster and other insect model systems. In this paper, we provide a comparative analysis of early embryonic transcriptomes across species, and use our data for a phylogenomic re-evaluation of dipteran phylogenetic relationships. We show how comparative transcriptomics can be used to create useful resources for evo-devo, and to investigate phylogenetic relationships. Our results demonstrate that de novo assembly of short (Illumina) reads yields high-quality, high-coverage transcriptomic data sets. We use these ...Continue Reading

References

Feb 12, 1988·Science·K G FieldR A Raff
Mar 25, 1981·Journal of Molecular Biology·T Smith, M S Waterman
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Aug 1, 1997·Mechanisms of Development·François BonnetonGabriel A Dover
Mar 31, 1999·Proceedings of the National Academy of Sciences of the United States of America·Michael StauberUrs Schmidt-Ott
Mar 25, 2000·Science·Mark D AdamsJ C Venter
Apr 26, 2000·Proceedings of the National Academy of Sciences of the United States of America·A AdoutteR de Rosa
Sep 20, 2000·Proceedings of the National Academy of Sciences of the United States of America·Michael StauberUrs Schmidt-Ott
Jan 5, 2001·Nucleic Acids Research·T Sicheritz-Pontén, S G Andersson
Jul 24, 2001·Development Genes and Evolution·Alistair P McGregorGabriel A Dover
Aug 2, 2001·Evolution & Development·P J ShawGabriel A Dover
Aug 30, 2001·Proceedings of the National Academy of Sciences of the United States of America·M S Rosenberg, S Kumar
Dec 1, 2001·Annual Review of Entomology·Gregory K Davis, Nipam H Patel
Dec 26, 2001·Bioinformatics·H Shimodaira, M Hasegawa
Jan 5, 2002·Proceedings of the National Academy of Sciences of the United States of America·Michael StauberUrs Schmidt-Ott
Sep 14, 2002·Systematic Biology·Derrick J Zwickl, David M Hillis
Oct 5, 2002·Science·Robert A HoltStephen L Hoffman
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Jun 4, 2004·Molecular Biology and Evolution·Hervé PhilippeDidier Casane
Aug 7, 2004·Science·Dave KosmanEthan Bier
Sep 18, 2004·Bioinformatics·C J Creevey, J O McInerney
Mar 5, 2005·Molecular Biology and Evolution·Antonis Rokas, Sean B Carroll
Apr 30, 2005·Nature Reviews. Genetics·Frédéric DelsucHervé Philippe
Sep 30, 2005·Development Genes and Evolution·Joanna Richardson, Pat Simpson
Mar 25, 2006·Nucleic Acids Research·Iain M WallaceCedric Notredame
Mar 24, 2007·Bioinformatics·Baris E SuzekCathy H Wu
May 19, 2007·Science·Vishvanath NeneDavid W Severson
Jun 15, 2007·Genome Biology·Jaime Huerta-CepasToni Gabaldón
Jul 25, 2007·Genome Biology·Pavel TomancakGerald M Rubin
Oct 4, 2007·Molecular Phylogenetics and Evolution·Christopher A DesjardinsCharles Mitter
Nov 13, 2007·Nature·Drosophila 12 Genomes ConsortiumIain MacCallum
Dec 11, 2007·Developmental Biology·Svetlana SurkovaJohn Reinitz
Jan 4, 2008·Proceedings of the National Academy of Sciences of the United States of America·Ab Matteen RafiqiUrs Schmidt-Ott
Jan 25, 2008·Development Genes and Evolution·Michael StauberUrs Schmidt-Ott
Mar 26, 2008·Nature·Tribolium Genome Sequencing ConsortiumGregor Bucher
Mar 29, 2008·Briefings in Bioinformatics·Kazutaka Katoh, Hiroyuki Toh
May 14, 2008·Bioinformatics·André WeheOliver Eulenstein
Jul 22, 2008·Evolution & Development·Steffen LemkeUrs Schmidt-Ott
Jul 30, 2008·Nature Reviews. Genetics·Chris P Ponting
Oct 23, 2008·Nucleic Acids Research·Sarah HunterCorin Yeats
Nov 6, 2008·Genome Biology·Toni Gabaldón
Nov 22, 2008·Evolution & Development·Marc F ScheteligErnst A Wimmer
Jan 6, 2009·Insect Biochemistry and Molecular Biology·International Silkworm Genome Consortium
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Mar 5, 2009·PloS One·Brant K PetersonMichael B Eisen
Mar 17, 2009·Trends in Genetics : TIG·Bárbara Negre, Pat Simpson
Jun 10, 2009·Bioinformatics·Salvador Capella-GutiérrezToni Gabaldón
Jun 19, 2009·Bioinformatics·Nicolas LartillotSamuel Blanquart
Sep 10, 2009·Bioinformatics·Timo LassmannCarsten O Daub
Jan 15, 2010·BMC Bioinformatics·Jaime Huerta-CepasToni Gabaldón
Jan 19, 2010·Proceedings of the National Academy of Sciences of the United States of America·Chris Todd HittingerAntonis Rokas
Feb 11, 2010·Genome Biology·Michel C MilinkovitchToni Gabaldón
Feb 27, 2010·PLoS Biology·International Aphid Genomics Consortium
May 1, 2010·Development·Steffen LemkeUrs Schmidt-Ott
May 4, 2010·Developmental Biology·Mónica A García-SolacheMichael Akam
Oct 12, 2010·Cellular and Molecular Life Sciences : CMLS·Johannes Jaeger
Nov 12, 2010·Nucleic Acids Research·David CroftLincoln Stein
Nov 16, 2010·Bioinformatics·Jaime Huerta-Cepas, Toni Gabaldón
Dec 15, 2010·Nature·Alex T KalinkaPavel Tomancak
Dec 24, 2010·Nature·Brenton R GraveleySusan E Celniker
Jan 27, 2011·BMC Genomics·Ben Ewen-CampenCassandra G Extavour
Feb 22, 2011·Nucleic Acids Research·Marina Marcet-Houben, Toni Gabaldón
Mar 16, 2011·Proceedings of the National Academy of Sciences of the United States of America·Brian M WiegmannDavid K Yeates
Apr 5, 2011·Cold Spring Harbor Protocols·Ab Matteen RafiqiUrs Schmidt-Ott
Apr 5, 2011·Cold Spring Harbor Protocols·Ab Matteen RafiqiUrs Schmidt-Ott
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Jul 19, 2012·PLoS Computational Biology·Anton CrombachJohannes Jaeger
Aug 10, 2012·Development·Ab Matteen RafiqiUrs Schmidt-Ott

Citations

Apr 19, 2013·Development Genes and Evolution·Karl R WottonEva Jiménez-Guri
Jan 11, 2014·PloS One·Karl R WottonJohannes Jaeger
Jan 11, 2014·PloS One·Eva Jiménez-GuriJohannes Jaeger
Nov 13, 2014·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Sophie Pantalacci, Marie Sémon
Nov 28, 2013·Nucleic Acids Research·Jaime Huerta-CepasToni Gabaldón
Sep 12, 2015·Annual Review of Cell and Developmental Biology·Dawn ThompsonSushmita Roy
Mar 7, 2015·Molecular Biology and Evolution·Kohtaro TanakaÉlio Sucena
Jul 12, 2016·Current Opinion in Genetics & Development·Urs Schmidt-Ott, Jeremy A Lynch
Sep 27, 2016·Yeast·Dawn A Thompson, Francisco A Cubillos
Mar 7, 2014·Journal of Biomolecular Screening·Yann AbrahamChristian N Parker
Nov 22, 2017·EvoDevo·Karl R WottonEva Jiménez-Guri
Oct 24, 2018·Molecular Biology and Evolution·Amanda M Bonner, R Scott Hawley
Apr 26, 2019·Biological Reviews of the Cambridge Philosophical Society·Miguel A Naranjo-Ortiz, Toni Gabaldón
Aug 14, 2013·The Journal of Biological Chemistry·Sebastien HannedoucheFrederic Bassilana
Mar 6, 2019·International Journal of Molecular Sciences·Yuyu WangAntonis Rokas
Sep 19, 2018·Royal Society Open Science·Eva Jiménez-GuriJohannes Jaeger

Datasets Mentioned

BETA
ERP001635

Methods Mentioned

BETA
RNA-seq
Illumina sequencing
cDNA library construction
PCR
electrophoresis
PCA

Related Concepts

Bayesian Prediction
Diptera
Drosophila melanogaster
Phylogeny
RNA
Sequence Determinations, RNA
Gene Duplication
Genomics
Prenidation Embryo Development, Animal
Array-Based Comparative Genomic Hybridization

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Alzheimer's Disease: MS4A

Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.

Pediculosis pubis

Pediculosis pubis is a disease caused by a parasitic insect known as Pthirus pubis, which infests human pubic hair, as well as other areas with hair including eye lashes. Here is the latest research.

Rh Isoimmunization

Rh isoimmunization is a potentially preventable condition that occasionally is associated with significant perinatal morbidity or mortality. Discover the latest research on Rh Isoimmunization here.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells. It also follows CRISPR-Cas9 approaches to generating genetic mutants as a means of understanding the effect of genetics on phenotype.

Enzyme Evolution

This feed focuses on molecular models of enzyme evolution and new approaches (such as adaptive laboratory evolution) to metabolic engineering of microorganisms. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Pharmacology of Proteinopathies

This feed focuses on the pharmacology of proteinopathies - diseases in which proteins abnormally aggregate (i.e. Alzheimer’s, Parkinson’s, etc.). Discover the latest research in this field with this feed.

Alignment-free Sequence Analysis Tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.